Assembly and Dynamics of Bacterial Chemosensory Signaling Arrays
Lead Research Organisation:
University of Oxford
Department Name: Wellcome Trust Centre for Human Genetics
Abstract
For nearly six decades, chemotaxis - a ubiquitous biological behavior enabling the movement of a cell or organism toward or away from chemicals -has severed as a paradigmatic model for the study of cellular sensory signal transduction and motile behavior. The relatively simple chemotaxis machinery of the bacterium Escherichia coli is the best understood biological signal transduction system and serves as a powerful tool for investigating the molecular mechanisms that proteins use to detect, process, and transmit stimulus information. E. coli cells respond to changes in their chemical environment through a sensory apparatus that is an ordered array (chemosensory array) of hundreds of basic core signalling units consisting of three essential components, the transmembrane chemoreceptors that detects the environment, the histidine kinase that passes the signal to the downstream effector, and the adaptor protein. The core units further assemble into a two-dimensional lattice array which allows cells to amplify and integrate many varied and possibly conflicting signals to locate optimal growing conditions. In bacterial pathogens, chemotaxis response is crucial for colonization and infection. Thus, the signal transduction systems that mediate such responses are potential new targets for antimicrobial drug development.
To understand the underlying molecular mechanisms of chemosensory array assembly, activation and high cooperativity, it is essential to determine the precise interactions between the core signalling components, in the context of the array, and its dynamical properties. In this project, we propose to use a combination of cutting-edge cryoEM structural methods and computational modeling and multi-scale molecular simulations, as well as in vivo functional assays for structural validation, to investigate the structural and dynamical mechanisms underlying signal transduction and regulation in the chemosensory array. Our results will establish, in atomistic detail, how individual signals are transmitted across the receptor, adaptively regulated, and subsequently integrated over multiple receptor proteins to jointly affect kinase activity, highlighting general features of cooperative protein signaling. The significant overlap in molecular machinery employed by diverse chemotactic species will greatly extend the relevance of our results, including to signal transduction within a wide-range of human and plant pathogens.
To understand the underlying molecular mechanisms of chemosensory array assembly, activation and high cooperativity, it is essential to determine the precise interactions between the core signalling components, in the context of the array, and its dynamical properties. In this project, we propose to use a combination of cutting-edge cryoEM structural methods and computational modeling and multi-scale molecular simulations, as well as in vivo functional assays for structural validation, to investigate the structural and dynamical mechanisms underlying signal transduction and regulation in the chemosensory array. Our results will establish, in atomistic detail, how individual signals are transmitted across the receptor, adaptively regulated, and subsequently integrated over multiple receptor proteins to jointly affect kinase activity, highlighting general features of cooperative protein signaling. The significant overlap in molecular machinery employed by diverse chemotactic species will greatly extend the relevance of our results, including to signal transduction within a wide-range of human and plant pathogens.
Technical Summary
The mechanism of stimulus-response coupling in bacterial chemotaxis has emerged as a paradigm for understanding the principles of intracellular signal transduction both in bacterial and eukaryotic cells. Bacteria use chemotaxis signaling pathways to monitor and response their environment changes. The essential core signaling unit comprises transmembrane receptors, a histidine kinase CheA, and a coupling protein CheW. A few hundred core signaling complexes assemble into a lattice array responsible for the remarkable cooperativity in chemotaxis signaling. Despite current atomic structures of the individual soluble domains of the receptor, CheA, and CheW and sub-complexes of the core unit, high resolution structures of the full core complex and its extended higher order array assembly, as well as the conformational states associated with signal transduction and transmission, have remained unattainable. The large size and dynamic nature of the signalling array have challenged conventional structural methods. We recently developed a novel in vitro reconstitution system to generate arrays of the core signaling units that mimic the native chemosensory apparatus, and have obtained a density map of the array at 9Å resolution by cryo-electron tomography (cryoET) and sub-tomogram averaging of data recorded on a CCD camera. Building on this success, we aim to 1) determine the structures of the core signaling complex and its extended array to near-atomic resolution using new direct electron detector and cryoET and sub-tomogram averaging, 2) develop atomic models of the dynamic signaling arrays by integrating the cryoEM structural "snapshots" of different states with large-scale MD simulations, and 3) functionally characterize the molecular interfaces within native cells. Through this integrative approach, the proposed studies will provide new and comprehensive insights into the mechanisms of chemotactic array assembly, activation and cooperativity.
