Xin Zhang

Verified email at psu.edu

Associate Professor, Department of Biochemistry and Molecular Biology, Department of Chemistry
Penn State University



                          

http://researchid.co/zhanglab
46

Scopus Publications

1675

Scholar Citations

23

Scholar h-index

32

Scholar i10-index

Scopus Publications

  • AggFluor: Fluorogenic Toolbox Enables Direct Visualization of the Multi-Step Protein Aggregation Process in Live Cells
    Charles H. Wolstenholme, Hang Hu, Songtao Ye, Brian E. Funk, Divya Jain, Chia-Heng Hsiung, Gang Ning, Yu Liu, Xiaosong Li, and Xin Zhang

    Journal of the American Chemical Society, ISSN: 00027863, eISSN: 15205126, Volume: 142, Pages: 17515-17523, Published: 14 October 2020 American Chemical Society (ACS)
    Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers and insoluble aggregates, a process that is associated with an increasing number of diseases that are not curable or manageable. Herein, we present a chemical toolbox, AggFluor, that allows for live cell imaging and differentiation of complex aggregated conformations in live cells. Based on the chromophore core of green fluorescent proteins, AggFluor is comprised of a series of molecular rotor fluorophores that span a wide range of viscosity sensitivity. As a result, these compounds exhibit differential turn-on fluorescence when incorporated in either soluble oligomers or insoluble aggregates. This feature allows us to develop, for the first time, a dual-color imaging strategy to distinguish unfolded protein oligomers from insoluble aggregates in live cells. Furthermore, we have demonstrated how small molecule proteostasis regulators can drive formation and disassembly of protein aggregates in both conformational states. In summary, AggFluor is the first set of rationally designed molecular rotor fluorophores that evenly cover a wide range of viscosity sensitivities. This set of fluorescent probes not only change the status quo of current imaging methods to visualize protein aggregation in live cells, but also can be generally applied to study other biological processes that involve local viscosity changes with temporal and spatial resolutions.

  • Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies
    Conner A. Hoelzel and Xin Zhang

    ChemBioChem, ISSN: 14394227, eISSN: 14397633, Pages: 1935-1946, Published: 16 July 2020 Wiley
    Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self‐labeling protein tags, focusing mainly on the application of HaloTag and SNAP‐tag systems. We describe the latest developments in small‐molecule probes that enable fluorogenic (no wash) imaging and super‐resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP‐tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self‐labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.

  • Fluorogenic detection of protein aggregates in live cells using the AggTag method
    Kwan Ho Jung and Xin Zhang

    Methods in Enzymology, ISSN: 00766879, eISSN: 15577988, Volume: 639, Pages: 1-22, Published: 2020 Elsevier
    Protein aggregation is a process that occurs through the self-assembly of misfolded proteins to form soluble oligomers and insoluble aggregates. While there has been significant interest in protein aggregation for neurodegenerative diseases, progress in this field of research has been limited by the lack of effective methods to detect and interrogate these species in live cells. To resolve this issue, we have developed a new imaging method named the AggTag to report on protein aggregation in live cells with fluorescence microscopy. The AggTag method utilizes a genetic fusion of a protein of interest (POI) to a protein tag to conjugate with the AggTag probe, which contains a fluorophore that turns on its fluorescence upon interaction with protein aggregates. Unlike the conventional methods, this method enables one to detect soluble misfolded oligomers that were previously invisible. Furthermore, the AggTag method has been applied for the simultaneous detection of co-aggregation between two different POIs by a dual-color and orthogonal tagging system. This chapter aims to provide step-by-step procedures of the AggTag method for researchers who intend to study aggregation of POIs in mammalian cell lines.

  • Super-Resolution Optical Lithography with DNA
    Shi Ho Kim, Yu Liu, Conner Hoelzel, Xin Zhang, and Tae-Hee Lee

    Nano Letters, ISSN: 15306984, eISSN: 15306992, Pages: 6035-6042, Published: 11 September 2019 American Chemical Society (ACS)
    We developed an efficient, versatile, and accessible super-resolution microscopy method to construct a nanoparticle assembly at a spatial resolution below the optical diffraction limit. The method utilizes DNA and a photo-activated DNA crosslinker. Super-resolution optical techniques have been used only as a means to make measurements below the light diffraction limit. Furthermore, no optical technique is currently available to construct nanoparticle assemblies with a precisely designed shape and internal structure at a resolution of a few tens of nanometers (nm). Here we demonstrate that we can fulfill this deficiency by utilizing spontaneous structural dynamics of DNA hairpins combined with single-molecule fluorescence resonance energy transfer (smFRET) microscopy and a photo-activated DNA crosslinker. The stochastic fluorescence blinking due to the spontaneous folding and unfolding motions of DNA hairpins enables us to precisely localize a folded hairpin and solidify it only when it is within a pre-designed target area whose size is below the diffraction limit. As the method is based on an optical microscope and an easily clickable DNA crosslinking reagent, it will provide an efficient means to create large nanoparticle assemblies with a shape and internal structure at an optical super-resolution, opening a wide window of opportunities toward investigating their photophysical and optoelectronic properties and developing novel devices.

  • A Fluorogenic AggTag Method Based on Halo- and SNAP-Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells
    Kwan Ho Jung, Sojung F. Kim, Yu Liu, and Xin Zhang

    ChemBioChem, ISSN: 14394227, eISSN: 14397633, Pages: 1078-1087, Published: 15 April 2019 Wiley
    Protein aggregation involves the assembly of partially misfolded proteins into oligomeric and higher‐order structures that have been associated with several neurodegenerative diseases. However, numerous questions relating to protein aggregation remain unanswered due to the lack of available tools for visualization of these species in living cells. We recently developed a fluorogenic method named aggregation tag (AggTag), and presented the AggTag probe P1, based on a Halo‐tag ligand, to report on the aggregation of a protein of interest (POI) in live cells. However, the Halo‐tag‐based AggTag method only detects the aggregation of one specific POI at a time. In this study, we have expanded the AggTag method by using SNAP‐tag technology to enable fluorogenic and biorthogonal detection of the aggregation of two different POIs simultaneously in live cells. A new AggTag probe—P2, based on a SNAP‐tag ligand bearing a green solvatochromic fluorophore—was synthesized for this purpose. Using confocal imaging and chemical crosslinking experiments, we confirmed that P2 can also report both on soluble oligomers and on insoluble aggregates of a POI fused with SNAP‐tag in live cells. Ultimately, we showed that the orthogonal fluorescence of P1 and P2 allows for simultaneous visualization of two different pathogenic protein aggregates in the same cell.

  • Monitoring proteome stress in live cells using halotag-based fluorogenic sensor
    Yu Liu, Matthew Fares, and Xin Zhang

    Methods in Molecular Biology, ISSN: 10643745, Volume: 1873, Pages: 171-182, Published: 2019 Springer New York
    Fluorescent folding sensor is a powerful tool to detect proteome stresses, including heat, osmotic, oxidative, and drug induced stresses. Monitoring proteome stress using these sensors allows us to dissect the mechanism of cellular stress and find therapeutics that ameliorate stress related diseases. Here we present a HaloTag-based fluorogenic proteome stress sensor (AgHalo) to robustly detect and quantify proteome stresses in live cells. We describe how proteome stresses are monitored in both bacterial and mammalian live cells using fluorescence confocal microscope and fluorescence plate reader.