Planned Impact
Understanding the mechanism of signaling in bacterial chemotaxis is of great interest for many areas of biology and medicine. Our proposed efforts for a comprehensive and integrated structural and functional analysis of the conserved bacterial chemosensory array will provide new insights into receptor-kinase coupling, signaling complex and array formation, and conformational dynamics essential for signaling, and will contribute to a deep understanding of signal transduction and signal processing that will also present new targets for antimicrobial drug development. Impact will arise in several ways.
Firstly, our work will inform fundamental microbiology, providing structural paradigms that explain function.
Secondly, it will provide new methods, protocols, reagents and software tools that may be of general value to structural biologists and computational biologists.
Thirdly, the proposed study is basic research of potential value to the commercial sector, in particular in the biotechnology and pharmaceutical industries on antimicrobial drug development. By inhibiting the proteins involved in chemotaxis, one can develop novel antibiotics to control multi-drug-resistant strains of bacteria. Given, the drug discovery process can take up to 20 years, it is imperative we prepare well in advance to counteract the threat of a society where resistant bacterial strains are common-place and untreatable. Therefore, if we are sufficiently well equipped, the impact of this proposal will be long lasting and life-changing for the future generations.
Fourthly, increased public understanding is an important benefit to the wider public. Structural and Computational approaches to the biosciences has a major advantage in that they are able to produce artistic and descriptive illustrations of biomolecules, that facilitate the accessibility of these ubiquitous macromolecular machines to the general public. Furthermore, molecular simulation enables the reanimation of statically resolved structures into movies that demonstrate the dynamics visually. By tuning the science to an appropriate level of detail, by using graphics tools such as Blender, one can make the research available as museum displays and as educational tools in schools.
The final area of impact for this research project will be in the training and career development of a cohort of young research scientists. We have been able to work with very talented, energetic, enthusiastic scientists, some experienced, and others at an early career stage, and we believe our laboratories have provided them with an excellent training environment. Of the order of a dozen of these have since gone on to leadership positions, in academia and industry.
This work is directly related to the BBSRC strategic priority areas of Bioscience for Health ("Develop and apply new tools in areas such as chemical biology, high resolution structural analysis"), to World-class Bioscience ("predictive, integrative and systems approaches in bioscience at a range of scales from molecules to...") and to Exploiting New Ways of Working by developing "the next generation of bioscience tools to drive new and deeper understanding in bioscience". This proposal directly relates to Combatting antimicrobial resistance by studying digital pathways within pathogenic organisms, while there are also elements to this proposal that comprise the systems approaches to and technology development for the biosciences. Therefore, this promotes partnerships with the pharmaceutical industry, in addition to the development of academic collaborations.
Thus, the overall impact will be to advance UK knowledge and technological development as well as promoting health and wellbeing through better drug design. Ultimately this will add significantly to the competitiveness of UK industry.
Firstly, our work will inform fundamental microbiology, providing structural paradigms that explain function.
Secondly, it will provide new methods, protocols, reagents and software tools that may be of general value to structural biologists and computational biologists.
Thirdly, the proposed study is basic research of potential value to the commercial sector, in particular in the biotechnology and pharmaceutical industries on antimicrobial drug development. By inhibiting the proteins involved in chemotaxis, one can develop novel antibiotics to control multi-drug-resistant strains of bacteria. Given, the drug discovery process can take up to 20 years, it is imperative we prepare well in advance to counteract the threat of a society where resistant bacterial strains are common-place and untreatable. Therefore, if we are sufficiently well equipped, the impact of this proposal will be long lasting and life-changing for the future generations.
Fourthly, increased public understanding is an important benefit to the wider public. Structural and Computational approaches to the biosciences has a major advantage in that they are able to produce artistic and descriptive illustrations of biomolecules, that facilitate the accessibility of these ubiquitous macromolecular machines to the general public. Furthermore, molecular simulation enables the reanimation of statically resolved structures into movies that demonstrate the dynamics visually. By tuning the science to an appropriate level of detail, by using graphics tools such as Blender, one can make the research available as museum displays and as educational tools in schools.
The final area of impact for this research project will be in the training and career development of a cohort of young research scientists. We have been able to work with very talented, energetic, enthusiastic scientists, some experienced, and others at an early career stage, and we believe our laboratories have provided them with an excellent training environment. Of the order of a dozen of these have since gone on to leadership positions, in academia and industry.
This work is directly related to the BBSRC strategic priority areas of Bioscience for Health ("Develop and apply new tools in areas such as chemical biology, high resolution structural analysis"), to World-class Bioscience ("predictive, integrative and systems approaches in bioscience at a range of scales from molecules to...") and to Exploiting New Ways of Working by developing "the next generation of bioscience tools to drive new and deeper understanding in bioscience". This proposal directly relates to Combatting antimicrobial resistance by studying digital pathways within pathogenic organisms, while there are also elements to this proposal that comprise the systems approaches to and technology development for the biosciences. Therefore, this promotes partnerships with the pharmaceutical industry, in addition to the development of academic collaborations.
Thus, the overall impact will be to advance UK knowledge and technological development as well as promoting health and wellbeing through better drug design. Ultimately this will add significantly to the competitiveness of UK industry.
Organisations
- University of Oxford (Lead Research Organisation)
- HARVARD UNIVERSITY (Collaboration)
- Columbia University (Collaboration)
- University of Virginia (UVa) (Collaboration)
- Case Western Reserve University (Collaboration)
- University of Utah (Collaboration)
- University of Warwick (Collaboration)
- Trinity College Dublin (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- University of Delaware (Collaboration)
- Vanderbilt University (Collaboration)
- Northwestern University (Collaboration)
- UNIVERSITY OF YORK (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- Rosalind Franklin Institute (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- University of Pittsburgh (Collaboration)
- UNIVERSITY OF SOUTHAMPTON (Collaboration)
- University of Bristol (Collaboration)
Publications
Abraham M
(2019)
Sharing Data from Molecular Simulations
in Journal of Chemical Information and Modeling
Abraham M
(2019)
Sharing Data from Molecular Simulations
Alvarez FJD
(2020)
Purification and Characterization of MxB.
in Methods in molecular biology (Clifton, N.J.)
Ansell TB
(2023)
LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
in Nature communications
Ansell TB
(2021)
Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.
in Journal of chemical theory and computation
Ashraf K
(2022)
Structural basis of lipopolysaccharide maturation by the O-antigen ligase
in Nature
Autzen HE
(2018)
Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment.
in Biochemistry
Baker A
(2020)
The SARS-COV-2 Spike Protein Binds Sialic Acids and Enables Rapid Detection in a Lateral Flow Point of Care Diagnostic Device
in ACS Central Science
Beale EV
(2020)
A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction.
in Frontiers in molecular biosciences
Bolla JR
(2020)
A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins.
in Angewandte Chemie (International ed. in English)
Brown CM
(2023)
Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane.
in Proceedings of the National Academy of Sciences of the United States of America
Burt A
(2020)
Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain.
in Nature communications
Burt A
(2021)
Alternative Architecture of the E. coli Chemosensory Array.
in Biomolecules
Bushell SR
(2019)
The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K.
in Nature communications
Bárcena M
(2021)
Structural biology in the fight against COVID-19.
in Nature structural & molecular biology
Caffalette C
(2019)
A lipid gating mechanism for the channel-forming O antigen ABC transporter
in Nature Communications
Caldwell TA
(2022)
Conformational dynamics of the membrane enzyme LspA upon antibiotic and substrate binding.
in Biophysical journal
Cassidy CK
(2018)
CryoEM-based hybrid modeling approaches for structure determination.
in Current opinion in microbiology
Cassidy CK
(2023)
Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells.
in mBio
Cassidy CK
(2020)
Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations.
in Communications biology
Chavent M
(2018)
Interactions of the EphA2 Kinase Domain with PIPs in Membranes: Implications for Receptor Function
in Structure
Cook J
(2023)
Activator-induced conformational changes regulate division-associated peptidoglycan amidases
in Proceedings of the National Academy of Sciences
Cook J
(2020)
Insights into bacterial cell division from a structure of EnvC bound to the FtsX periplasmic domain.
in Proceedings of the National Academy of Sciences of the United States of America
Corey RA
(2019)
Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations.
in Journal of chemical theory and computation
Corey RA
(2022)
Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of complexes III and IV.
in Chemical science
Corey RA
(2021)
Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins.
in Science advances
Corey RA
(2020)
The energetics of protein-lipid interactions as viewed by molecular simulations.
in Biochemical Society transactions
Couves EC
(2023)
Structural basis for membrane attack complex inhibition by CD59.
in Nature communications
Deme JC
(2020)
Structures of the stator complex that drives rotation of the bacterial flagellum.
in Nature microbiology
Depelteau JS
(2022)
UVC inactivation of pathogenic samples suitable for cryo-EM analysis.
in Communications biology
Dietz L
(2023)
Structural basis for SMAC-mediated antagonism of caspase inhibition by the giant ubiquitin ligase BIRC6.
in Science (New York, N.Y.)