  • A HaloTag-Based Multicolor Fluorogenic Sensor Visualizes and Quantifies Proteome Stress in Live Cells Using Solvatochromic and Molecular Rotor-Based Fluorophores
    Yu Liu, Kun Miao, Yinghao Li, Matthew Fares, Shuyuan Chen, and Xin Zhang

    Biochemistry, ISSN: 00062960, eISSN: 15204995, Pages: 4663-4674, Published: 7 August 2018 American Chemical Society (ACS)
    Protein homeostasis, or proteostasis, is essential for cellular fitness and viability. Many environmental factors compromise proteostasis, induce global proteome stress, and cause diseases. The proteome stress sensor is a powerful tool for dissecting the mechanism of cellular stress and finding therapeutics that ameliorate these diseases. In this work, we present a multicolor HaloTag-based sensor (named AgHalo) to visualize and quantify proteome stresses in live cells. The current AgHalo sensor is equipped with three fluorogenic probes that turn on fluorescence when the sensor forms either soluble oligomers or insoluble aggregates upon exposure to stress conditions, both in vitro and in cellulo. In addition, AgHalo probes can be combined with commercially available always-fluorescent HaloTag ligands to enable two-color imaging, allowing for direct visualization of the AgHalo sensor both before and after cells are subjected to stress conditions. Finally, pulse-chase experiments can be performed to discern changes in the cellular proteome in live cells by first forming the AgHalo conjugate and then either applying or removing stress at any desired time point. In summary, the AgHalo sensor can be used to visualize and quantify proteome stress in live cells, a task that is difficult to accomplish using previous always-fluorescent methods. This sensor should be suited to evaluating cellular proteostasis under various exogenous stresses, including chemical toxins, drugs, and environmental factors.

  • NMR Measurements Reveal the Structural Basis of Transthyretin Destabilization by Pathogenic Mutations
    Benjamin I. Leach, Xin Zhang, Jeffery W. Kelly, H. Jane Dyson, and Peter E. Wright

    Biochemistry, ISSN: 00062960, eISSN: 15204995, Pages: 4421-4430, Published: 31 July 2018 American Chemical Society (ACS)
    Inherited mutations of transthyretin (TTR) destabilize its structure, leading to aggregation and familial amyloid disease. Although numerous crystal structures of wild-type (WT) and mutant TTRs have been determined, they have failed to yield a comprehensive structural explanation for destabilization by pathogenic mutations. To identify structural and dynamic variations that are not readily observed in the crystal structures, we used NMR to study WT TTR and three kinetically and/or thermodynamically destabilized pathogenic variants (V30M, L55P, and V122I). Sequence-corrected chemical shifts reveal important structural differences between WT and mutant TTR. The L55P mutation linked to aggressive early onset cardiomyopathy and polyneuropathy induces substantial structural perturbations in both the DAGH and CBEF β-sheets, whereas the V30M polyneuropathy-linked substitution perturbs primarily the CBEF sheet. In both variants, the structural perturbations propagate across the entire width of the β-sheets from the site of mutation. Structural changes caused by the V122I cardiomyopathy-associated mutation are restricted to the immediate vicinity of the mutation site, directly perturbing the subunit interfaces. NMR relaxation dispersion measurements show that WT TTR and the three pathogenic variants undergo millisecond time scale conformational fluctuations to populate a common excited state with an altered structure in the subunit interfaces. The excited state is most highly populated in L55P. The combined application of chemical shift analysis and relaxation dispersion to these pathogenic variants reveals differences in ground state structure and in the population of a transient excited state that potentially facilitates tetramer dissociation, providing new insights into the molecular mechanism by which mutations promote TTR amyloidosis.

  • Modulation of Fluorescent Protein Chromophores to Detect Protein Aggregation with Turn-On Fluorescence
    Yu Liu, Charles H. Wolstenholme, Gregory C. Carter, Hongbin Liu, Hang Hu, Leeann S. Grainger, Kun Miao, Matthew Fares, Conner A. Hoelzel, Hemant P. Yennawar, Gang Ning, Manyu Du, Lu Bai, Xiaosong Li, and Xin Zhang

    Journal of the American Chemical Society, ISSN: 00027863, eISSN: 15205126, Volume: 140, Pages: 7381-7384, Published: 20 June 2018 American Chemical Society (ACS)
    We present a fluorogenic method to visualize misfolding and aggregation of a specific protein-of-interest in live cells using structurally modulated fluorescent protein chromophores. Combining photophysical analysis, X-ray crystallography, and theoretical calculation, we show that fluorescence is triggered by inhibition of twisted-intramolecular charge transfer of these fluorophores in the rigid microenvironment of viscous solvent or protein aggregates. Bioorthogonal conjugation of the fluorophore to Halo-tag fused protein-of-interests allows for fluorogenic detection of both misfolded and aggregated species in live cells. Unlike other methods, our method is capable of detecting previously invisible misfolded soluble proteins. This work provides the first application of fluorescent protein chromophores to detect protein conformational collapse in live cells.

  • Role of HSP90 in the Regulation of de Novo Purine Biosynthesis
    Anthony M. Pedley, Georgios I. Karras, Xin Zhang, Susan Lindquist, and Stephen J. Benkovic

    Biochemistry, ISSN: 00062960, eISSN: 15204995, Pages: 3217-3221, Published: 12 June 2018 American Chemical Society (ACS)
    Despite purines making up one of the largest classes of metabolites in a cell, little is known about the regulatory mechanisms that facilitate efficient purine production. Under conditions resulting in high purine demand, enzymes within the de novo purine biosynthetic pathway cluster into multienzyme assemblies called purinosomes. Purinosome formation has been linked to molecular chaperones HSP70 and HSP90; however, the involvement of these molecular chaperones in purinosome formation remains largely unknown. Here, we present a new-found biochemical mechanism for the regulation of de novo purine biosynthetic enzymes mediated through HSP90. HSP90-client protein interaction assays were employed to identify two enzymes within the de novo purine biosynthetic pathway, PPAT and FGAMS, as client proteins of HSP90. Inhibition of HSP90 by STA9090 abrogated these interactions and resulted in a decrease in the level of available soluble client protein while having no significant effect on their interactions with HSP70. These findings provide a mechanism to explain the dependence of purinosome assembly on HSP90 activity. The combined efforts of molecular chaperones in the maturation of PPAT and FGAMS result in purinosome formation and are likely essential for enhancing the rate of purine production to meet intracellular purine demand.

  • Carbon nitride nanothread crystals derived from pyridine
    Xiang Li, Tao Wang, Pu Duan, Maria Baldini, Haw-Tyng Huang, Bo Chen, Stephen J. Juhl, Daniel Koeplinger, Vincent H. Crespi, Klaus Schmidt-Rohr, Roald Hoffmann, Nasim Alem, Malcolm Guthrie, Xin Zhang, and John V. Badding

    Journal of the American Chemical Society, ISSN: 00027863, eISSN: 15205126, Volume: 140, Pages: 4969-4972, Published: 18 April 2018 American Chemical Society (ACS)
    Carbon nanothreads are a new one-dimensional sp3 carbon nanomaterial. They assemble into hexagonal crystals in a room temperature, nontopochemical solid-state reaction induced by slow compression of benzene to 23 GPa. Here we show that pyridine also reacts under compression to form a well-ordered sp3 product: C5NH5 carbon nitride nanothreads. Solid pyridine has a different crystal structure from solid benzene, so the nontopochemical formation of low-dimensional crystalline solids by slow compression of small aromatics may be a general phenomenon that enables chemical design of properties. The nitrogen in the carbon nitride nanothreads may improve processability, alters photoluminescence, and is predicted to reduce the bandgap.

  • Heat Shock Protein Reports on Proteome Stress
    Yu Liu and Xin Zhang

    Biotechnology Journal, ISSN: 18606768, eISSN: 18607314, Published: April 2018 Wiley
    Proper regulation of protein homeostasis (proteostasis) is essential to maintain cellular fitness. Proteome stress causes imbalance of the proteostasis, leading to various diseases represented by neurodegenerative diseases, cancers, and metabolic disorders. The biosensor community recently embarked on the development of proteome stress sensors to report on the integrity of proteostasis in live cells. While most of these sensors are based on metastable mutants of specific client proteins, a recent sensor takes advantage of the specific association of heat shock protein 27 with protein aggregates and exhibits a diffusive to punctate fluorescent change in cells that are subjected to stress conditions. Thus, heat shock proteins can be also used as a family of sensors to monitor proteome stress.