Dijkman PM
(2020)
Conformational dynamics of a G protein-coupled receptor helix 8 in lipid membranes.
in Science advances
Dinsdale RL
(2021)
An outer-pore gate modulates the pharmacology of the TMEM16A channel.
in Proceedings of the National Academy of Sciences of the United States of America
Domanski J
(2018)
Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association.
in Journal of chemical theory and computation
Duyvesteyn HME
(2018)
Machining protein microcrystals for structure determination by electron diffraction.
in Proceedings of the National Academy of Sciences of the United States of America
El Ghachi M
(2018)
Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.
in Nature communications
Fiorentino F
(2021)
Dynamics of an LPS translocon induced by substrate and an antimicrobial peptide.
in Nature chemical biology
Fu X
(2019)
AutoCLEM: An Automated Workflow for Correlative Live-Cell Fluorescence Microscopy and Cryo-Electron Tomography.
in Scientific reports
Fuss MF
(2023)
Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation.
in Nature communications
Hadjidemetriou K
(2022)
Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches.
in Biochemical Society transactions
Description | Bacterial chemotaxis pathways, in particular that of E. coli, are the best characterized signal transduction systems in microbiology. This manuscript describes, in unprecedented detail, the highly-conserved sensory core signaling complex underlying chemotactic behavior in motile bacteria. Despite decades of structural studies, this large (~1MD) and dynamic complex has resisted high-resolution characterization, obscuring the molecular details of critical signal transduction mechanisms. We present the first sub-nanometer resolution structure, solved using cryo-electron tomography (cryoET) and subtomogram averaging, as well as an all-atom model of the E. coli core signaling complex derived from our cryoET data. The integration of cryoEM and computer simulation allows us to take the first in-depth look at the structure and dynamics of the E. coli chemosensory proteins in their native structural context. The results presented in the current manuscript provide particular insight into the workings of the sensory molecule at the heart of bacterial chemotaxis, namely the histidine kinase CheA. In particular, we identify multiple, distinct conformations of CheA catalytic domain and highlight specific structural elements responsible for stabilizing each. These findings rationalize several previous observations made by us and others in the field. Our atomic model provides a high-fidelity structural platform for investigating critical signaling-related changes throughout the signaling complex and will enable the broader chemotaxis community to design novel experiments to test and expand existing signal transduction models. Considering the highly-conserved nature of the signaling complex in diverse bacterial species, including numerous human and plant pathogens, our results should be of general interest to those studying microbial signal transduction. Furthermore, cutting-edge image processing methods and molecular modeling tools developed and applied in this study should benefit a wide-range of experimental and computational biologists alike, especially those involved in structure determination of large, dynamical multi-protein complexes. |
Exploitation Route | publication structure deposition |
Sectors | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
Description | The impact arises in several ways: 1.We provide new methods, protocols, reagents and software tools that may be of general value to structural biologists and computational biologists. 2. The structure models we derived is of potential value to the commercial sector, in particular in the biotechnology and pharmaceutical industries on antimicrobial drug development. By inhibiting the proteins and interfering protein-protein interactions involved in chemotaxis, one can develop novel antibiotics to control multi-drug-resistant strains of bacteria. 3. Increased public understanding is an important benefit to the wider public. Structural and Computational approaches to the biosciences has a major advantage in that they are able to produce artistic and descriptive illustrations of biomolecules, that facilitate the accessibility of these ubiquitous macromolecular machines to the general public. 4. Molecular simulation enables the reanimation of statically resolved structures into movies that demonstrate the dynamics visually. By tuning the science to an appropriate level of detail, by using graphics tools such as Blender, one can make the research available as museum displays and as educational tools in schools. 5. Our laboratories have provided a cohort of young research scientists with an excellent training environment. |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology |
Impact Types | Societal,Economic,Policy & public services |
Title | Structure and Dynamics of the E. coli Chemotaxis Core Signaling Complex by Cryo-electron Tomography and Molecular Simulations |
Description | electron density map of the E. coli 4Q core signaling unit: EMD-10050, and PDB code: 6S1K |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | provide an atomic model of the Escherichia coli chemotaxis core signaling unit. |
Description | Collaboration with Case Western |
Organisation | Case Western Reserve University |
Department | Department of Biochemistry |
Country | United States |
Sector | Academic/University |
PI Contribution | Molecular simulations of the copper transporter CusA revealing how Copper stabilises the efflux state. We also show how the periplasmic domains change conformation from resting to extrusion state and also how protons may use a water wire across the membrane to power transport via the Proton Motive Force. |
Collaborator Contribution | Ed Yu and his lab have provided novel structures of the CusA transporter in distinct states. |
Impact | mBio publication now accepted. |
Start Year | 2020 |
Description | Collaboration with Tanmay Bharat |
Organisation | University of Oxford |
Department | Sir William Dunn School of Pathology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Simulations of bacterial Surface Layer proteins. |
Collaborator Contribution | Structures and functional data for SLPs |
Impact | Structural basis of lipopolysaccharide mediated surface layer anchoring on Caulobacter crescentus cells Andriko von Kügelgen, Haiping Tang, Gail G. Hardy, Danguole Kureisaite-Ciziene, Yves V. Brun, Phillip J. Stansfeld, Carol V. Robinson, and Tanmay A.M. Bharat Cell pii: S0092-8674(19)31332-7. doi: 10.1016/j.cell.2019.12.006. A further publication is being finalised for submission. |
Start Year | 2018 |
Description | Collaboration with Trinity College Dublin |
Organisation | Trinity College Dublin |
Department | School of Biochemistry and Immunology |
Country | Ireland |
Sector | Academic/University |
PI Contribution | Collaboration to study lipoprotein maturation and transport. We provide the molecular simulation and computational data to add value to our collaborators' structures. |
Collaborator Contribution | Our collaborators provide the molecular structures and experimental data. |
Impact | Publications, seminars and contribution to an international website resource. |
Start Year | 2013 |
Description | Collaboration with University of Bristol |
Organisation | University of Bristol |
Department | School of Biochemistry Bristol |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Collaboration with Prof Ian Collinson and development of a collaborative award. |
Collaborator Contribution | Initial contact and development of research ideas |
Impact | Wellcome Trust collaborative award passed the triage stage and is now submitted as a full proposal. |
Start Year | 2020 |
Description | Collaboration with University of Columbia |
Organisation | Columbia University |
Country | United States |
Sector | Academic/University |
PI Contribution | Computational simulations and modelling to understand key biosynthetic pathways within the bacterial cell envelope. |
Collaborator Contribution | Molecular structures of key biosynthetic enzymes. |
Impact | Papers in progress. 1 paper ready for submission in Mar 2021. |
Start Year | 2020 |
Description | HIV-1 capsid maturation |
Organisation | National Institutes of Health (NIH) |
Country | United States |
Sector | Public |
PI Contribution | structural analysis of mature and immature HOV-1 capsid and in complex with maturation inhibitors |
Collaborator Contribution | mutagenisis, function assays (NIH and Vanderbilt) simulations and solid state NMR structural analysis (delaware) Solution NMR (pittsburgh) |
Impact | Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P* (2021) CryoET structures of immature HIV Gag reveal a complete six-helix bundle. Commun Biol. 4(1):481. Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P* (2020) Intrinsic curvature of HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27(9):855-862 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra Jr R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T (2017) Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun 8(1):1779 Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P* (2017) CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B 121(15):3853-3863 Krebs AS, Mendonça LM, Zhang P.* (2022) Structural Analysis of Retrovirus Assembly and Maturation. Viruses 14(1):54 Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. |
Start Year | 2018 |
Description | HIV-1 capsid maturation |
Organisation | University of Delaware |
Country | United States |
Sector | Academic/University |
PI Contribution | structural analysis of mature and immature HOV-1 capsid and in complex with maturation inhibitors |
Collaborator Contribution | mutagenisis, function assays (NIH and Vanderbilt) simulations and solid state NMR structural analysis (delaware) Solution NMR (pittsburgh) |