  • A Molecular Rotor-Based Halo-Tag Ligand Enables a Fluorogenic Proteome Stress Sensor to Detect Protein Misfolding in Mildly Stressed Proteome
    Matthew Fares, Yinghao Li, Yu Liu, Kun Miao, Zi Gao, Yufeng Zhai, and Xin Zhang

    Bioconjugate Chemistry, ISSN: 10431802, eISSN: 15204812, Pages: 215-224, Published: 17 January 2018 American Chemical Society (ACS)
    Cellular stress leads to disruption of protein homeostasis (proteostasis) that is associated with global misfolding and aggregation of the endogenous proteome. Monitoring stress-induced proteostasis deficiency remains one of the major technical challenges facing established sensors of this process. Available sensors use solvatochromic fluorophores to detect protein aggregation in forms of soluble oligomers or insoluble aggregates when cells are subjected to severe stress conditions. Misfolded monomers induced by mild stresses, however, remain largely invisible to these sensors. Here, we describe a fluorogenic proteome stress sensor by conjugating a fluorescent molecular rotor with a metastable Halo-tag protein domain that contains a K73T mutation (named AgHalo hereinafter). In nonstressed cells, the AaHalo sensor remains largely folded and the AgHalo•ligand conjugate is fluorescent dark in the folded state. Under various stress conditions, the AgHalo sensor has been established to form both soluble and insoluble aggregates along with metastable proteins of the endogenous cellular proteome. Thus, the AgHalo•ligand conjugate fluoresces strongly when the sensor forms misfolded monomers (a 16-fold increase) or aggregates in both soluble and insoluble forms (a 20-fold increase). Compared to the solvatochromic fluorophore-based sensor, we demonstrate that the molecular rotor-based sensor not only is more effective in detecting mild proteome stress that induces primarily misfolding conformations, but also exhibits a higher fluorescence signal in detecting more severe proteome stress that involves protein aggregates. Thus, the conjugation of a fluorescent molecular rotor to AgHalo further improves the capacity of this sensor to detect conditions of proteome stress. This work highlights the utility of molecular rotor-based fluorophores in direct visualization of the protein aggregation cascade in live cells, providing new methodologies for real-time analyses of cellular proteostasis upon exposure to different types of stress conditions.

  • The Cation−π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification
    Yu Liu, Kun Miao, Noah P. Dunham, Hongbin Liu, Matthew Fares, Amie K. Boal, Xiaosong Li, and Xin Zhang

    Biochemistry, ISSN: 00062960, eISSN: 15204995, Pages: 1585-1595, Published: 21 March 2017 American Chemical Society (ACS)
    The design of fluorogenic probes for a Halo tag is highly desirable but challenging. Previous work achieved this goal by controlling the chemical switch of spirolactones upon the covalent conjugation between the Halo tag and probes or by incorporating a "channel dye" into the substrate binding tunnel of the Halo tag. In this work, we have developed a novel class of Halo-tag fluorogenic probes that are derived from solvatochromic fluorophores. The optimal probe, harboring a benzothiadiazole scaffold, exhibits a 1000-fold fluorescence enhancement upon reaction with the Halo tag. Structural, computational, and biochemical studies reveal that the benzene ring of a tryptophan residue engages in a cation-π interaction with the dimethylamino electron-donating group of the benzothiadiazole fluorophore in its excited state. We further demonstrate using noncanonical fluorinated tryptophan that the cation-π interaction directly contributes to the fluorogenicity of the benzothiadiazole fluorophore. Mechanistically, this interaction could contribute to the fluorogenicity by promoting the excited-state charge separation and inhibiting the twisting motion of the dimethylamino group, both leading to an enhanced fluorogenicity. Finally, we demonstrate the utility of the probe in no-wash direct imaging of Halo-tagged proteins in live cells. In addition, the fluorogenic nature of the probe enables a gel-free quantification of fusion proteins expressed in mammalian cells, an application that was not possible with previously nonfluorogenic Halo-tag probes. The unique mechanism revealed by this work suggests that incorporation of an excited-state cation-π interaction could be a feasible strategy for enhancing the optical performance of fluorophores and fluorogenic sensors.

  • AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress
    Yu Liu, Matthew Fares, Noah P. Dunham, Zi Gao, Kun Miao, Xueyuan Jiang, Samuel S. Bollinger, Amie K. Boal, and Xin Zhang

    Angewandte Chemie - International Edition, ISSN: 14337851, eISSN: 15213773, Pages: 8672-8676, Published: 2017 Wiley
    Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins.

  • Fluorescence Turn-On Folding Sensor to Monitor Proteome Stress in Live Cells
    Yu Liu, Xin Zhang, Wentao Chen, Yun Lei Tan, and Jeffery W. Kelly

    Journal of the American Chemical Society, ISSN: 00027863, eISSN: 15205126, Volume: 137, Pages: 11303-11311, Published: 9 September 2015 American Chemical Society (ACS)
    Proteome misfolding and/or aggregation, caused by a thermal perturbation or a related stress, transiently challenges the cellular protein homeostasis (proteostasis) network capacity of cells by consuming chaperone/chaperonin pathway and degradation pathway capacity. Developing protein client-based probes to quantify the cellular proteostasis network capacity in real time is highly desirable. Herein we introduce a small-molecule-regulated fluorescent protein folding sensor based on a thermo-labile mutant of the de novo designed retroaldolase (RA) enzyme. Since RA enzyme activity is not present in any cell, the protein folding sensor is bioorthogonal. The fluorogenic small molecule was designed to become fluorescent when it binds to and covalently reacts with folded and functional RA. Thus, in the first experimental paradigm, cellular proteostasis network capacity and its dynamics are reflected by RA–small molecule conjugate fluorescence, which correlates with the amount of folded and functional RA present, provided that pharmacologic chaperoning is minimized. In the second experimental scenario, the RA–fluorogenic probe conjugate is pre-formed in a cell by simply adding the fluorogenic probe to the cell culture media. Unreacted probe is then washed away before a proteome misfolding stress is applied in a pulse-chase-type experiment. Insufficient proteostasis network capacity is reflected by aggregate formation of the fluorescent RA–fluorogenic probe conjugate. Removal of the stress results in apparent RA–fluorogenic probe conjugate re-folding, mediated in part by the heat-shock response transcriptional program augmenting cytosolic proteostasis network capacity, and in part by time-dependent RA–fluorogenic probe conjugate degradation by cellular proteolysis.

  • Individual and collective contributions of chaperoning and degradation to protein homeostasis in E. coli
    Younhee Cho, Xin Zhang, Kristine Faye R. Pobre, Yu Liu, David L. Powers, Jeffery W. Kelly, Lila M. Gierasch, and Evan T. Powers

    Cell Reports, eISSN: 22111247, Pages: 321-333, Published: 2015 Elsevier BV
    The folding fate of a protein in vivo is determined by the interplay between a protein's folding energy landscape and the actions of the proteostasis network, including molecular chaperones and degradation enzymes. The mechanisms of individual components of the E. coli proteostasis network have been studied extensively, but much less is known about how they function as a system. We used an integrated experimental and computational approach to quantitatively analyze the folding outcomes (native folding versus aggregation versus degradation) of three test proteins biosynthesized in E. coli under a variety of conditions. Overexpression of the entire proteostasis network benefited all three test proteins, but the effect of upregulating individual chaperones or the major degradation enzyme, Lon, varied for proteins with different biophysical properties. In sum, the impact of the E. coli proteostasis network is a consequence of concerted action by the Hsp70 system (DnaK/DnaJ/GrpE), the Hsp60 system (GroEL/GroES), and Lon.

  • De Novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters
    Yu Liu, Xin Zhang, Yun Lei Tan, Gira Bhabha, Damian C. Ekiert, Yakov Kipnis, Sinisa Bjelic, David Baker, and Jeffery W. Kelly

    Journal of the American Chemical Society, ISSN: 00027863, eISSN: 15205126, Volume: 136, Pages: 13102-13105, Published: 24 September 2014 American Chemical Society (ACS)
    Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme–small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores.

  • Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli
    Xin Zhang, Yu Liu, Joseph C. Genereux, Chandler Nolan, Meha Singh, and Jeffery W. Kelly

    ACS Chemical Biology, ISSN: 15548929, eISSN: 15548937, Pages: 1945-1949, Published: 19 September 2014 American Chemical Society (ACS)
    The biosynthesis of soluble, properly folded recombinant proteins in large quantities from Escherichia coli is desirable for academic research and industrial protein production. The basal E. coli protein homeostasis (proteostasis) network capacity is often insufficient to efficiently fold overexpressed proteins. Herein we demonstrate that a transcriptionally reprogrammed E. coli proteostasis network is generally superior for producing soluble, folded, and functional recombinant proteins. Reprogramming is accomplished by overexpressing a negative feedback deficient heat-shock response transcription factor before and during overexpression of the protein-of-interest. The advantage of transcriptional reprogramming versus simply overexpressing select proteostasis network components (e.g., chaperones and co-chaperones, which has been explored previously) is that a large number of proteostasis network components are upregulated at their evolved stoichiometry, thus maintaining the system capabilities of the proteostasis network that are currently incompletely understood. Transcriptional proteostasis network reprogramming mediated by stress-responsive signaling in the absence of stress should also be useful for protein production in other cells.

  • Chaperonins resculpt folding free energy landscapes to avoid kinetic traps and accelerate protein folding
    Xin Zhang and Jeffery W. Kelly

    Journal of Molecular Biology, ISSN: 00222836, eISSN: 10898638, Volume: 426, Pages: 2736-2738, Published: 29 July 2014 Elsevier BV

  • Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts
    Y. Liu, Y. L. Tan, X. Zhang, G. Bhabha, D. C. Ekiert, J. C. Genereux, Y. Cho, Y. Kipnis, S. Bjelic, D. Baker, and J. W. Kelly

    Proceedings of the National Academy of Sciences of the United States of America, ISSN: 00278424, eISSN: 10916490, Volume: 111, Pages: 4449-4454, Published: 25 March 2014 Proceedings of the National Academy of Sciences
    Significance Historically, the folding of individual proteins in buffers has been studied spectroscopically. The majority of spectroscopic methods (NMR and fluorescence excluded) cannot be used in a cell, because the protein of interest (POI) cannot be distinguished from the background proteome. Herein, we introduce folding probes, which when used in cell lysates with sufficient holdase activity, faithfully quantify the folded and functional fraction of a POI at a time point of interest in a cell by selectively reacting with that state to afford a fluorescent signal. This work provides a blueprint for how to convert enzyme inhibitors, ligands for nonenzyme proteins, etc. into folding probes to efficiently and specifically investigate how intracellular function is controlled by the proteostasis network as a function of cellular perturbations. Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein’s folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein’s functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.

  • Fidelity of cotranslational protein targeting by the signal recognition particle
    Xin Zhang and Shu-ou Shan

    Annual Review of Biophysics, ISSN: 1936122X, eISSN: 19361238, Pages: 381-408, Published: May 2014 Annual Reviews
    Accurate folding, assembly, localization, and maturation of newly synthesized proteins are essential to all cells and require high fidelity in the protein biogenesis machineries that mediate these processes. Here, we review our current understanding of how high fidelity is achieved in one of these processes, the cotranslational targeting of nascent membrane and secretory proteins by the signal recognition particle (SRP). Recent biochemical, biophysical, and structural studies have elucidated how the correct substrates drive a series of elaborate conformational rearrangements in the SRP and SRP receptor GTPases; these rearrangements provide effective fidelity checkpoints to reject incorrect substrates and enhance the fidelity of this essential cellular pathway. The mechanisms used by SRP to ensure fidelity share important conceptual analogies with those used by cellular machineries involved in DNA replication, transcription, and translation, and these mechanisms likely represent general principles for other complex cellular pathways.

  • Mechanisms of transthyretin inhibition of β-amyloid aggregation in vitro
    X. Li, X. Zhang, A. R. A. Ladiwala, D. Du, J. K. Yadav, P. M. Tessier, P. E. Wright, J. W. Kelly, and J. N. Buxbaum

    Journal of Neuroscience, ISSN: 02706474, eISSN: 15292401, Pages: 19423-19433, Published: 2013 Society for Neuroscience
    Tissue-specific overexpression of the human systemic amyloid precursor transthyretin (TTR) ameliorates Alzheimer's disease (AD) phenotypes in APP23 mice. TTR–β-amyloid (Aβ) complexes have been isolated from APP23 and some human AD brains. We now show that substoichiometric concentrations of TTR tetramers suppress Aβ aggregation in vitro via an interaction between the thyroxine binding pocket of the TTR tetramer and Aβ residues 18–21 (nuclear magnetic resonance and epitope mapping). The KD is micromolar, and the stoichiometry is <1 for the interaction (isothermal titration calorimetry). Similar experiments show that engineered monomeric TTR, the best inhibitor of Aβ fibril formation in vitro, did not bind Aβ monomers in liquid phase, suggesting that inhibition of fibrillogenesis is mediated by TTR tetramer binding to Aβ monomer and both tetramer and monomer binding of Aβ oligomers. The thousand-fold greater concentration of tetramer relative to monomer in vivo makes it the likely suppressor of Aβ aggregation and disease in the APP23 mice.

  • Bio-inspired protein-gold nanoconstruct with core-void-shell structure: Beyond a chemo drug carrier
    Xiangyou Liu, Wei Wei, Shijiao Huang, Shrong-Shi Lin, Xin Zhang, Chuanmao Zhang, Yuguang Du, Guanghui Ma, Mei Li, Stephen Mann, and Ding Ma

    Journal of Materials Chemistry B, ISSN: 20507518, eISSN: 2050750X, Pages: 3136-3143, Published: 7 July 2013 Royal Society of Chemistry (RSC)
    Chemotherapy has been widely used in clinical practice for cancer treatment. A major challenge for a successful chemotherapy is to potentiate the anticancer activity, whilst reducing the severe side effects. In this context, we design a bio-inspired protein-gold nanoconstruct (denoted as AFt-Au hereafter) with a core-void-shell structure which exhibits a high selectivity towards carcinoma cells. Anticancer drug 5-fluorouracil (5-FU) can be sequestered into the void space of the construct to produce an integrated nanoscale hybrid AFt-AuFU that exhibits an increased cellular uptake of 5-FU. More importantly, AFt-Au, serving as a bio-nano-chemosensitizer, renders carcinoma cells more susceptible to 5-FU by cell-cycle regulation, and thus, leads to a dramatic decrease of the IC50 value (i.e. the drug concentration required to kill 50% of the cell population) of 5-FU in HepG2 cells from 138.3 μM to 9.2 μM. Besides HepG2 cells, a remarkably enhanced anticancer efficacy and potentially reduced side effects are also achieved in other cell lines. Our further work reveals that the drug 5-FU is internalized into cells with AFt-Au primarily via receptor-mediated endocytosis (RME). After internalization, AFt-AuFU colocalizes with lysosomes which trigger the release of 5-FU under acidic conditions. Overall, our approach provides a novel procedure in nanoscience that promises an optimal chemotherapeutic outcome.

  • Signal recognition particle: An essential protein-targeting machine
    David Akopian, Kuang Shen, Xin Zhang, and Shu-ou Shan

    Annual Review of Biochemistry, ISSN: 00664154, eISSN: 15454509, Pages: 693-721, Published: June 2013 Annual Reviews
    The signal recognition particle (SRP) and its receptor compose a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization. The past decade has witnessed an explosion in in-depth mechanistic investigations of this targeting machine at increasingly higher resolutions. In this review, we summarize recent work that elucidates how the SRP and SRP receptor interact with the cargo protein and the target membrane, respectively, and how these interactions are coupled to a novel GTPase cycle in the SRP·SRP receptor complex to provide the driving force and enhance the fidelity of this fundamental cellular pathway. We also discuss emerging frontiers in which important questions remain to be addressed.

  • Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex
    Ottilie von Loeffelholz, Kèvin Knoops, Aileen Ariosa, Xin Zhang, Manikandan Karuppasamy, Karine Huard, Guy Schoehn, Imre Berger, Shu-ou Shan, and Christiane Schaffitzel

    Nature Structural and Molecular Biology, ISSN: 15459993, eISSN: 15459985, Pages: 604-610, Published: May 2013 Springer Science and Business Media LLC
    Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor.

  • Apoferritin-ceo2 nano-truffle that has excellent artificial redox enzyme activity
    Xiangyou Liu, Wei Wei, Quan Yuan, Xin Zhang, Ning Li, Yuguang Du, Guanghui Ma, Chunhua Yan, and Ding Ma

    Chemical Communications, ISSN: 13597345, eISSN: 1364548X, Pages: 3155-3157, Published: 29 February 2012 Royal Society of Chemistry (RSC)
    4.5 nm nanoceria particles are successfully encapsulated into the apoferritin cavity via a dissociation-reconstruction route. The apoferritin coating not only improves the biocompatibility and changes the cellular uptake route of nanoceria, but also manipulates the electron localization at the surface of the nanoparticle thereby ameliorating the ROS-scavenging activity.

  • Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
    Ming-Jun Yang and Xin Zhang

    Proteins: Structure, Function and Bioinformatics, ISSN: 08873585, eISSN: 10970134, Pages: 1774-1785, Published: June 2011 Wiley
    Two homologous GTPases (guanine‐triphosphatases) in the signal recognition particle (SRP) and its receptor (SR) use their cumulative energy during GTP (guanine‐triphosphate) hydrolysis to control the co‐translational protein targeting process. Distinct from classical GTPases, which rely on external factors to hydrolyze GTP, SRP GTPases stimulate one another's activity in a self‐sufficient manner upon SRP–SR complex association. Although both ground‐state and putative transition‐state GTP analogs have been used to recapitulate the state of GTPase activation, the underlying mechanism of the activated state still remains elusive. In particular, several residues that were placed in pending positions have been shown to be important to GTP hydrolysis in biochemical studies. Here, we examined the stability and dynamics of three interaction networks involving these residues and discovered that they contribute to the GTPase activation via well‐tuned conformational changes. The crystallographically identified pending residues Ffh:R191/FtsY:R195 undergo extensive conformational rearrangements to form persisted interactions with FtsY:E284/Ffh:E274, explaining the biochemically observed defective effect of R191 mutant to the activation of both GTPases. In addition, the side chain of FtsY:R142, one of the most important catalytic residues, rotates to an extended conformation that could more efficiently maintain the electrostatic balance for GTP hydrolysis. Finally, the invariant residues Ffh:G190 and FtsY:G194, instead of the supposed auxiliary water molecules, are proposed to stabilize the nucleophilic waters during GTPase activation. In complementary to experimental observations, these findings suggest a more favorable interaction model for SRP GTPase activation and would thus benefit to our understanding of how SRP GTPases regulate the protein targeting pathway. Proteins 2011; © 2011 Wiley‐Liss, Inc.

  • Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting KUANG
    K. Shen, X. Zhang, and S.-o. Shan
    ISSN: 13558382, eISSN: 14699001, Pages: 892-902, Published: May 2011 Cold Spring Harbor Laboratory
    During cotranslational protein targeting by the Signal Recognition Particle (SRP), the correct cargo accelerates stable complex assembly between the SRP and SRP receptor (FtsY) by several orders of magnitude, thus enabling rapid and faithful cargo delivery to the target membrane. The molecular mechanism underlying this cargo-induced rate acceleration has been unclear. Here we show that the SRP RNA allows assembly of the SRP-FtsY complex to be specifically stimulated by a correct cargo, and, reciprocally, a correct cargo enables the SRP RNA to optimize its electrostatic interactions with FtsY. These results combined with recent structural work led us to suggest a "conformational selection" model that explains the synergistic action of the SRP RNA with the cargo in accelerating complex assembly. In addition to its previously proposed role in preventing the premature dissociation of SRP and FtsY, we found that the SRP RNA also plays an active role in ensuring the formation of productive assembly intermediates, thus guiding the SRP and FtsY through the most efficient pathway of assembly.

  • Direct visualization reveals dynamics of a transient intermediate during protein assembly
    X. Zhang, V. Q. Lam, Y. Mou, T. Kimura, J. Chung, S. Chandrasekar, J. R. Winkler, S. L. Mayo, and S.-o. Shan

    Proceedings of the National Academy of Sciences of the United States of America, ISSN: 00278424, eISSN: 10916490, Volume: 108, Pages: 6450-6455, Published: 19 April 2011 Proceedings of the National Academy of Sciences
    Interactions between proteins underlie numerous biological functions. Theoretical work suggests that protein interactions initiate with formation of transient intermediates that subsequently relax to specific, stable complexes. However, the nature and roles of these transient intermediates have remained elusive. Here, we characterized the global structure, dynamics, and stability of a transient, on-pathway intermediate during complex assembly between the Signal Recognition Particle (SRP) and its receptor. We show that this intermediate has overlapping but distinct interaction interfaces from that of the final complex, and it is stabilized by long-range electrostatic interactions. A wide distribution of conformations is explored by the intermediate; this distribution becomes more restricted in the final complex and is further regulated by the cargo of SRP. These results suggest a funnel-shaped energy landscape for protein interactions, and they provide a framework for understanding the role of transient intermediates in protein assembly and biological regulation.

  • Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding
    Ming-Jun Yang, Xue-Qin Pang, Xin Zhang, and Ke-Li Han

    Journal of Structural Biology, ISSN: 10478477, eISSN: 10958657, Volume: 173, Pages: 57-66, Published: January 2011 Elsevier BV
    Two GTPases in the signal recognition particle (SRP) and SRP receptor (SR) interact with one another to mediate the cotranslational protein targeting pathway. Previous studies have shown that a universally conserved SRP RNA facilitates an efficient SRP-SR interaction in the presence of a signal sequence bound to SRP. However, a remarkable exception has been found in chloroplast SRP (cpSRP) pathway, in which the SRP RNA is missing. Based on biochemical and structural analyses, it is proposed that free cpSRP receptor (cpFtsY) has already been preorganized into a closed state for efficient cpSRP-cpFtsY association. However, no direct evidence has been reported to support this postulation thus far. In this study, we characterized the structural dynamics of cpFtsY and its conformational rearrangements induced by GTP binding using molecular dynamics (MD) simulations. Our results showed that the GTP-binding event triggered substantial conformational changes in free cpFtsY, including the relative orientation of N-G domain and several conserved motifs that are critical in complex formation. These rearrangements enabled the cpFtsY to relax into a preorganized 'closed' state that favored the formation of a stable complex with cpSRP54. Interestingly, the intrinsic flexibility of αN1 helix facilitated these rearrangements. In addition, GTP binding in cpFtsY was mediated by conserved residues that have been shown in other SRP GTPases. These findings suggested that GTP-bound cpFtsY could fluctuate into conformations that are favorable to form the stable complex, providing explanation of why SRP-SR interaction bypasses the requirement of the SRP RNA at a molecular level.

  • Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations
    Mingjun Yang, Xin Zhang, and Keli Han

    Proteins: Structure, Function and Bioinformatics, ISSN: 08873585, eISSN: 10970134, Pages: 2222-2237, Published: 1 August 2010 Wiley
    Signal recognition particle (SRP) and its receptor (SR) play essential role in the SRP‐dependent protein targeting pathway. They interact with one another to precisely regulate the targeting reaction. The mechanism of this interaction consists of at least two discrete conformational states: complex formation and GTPase activation. Although structural studies have provided valuable insights into the understanding of the SRP‐SR interaction, it still remains unclear that how SRP and SR GTPases use their intrinsic conformational flexibilities to exert multiple allosteric regulations on this interaction process. Here, we use computational simulations to present the dynamic behavior of the SRP GTPases at an atomic level to gain further understanding of SRP‐SR interaction. We show that: (i) equilibrium conformational fluctuations contain a cooperative inter‐ and intradomain structural rearrangements that are functionally relevant to complex formation, (ii) a series of residues in different domains are identified to correlate with each other during conformational rearrangements, and (iii) α3 and α4 helices at domain interface actively rearrange their relative conformation to function as a bridge between the N domain and the core region of the G domain. These results, in addition to structural studies, would harness our understanding of the molecular mechanism for SRP and SR interaction. Proteins 2010. © 2010 Wiley‐Liss, Inc.

  • Sequential checkpoints govern substrate selection during cotranslational protein targeting
    X. Zhang, R. Rashid, K. Wang, and S. o. Shan

    Science, ISSN: 00368075, eISSN: 10959203, Volume: 328, Issue: 5979, Pages: 757-760, Published: 7 May 2010 American Association for the Advancement of Science (AAAS)
    Target Acquisition The proper localization of proteins to the correct intracellular destinations is essential for the structure and function of all cells. Most membrane and secretory proteins are targeted to membranes by virtue of a signal sequence that is recognized by signal recognition particle (SRP) as the protein is being translated, forming a complex that docks with target membranes bearing the SRP receptor. Now, Zhang et al. (p. 757) have found, using cell-free bacterial extracts, that the initial binding of cargo by SRP is not sufficient to discriminate against all the incorrect cargos. Instead, a series of fidelity checkpoints during subsequent steps of the protein-targeting and translocation pathway help reject incorrect cargos. Protein cargo is monitored at several points during membrane translocation to improve targeting fidelity. Proper protein localization is essential for all cells. However, the precise mechanism by which high fidelity is achieved is not well understood for any protein-targeting pathway. To address this fundamental question, we investigated the signal recognition particle (SRP) pathway in Escherichia coli, which delivers proteins to the bacterial inner membrane through recognition of signal sequences on cargo proteins. Fidelity was thought to arise from the inability of SRP to bind strongly to incorrect cargos. Using biophysical assays, we found that incorrect cargos were also rejected through a series of checkpoints during subsequent steps of targeting. Thus, high fidelity of substrate selection is achieved through the cumulative effect of multiple checkpoints; this principle may be generally applicable to other pathways involving selective signal recognition.

  • Signal recognition particle (SRP) and SRP receptor: A new paradigm for multistate regulatory GTPases
    Shu-ou Shan, Sandra L. Schmid, and Xin Zhang

    Biochemistry, ISSN: 00062960, Pages: 6696-6704, Published: 28 July 2009 American Chemical Society (ACS)
    The GTP-binding proteins or GTPases comprise a superfamily of proteins that provide molecular switches in numerous cellular processes. The "GTPase switch" paradigm, in which a GTPase acts as a bimodal switch that is turned "on" and "off" by external regulatory factors, has been used to interpret the regulatory mechanism of many GTPases for more than two decades. Nevertheless, recent work has unveiled an emerging class of "multistate" regulatory GTPases that do not adhere to this classical paradigm. Instead of relying on external nucleotide exchange factors or GTPase activating proteins to switch between the on and off states, these GTPases have the intrinsic ability to exchange nucleotides and to sense and respond to upstream and downstream factors. In contrast to the bimodal nature of the GTPase switch, these GTPases undergo multiple conformational rearrangements, allowing multiple regulatory points to be built into a complex biological process to ensure the efficiency and fidelity of the pathway. We suggest that these multistate regulatory GTPases are uniquely suited to provide spatial and temporal control of complex cellular pathways that require multiple molecular events to occur in a highly coordinated fashion.

  • Determination of the structure form of the fourth ligand of zinc in acutolysin a using combined quantum mechanical and molecular mechanical simulation
    Emilia L. Wu, Kin-Yiu Wong, Xin Zhang, Keli Han, and Jiali Gao

    Journal of Physical Chemistry B, ISSN: 15206106, Volume: 113, Pages: 2477-2485, Published: 26 February 2009 American Chemical Society (ACS)
    Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. On the basis of these theoretical results, we note that the experimental observed pH dependence of the proteolytic and hemorrhagic activity of Acutolysin A can be attributed to the deprotonation of the zinc-bound water to yield a better nucleophile, the hydroxide ion. Structural analyses revealed structural details useful for the understanding of acutolysin catalytic mechanism.

  • Multiple conformational switches in a GTPase complex control co-translational protein targeting
    Xin Zhang, Christiane Schaffitzel, Nenad Ban, and Shu-ou Shan

    Proceedings of the National Academy of Sciences of the United States of America, ISSN: 00278424, eISSN: 10916490, Volume: 106, Pages: 1754-1759, Published: 10 February 2009 Proceedings of the National Academy of Sciences
    The “GTPase switch” paradigm, in which a GTPase switches between an active, GTP-bound state and an inactive, GDP-bound state through the recruitment of nucleotide exchange factors (GEFs) or GTPase activating proteins (GAPs), has been used to interpret the regulatory mechanism of many GTPases. A notable exception to this paradigm is provided by two GTPases in the signal recognition particle (SRP) and the SRP receptor (SR) that control the co-translational targeting of proteins to cellular membranes. Instead of the classical “GTPase switch,” both the SRP and SR undergo a series of discrete conformational rearrangements during their interaction with one another, culminating in their reciprocal GTPase activation. Here, we show that this series of rearrangements during SRP-SR binding and activation provide important control points to drive and regulate protein targeting. Using real-time fluorescence, we showed that the cargo for SRP—ribosomes translating nascent polypeptides with signal sequences—accelerates SRP·SR complex assembly over 100-fold, thereby driving rapid delivery of cargo to the membrane. A series of subsequent rearrangements in the SRP·SR GTPase complex provide important driving forces to unload the cargo during late stages of protein targeting. Further, the cargo delays GTPase activation in the SRP·SR complex by 8–12 fold, creating an important time window that could further improve the efficiency and fidelity of protein targeting. Thus, the SRP and SR GTPases, without recruiting external regulatory factors, constitute a self-sufficient system that provides exquisite spatial and temporal control of a complex cellular process.

  • Demonstration of a Multistep Mechanism for Assembly of the SRP·SRP Receptor Complex: Implications for the Catalytic Role of SRP RNA
    Xin Zhang, Simon Kung, and Shu-ou Shan

    Journal of Molecular Biology, ISSN: 00222836, Volume: 381, Pages: 581-593, Published: 5 September 2008 Elsevier BV
    Two GTPases in the signal recognition particle (SRP) and its receptor (SR) control the delivery of newly synthesized proteins to the endoplasmic reticulum or plasma membrane. During the protein targeting reaction, the 4.5S SRP RNA accelerates the association between the two GTPases by 400-fold. Using fluorescence resonance energy transfer, we demonstrate here that formation of a stable SRP x SR complex involves two distinct steps: a fast initial association between SRP and SR to form a GTP-independent early complex and then a GTP-dependent conformational rearrangement to form the stable final complex. We also found that the 4.5S SRP RNA significantly stabilizes the early GTP-independent intermediate. Furthermore, mutational analyses show that there is a strong correlation between the ability of the mutant SRP RNAs to stabilize the early intermediate and their ability to accelerate SRP x SR complex formation. We propose that the SRP RNA, by stabilizing the early intermediate, can give this transient intermediate a longer life time and therefore a higher probability to rearrange to the stable final complex. This provides a coherent model that explains how the 4.5S RNA exerts its catalytic role in SRP x SR complex assembly.