Impact | Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P* (2021) CryoET structures of immature HIV Gag reveal a complete six-helix bundle. Commun Biol. 4(1):481. Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P* (2020) Intrinsic curvature of HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27(9):855-862 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra Jr R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T (2017) Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun 8(1):1779 Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P* (2017) CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B 121(15):3853-3863 Krebs AS, Mendonça LM, Zhang P.* (2022) Structural Analysis of Retrovirus Assembly and Maturation. Viruses 14(1):54 Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. |
Start Year | 2018 |
Description | HIV-1 capsid maturation |
Organisation | University of Pittsburgh |
Country | United States |
Sector | Academic/University |
PI Contribution | structural analysis of mature and immature HOV-1 capsid and in complex with maturation inhibitors |
Collaborator Contribution | mutagenisis, function assays (NIH and Vanderbilt) simulations and solid state NMR structural analysis (delaware) Solution NMR (pittsburgh) |
Impact | Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P* (2021) CryoET structures of immature HIV Gag reveal a complete six-helix bundle. Commun Biol. 4(1):481. Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P* (2020) Intrinsic curvature of HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27(9):855-862 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra Jr R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T (2017) Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun 8(1):1779 Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P* (2017) CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B 121(15):3853-3863 Krebs AS, Mendonça LM, Zhang P.* (2022) Structural Analysis of Retrovirus Assembly and Maturation. Viruses 14(1):54 Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. |
Start Year | 2018 |
Description | HIV-1 capsid maturation |
Organisation | Vanderbilt University |
Country | United States |
Sector | Academic/University |
PI Contribution | structural analysis of mature and immature HOV-1 capsid and in complex with maturation inhibitors |
Collaborator Contribution | mutagenisis, function assays (NIH and Vanderbilt) simulations and solid state NMR structural analysis (delaware) Solution NMR (pittsburgh) |
Impact | Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P* (2021) CryoET structures of immature HIV Gag reveal a complete six-helix bundle. Commun Biol. 4(1):481. Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P* (2020) Intrinsic curvature of HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27(9):855-862 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra Jr R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T (2017) Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun 8(1):1779 Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P* (2017) CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B 121(15):3853-3863 Krebs AS, Mendonça LM, Zhang P.* (2022) Structural Analysis of Retrovirus Assembly and Maturation. Viruses 14(1):54 Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P* (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv 7(47):eabj5715 Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. |
Start Year | 2018 |
Description | HIV-1 interaction with CPSF6 |
Organisation | Harvard University |
Country | United States |
Sector | Academic/University |
PI Contribution | We contributed structural analysis |
Collaborator Contribution | light microscpy, mutagenesis |
Impact | Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. Ning J, Zhong Z, Fischer DK, Harris G, Watkins SC, Ambrose Z, Zhang P* (2018) Truncated CPSF6 forms higher order complexes that bind and disrupt HIV-1 capsid. J Virol 92(13). pii: e00368-18 |
Start Year | 2018 |
Description | HIV-1 interaction with CPSF6 |
Organisation | University of Pittsburgh |
Country | United States |
Sector | Academic/University |
PI Contribution | We contributed structural analysis |
Collaborator Contribution | light microscpy, mutagenesis |
Impact | Zhong Z, Ning J, Boggs E, Jang S, Wallace C, Telmer C, Bruchez M, Ahn J, Engelman A, Zhang P, Watkins S, and Ambrose Z (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner. mBio12(2): e03142-20. Ning J, Zhong Z, Fischer DK, Harris G, Watkins SC, Ambrose Z, Zhang P* (2018) Truncated CPSF6 forms higher order complexes that bind and disrupt HIV-1 capsid. J Virol 92(13). pii: e00368-18 |
Start Year | 2018 |
Description | SARS-CoV-2 vaccine development |
Organisation | University of Oxford |
Department | Oxford Hub |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We performed structural analysis by cryoET and subtomogram averaging |
Collaborator Contribution | Gilbert's contributed the ChadOx vaccine and andybody assays. Crispin's group contributed Mass spec analysis |
Impact | Watanabe Y, Mendonça L, Allen E, Howe A, Lee M, Allen J, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska,M, Belij-Rammerstorfer S, Morris S, Krebs A, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton G, Green C, Lambe T, Zhang P*, Gilbert S, Crispin M (2021) Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19 vaccine. ACS Central Science Article ASAP DOI: 10.1021/acscentsci.1c00080 |