  • High-order symplectic integration in quasi-classical trajectory simulation: Case study for O( 1D) + H 2
    Xin Zhang and Ke-Li Han

    International Journal of Quantum Chemistry, ISSN: 00207608, eISSN: 1097461X, Volume: 106, Pages: 1815-1819, Published: July 2006 Wiley
    Classical trajectory calculations for the o(d-1) + h-2 reaction system are employed to assess the effectiveness of the symplectic integrators. the sixth-order symplectic integrator has been found to be the most suitable method for the quasiclassical trajectory calculation of a long-lived complex-forming reaction system. in comparison with the traditional fourth-order runge-kutta initialized fourth-order admas-moulton-hamming predictor-corrector integrator (rk4-amh4), the sixth-order symplectic integrator is six times less computationally expensive and exhibits better energy conservation. (c) 2006 wiley periodicals, inc.

  • First principles quantum dynamics study reveals subtle resonance in polyatomic reaction: The case of F + CH4 → HF + CH3
    Tianshu Chu, Xin Zhang, Liping Ju, Li Yao, Ke-Li Han, Mingliang Wang, and John. Z.H. Zhang

    Chemical Physics Letters, ISSN: 00092614, Volume: 424, Issue: 4-6, Pages: 243-246, Published: 24 June 2006 Elsevier BV
    First principles quantum dynamics calculation has been carried out to investigate a recently observed resonance feature in the f + ch4 reaction by molecular beam experiment [w.c. shin, j.j. lin, k.p. liu, phys. rev. lett., 92 (2004) 103201]. the generalized semi-rigid vibrating rotor target (gsvrt) method is employed to perform the quantum dynamics calculation on new ab initio potential energy surfaces (pes) constructed from the extensive high level ab initio calculations. a resonance near the reaction threshold energy is observed in both the calculated microscopic reaction probabilities and integral cross-sections on the zyh2 pes. the calculated resonance on the zyh2 pes is in good agreement with the experimental observation. this resonance feature is highly quantum mechanical and sensitive to the accuracy of ab initio energies. (c) 2006 elsevier b.v. all rights reserved.

  • Ab initio study of the H + ClONO2 reaction
    Xiaofang Chen, Xin Zhang, Keli Han, and António J.C. Varandas

    Chemical Physics Letters, ISSN: 00092614, Volume: 421, Issue: 4-6, Pages: 453-459, Published: 15 April 2006 Elsevier BV
    The mechanism of the H + ClONO2 reaction is examined by performing QCISD calculations at geometries optimized at the MP2 level. Each of the six reaction channels involves stereoisomeric transition states that have identical energy barriers. The lowest energy barrier is 24.2 kcal mol(-1) for the indirect metathetical pathway leading to OH + cis-CIONO, being the corresponding rate constant calculated employing TST theory. The NO2-elimination channel and the indirect metathetical pathway leading to OH + trans-ClONO should compete with each other as they have barriers of 24.8 and 25.1 kcal mol(-1). For Cl-substitution, Cl-abstraction, and N-attack, the barriers are 27.4, 35.1, and 41.3 kcal mol(-1). (c) 2005 Elsevier B.V. All rights reserved.

  • Theoretical study of the mechanism for spin-forbidden quenching process O(1D) + CO2(1Σg+) → O(3P) + CO2(1Σg+)
    Guanghui Yang, Li Yao, Xin Zhang, Qingtian Meng, and Ke-Li Han

    International Journal of Quantum Chemistry, ISSN: 00207608, Volume: 105, Pages: 154-159, Published: 15 October 2005 Wiley
    The mechanism of the spin-forbidden quenching process O(1D) + CO2(1Σ) O(3P) + CO2(1Σ) was investigated by ab initio quantum chemistry methods. The calculations showed the singlet potential surface [O(1D)+CO2] is attractive where a strongly bound intermediate complex CO3 is formed in the potential basin without a transition state, whereas the complex CO3 that is formed on the triplet surface [O(3P)+CO3] must overcome a barrier. The complex channel was documented by searching minimum energy intersection points in the region of the bound complex CO3 and calculating spin-orbit coupling at the point. A direct channel was proposed by a study of cross point of singlet and triplet PESs with different collision angles and calculations of spin-orbit coupling at those cross points in a nonbound region of the [O(1D)+CO3] system. The mechanism of the energy transfer is discussed on the basis of the theoretical results. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

  • A modified potential energy surface for the C2H + H2 → C2H2 + H reaction and a theoretical study on its rate constants
    Li-Ping Ju, Ting-Xian Xie, Xin Zhang, and Ke-Li Han

    Chemical Physics Letters, ISSN: 00092614, Volume: 409, Issue: 4-6, Pages: 249-254, Published: 30 June 2005 Elsevier BV
    Abstract In this Letter, we report on the finding of a lower barrier height of the Wang and Bowman (WB) [D.S. Wang, J.M. Bowman, J. Chem. Phys. 101 (1994) 8646] potential energy surface (PES) for the C 2 H + H 2  → C 2 H 2  + H reaction basing on ab initio calculation at the QCISD (T, full)/aug-cc-pVTZ//QCISD (full)/cc-pVTZ level. The barrier height of the modified WB (designated as MWB) PES is 2.29 kcal/mol. The rate constants have also been calculated based on the MWB PES and the ab initio calculation in the present work by the P olyrate version 9.1 program. The rate constants calculated from the MWB PES agree well with the experimental data as well as the ab initio results in the present work.

  • A quantum wave-packet study of intersystem crossing effects in the O (P 2,1,0 3, D21) + H2 reaction
    Tian-Shu Chu, Xin Zhang, and Ke-Li Han

    Journal of Chemical Physics, ISSN: 00219606, Volume: 122, Published: 1 June 2005 AIP Publishing
    We present for the first time an exact quantum study of spin-orbit-induced intersystem crossing effects in the title reaction. The time-dependent wave-packet method, combined with an extended split operator scheme, is used to calculate the fine-structure resolved cross section. The calculation involves four electronic potential-energy surfaces of the 1A' state [J. Dobbyn and P. J. Knowles, Faraday Discuss. 110, 247 (1998)], the 3A' and the two degenerate 3A" states [S. Rogers, D. Wang, A. Kuppermann, and S. Wald, J. Phys. Chem. A 104, 2308 (2000)], and the spin-orbit couplings between them [B. Maiti, and G. C. Schatz, J. Chem. Phys. 119, 12360 (2003)]. Our quantum dynamics calculations clearly demonstrate that the spin-orbit coupling between the triplet states of different symmetries has the greatest contribution to the intersystem crossing, whereas the singlet-triplet coupling is not an important effect. A branch ratio of the spin state Pi32 to Pi12 of the product OH was calculated to be approximately 2.75, with collision energy higher than 0.6 eV, when the wave packet was initially on the triplet surfaces. The quantum calculation agrees quantitatively with the previous quasiclassical trajectory surface hopping study.

  • Theoretical Study on the Formation Mechanism of Iso-CH2I-Cl
    Guanghui Yang, Qingtian Meng, Xin Zhang, and Keli Han

    International Journal of Quantum Chemistry, ISSN: 00207608, Pages: 719-724, Published: 15 March 2004 Wiley
    The dissociation and isomerization reaction mechanism on the ground-state potential energy surface for CH2ClI are investigated by ab initio calculations. It is found that the isomer iso-CH2I-Cl can be produced from either the recombination of the photodissociation. fragments or the isomerization reaction of CH2ClI, rather than from isomerization reaction of iso-CH2Cl-I. Further explanations of experimental results are also presented. (C) 2003 Wiley Periodicals, Inc.

  • Quantum dynamics study of isotope effect for H+CH4 reaction using the SVRT model
    Xin Zhang, Guang-Hui Yang, Ke-Li Han, M. L. Wang, and John Z. H. Zhang

    Journal of Chemical Physics, ISSN: 00219606, Volume: 118, Pages: 9266-9271, Published: 22 May 2003 AIP Publishing
    The semirigid vibrating rotor target model is applied to study the isotope effect in reaction H+CH4→H2+CH3 using time-dependent wave-packet method. The reaction probabilities for producing H2 and HD product channels are calculated. The energy dependence of the reaction probabilities shows oscillating structures for both reaction channels. At low temperature or collision energies, the H atom abstraction is favored due to tunnelling effect. In partially deuterated CHxDy (x+y=4), the breaking of the C–H bond is favored over that of the C–D bond in the entire energy range studied. In H+CHD3 reaction at high energies, the HD product dominates simply due to statistical factor.

  • SVRT calculation for bond-selective reaction H+HOD→H2+OD, HD+OH
    Xin Zhang, KeLi Han, and John Z. H. Zhang

    Journal of Chemical Physics, ISSN: 00219606, Volume: 116, Pages: 10197-10200, Published: 23 June 2002 AIP Publishing
    The semirigid vibrating rotor target (SVRT) model is applied to study bond-selective branching reaction H+HOD→H2+OD, HD+OH on the Schatz–Elgersma potential energy surface when one of the stretching modes of HOD is excited. Using the SVRT model, the time-dependent wavepacket calculation is carried out in four-mathematical dimensions with the remaining two internal coordinates fixed. The reaction probabilities for producing two product branches are calculated from two separate dynamics calculations. The results show that for reaction H+HOD(100)→HD+OH when O–D stretching mode is excited, the SVRT calculation gives excellent results. The SVRT result is slightly worse for reaction H+HOD(001)→H2+OD when the O–H stretching mode is excited. The current study demonstrates that the SVRT model is also applicable for giving accurate results for polyatomic reactions when the chemical bond that is broken is vibrationally excited.

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    Y Cho, X Zhang, KFR Pobre, Y Liu, DL Powers, JW Kelly, LM Gierasch, ...
    Cell reports 11 (2), 321-333 2015

  • De Novo-Designed Enzymes as Small-Molecule-Regulated Fluorescence Imaging Tags and Fluorescent Reporters
    Y Liu, X Zhang, YL Tan, G Bhabha, DC Ekiert, Y Kipnis, S Bjelic, D Baker, ...
    Journal of the American Chemical Society 136 (38), 13102-13105 2014

  • Heat-Shock Response Transcriptional Program Enables High-Yield and High-Quality Recombinant Protein Production in Escherichia coli
    X Zhang, Y Liu, JC Genereux, C Nolan, M Singh, JW Kelly
    ACS chemical biology 9 (9), 1945-1949 2014

  • Chaperonins resculpt folding free energy landscapes to avoid kinetic traps and accelerate protein folding.
    X Zhang, JW Kelly
    Journal of molecular biology 426 (15), 2736 2014

  • Fidelity of cotranslational protein targeting by the signal recognition particle
    X Zhang, S Shan
    Annual review of biophysics 43, 381-408 2014

  • Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts
    Y Liu, YL Tan, X Zhang, G Bhabha, DC Ekiert, JC Genereux, Y Cho, ...
    Proceedings of the National Academy of Sciences 111 (12), 4449-4454 2014

  • Protein Conformational Dynamics
    KL Han, X Zhang, M Yang
    Springer Science & Business Media 2014

  • Mechanisms of transthyretin inhibition of β-amyloid aggregation in vitro
    X Li, X Zhang, ARA Ladiwala, D Du, JK Yadav, PM Tessier, PE Wright, ...
    Journal of Neuroscience 33 (50), 19423-19433 2013

  • Signal recognition particle: an essential protein-targeting machine
    D Akopian, K Shen, X Zhang, S Shan
    Annual review of biochemistry 82, 693-721 2013

MOST CITED SCHOLAR PUBLICATIONS

  • Signal recognition particle: an essential protein-targeting machine
    D Akopian, K Shen, X Zhang, S Shan
    Annual review of biochemistry 82, 693-721 2013
    Citations: 281

  • High‐order symplectic integration in quasi‐classical trajectory simulation: Case study for O(1D) + H2
    X Zhang, KL Han
    International journal of quantum chemistry 106 (8), 1815-1819 2006
    Citations: 148

  • Multiple conformational switches in a GTPase complex control co-translational protein targeting
    X Zhang, C Schaffitzel, N Ban, S Shan
    Proceedings of the National Academy of Sciences 106 (6), 1754-1759 2009
    Citations: 115

  • A quantum wave-packet study of intersystem crossing effects in the reaction
    TS Chu, X Zhang, KL Han
    The Journal of chemical physics 122 (21), 214301 2005
    Citations: 106

  • Sequential checkpoints govern substrate selection during cotranslational protein targeting
    X Zhang, R Rashid, K Wang, S Shan
    Science 328 (5979), 757-760 2010
    Citations: 97

  • Mechanisms of transthyretin inhibition of β-amyloid aggregation in vitro
    X Li, X Zhang, ARA Ladiwala, D Du, JK Yadav, PM Tessier, PE Wright, ...
    Journal of Neuroscience 33 (50), 19423-19433 2013
    Citations: 89

  • Demonstration of a multistep mechanism for assembly of the SRP SRP receptor complex: Implications for the catalytic role of SRP RNA
    X Zhang, S Kung, S Shan
    Journal of molecular biology 381 (3), 581-593 2008
    Citations: 84

  • Time-dependent quantum wave packet calculation for nonadiabatic reaction
    Y Zhang, TX Xie, KL Han, JZH Zhang
    The Journal of chemical physics 119 (24), 12921-12925 2003
    Citations: 77

  • MRCI potential curve and analytical potential energy function of the ground state of H2
    CL Yang, YJ Huang, X Zhang, KL Han
    Journal of Molecular Structure: THEOCHEM 625 (1-3), 289-293 2003
    Citations: 49

  • Fidelity of cotranslational protein targeting by the signal recognition particle
    X Zhang, S Shan
    Annual review of biophysics 43, 381-408 2014
    Citations: 48

  • Modulation of fluorescent protein chromophores to detect protein aggregation with turn-on fluorescence
    Y Liu, CH Wolstenholme, GC Carter, H Liu, H Hu, LS Grainger, K Miao, ...
    Journal of the American Chemical Society 140 (24), 7381-7384 2018
    Citations: 42

  • Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding
    MJ Yang, XQ Pang, X Zhang, KL Han
    Journal of structural biology 173 (1), 57-66 2011
    Citations: 38

  • Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases
    S Shan, SL Schmid, X Zhang
    Biochemistry 48 (29), 6696-6704 2009
    Citations: 37

  • Analytical potential energy function and spectroscopic parameters for the ground and excited states of NaH
    CL Yang, X Zhang, KL Han
    Journal of Molecular Structure: THEOCHEM 676 (1-3), 209-213 2004
    Citations: 35

  • AgHalo: A Facile Fluorogenic Sensor to Detect Drug‐Induced Proteome Stress
    Y Liu, M Fares, NP Dunham, Z Gao, K Miao, X Jiang, SS Bollinger, ...
    Angewandte Chemie 129 (30), 8798-8802 2017
    Citations: 34

  • The cation− π interaction enables a halo-tag fluorogenic probe for fast no-wash live cell imaging and gel-free protein quantification
    Y Liu, K Miao, NP Dunham, H Liu, M Fares, AK Boal, X Li, X Zhang
    Biochemistry 56 (11), 1585-1595 2017
    Citations: 34

  • Quantum dynamics study of isotope effect for reaction using the SVRT model
    X Zhang, GH Yang, KL Han, ML Wang, JZH Zhang
    The Journal of chemical physics 118 (20), 9266-9271 2003
    Citations: 32

  • Direct visualization reveals dynamics of a transient intermediate during protein assembly
    X Zhang
    Multistate GTPase Control Co-translational Protein Targeting, 27-48 2012
    Citations: 31

  • Theoretical study on analytical potential function and spectroscopic parameters for CaF molecule
    CL Yang, X Zhang, KL Han
    Journal of Molecular Structure: THEOCHEM 678 (1-3), 183-188 2004
    Citations: 30

  • Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting
    K Shen, X Zhang, S Shan
    Rna 17 (5), 892-902 2011
    Citations: 29