Start Year | 2020 |
Description | SARS-CoV-2 vaccine development |
Organisation | University of Southampton |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We performed structural analysis by cryoET and subtomogram averaging |
Collaborator Contribution | Gilbert's contributed the ChadOx vaccine and andybody assays. Crispin's group contributed Mass spec analysis |
Impact | Watanabe Y, Mendonça L, Allen E, Howe A, Lee M, Allen J, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska,M, Belij-Rammerstorfer S, Morris S, Krebs A, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton G, Green C, Lambe T, Zhang P*, Gilbert S, Crispin M (2021) Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19 vaccine. ACS Central Science Article ASAP DOI: 10.1021/acscentsci.1c00080 |
Start Year | 2020 |
Description | Sorting nexins (SNX) in membrane trafficking |
Organisation | University of Pittsburgh |
Country | United States |
Sector | Academic/University |
PI Contribution | We carried out cryoEM structure determination and structural analysis. |
Collaborator Contribution | Ford's lab made the proteins and carried functional analysis and determined crystal structures. |
Impact | Varlakhanova NV, Alvarez FJD, Brady TM, Tornabene BA, Hosford CJ, Chappie JS, Zhang P, Ford MGJ (2018) Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture. J Cell Biol 217(10):3608-3624 Sun D, Varlakhanova NV, Tornabene BA, Ramachandran R, Zhang P*, Ford MGJ (2020) The cryo-EM structure of the SNX-BAR Mvp1 tetramer. Nat Commun 11(1):1506. |
Start Year | 2018 |
Description | Structure and mechanism of bactericidal mammalian perforin-2 |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We carried out structural determination |
Collaborator Contribution | Gilbert's lab provided the biological system and functional analysis |
Impact | Ni T, Jiao F, Yu X, Aden S, Ginger L, Williams SI, Bai F, Pražák V, Karia D, Stansfeld P, Zhang P, Munson G, Anderluh G, Scheuring S, Gilbert RJC (2020) Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity. Sci Adv 6(5):eaax8286. Yu X, Ni T, Munson G, Zhang P*, Gilbert RJC (2022) Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation. EMBO J e111857. |
Start Year | 2018 |
Description | University of Virginia |
Organisation | University of Virginia (UVa) |
Department | School of Medicine |
Country | United States |
Sector | Academic/University |
PI Contribution | Molecular simulations of molecular structures solved by the Zimmer research group. |
Collaborator Contribution | Provision of novel molecular protein structures. |
Impact | Understanding of the mechanisms of polysaccharide transport. |
Start Year | 2018 |
Description | bacterial carboxysomes |
Organisation | University of Liverpool |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Structural characterization of carboxysome components and thylakoid membrane biogenesis |
Collaborator Contribution | Sample preparation |
Impact | Ni T, Sun Y, Burn W, Al-Hazeem MMJ, Zhu Y, Yu X, Liu LN, Zhang P* (2022) Structure and assembly of cargo Rubisco in two native a-carboxysomes. Nat Commun.13:4299. Huokko T, Ni T, Dykes GF, Simpson DM, Brownridge P, Conradi FD, Beynon RJ, Nixon PJ, Mullineaux CW, Zhang P, Liu LN (2021) Probing the biogenesis pathway and dynamics of thylakoid membranes. Nat Commun. 12(1):3475. |
Start Year | 2018 |
Description | cryoEM software development |
Organisation | University of York |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | software development for cryoEM |
Collaborator Contribution | guiding and validating new software |
Impact | Olek M, Cowtan K, Webb D, Chaban Y, Zhang P. (2021) IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice. Structure, doi: 10.1016/j.str.2022.01.005 |
Start Year | 2019 |
Description | in situ structure determination of pMMO in methanotrophs |
Organisation | Northwestern University |
Country | United States |
Sector | Academic/University |
PI Contribution | structure determination and analysis by cryoET and subtomogram averaging |
Collaborator Contribution | sample preparation |
Impact | Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P* (2022) Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 13(1):5221. |
Start Year | 2018 |
Description | in situ virus structures |
Organisation | University of Oxford |
Department | Oxford Hub |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | we perform cryoET subtomogram averaging of virus structures inside of native infected cells |
Collaborator Contribution | Viruses and infection studies |
Impact | Sutton G, Sun D, Fu X, Kotecha A, Hecksel CW, Clare DK, Zhang P*, Stuart DI, Boyce M (2020) Assembly intermediates of orthoreovirus captured in the cell. Nat Commun 11(1), 4445 Duyvesteyn HME, Kotecha A, Ginn HM, Hecksel CW, Beale EV, de Haas F, Evans G, Zhang P, Chiu W, Stuart DI (2018) Machining protein microcrystals for structure determination by electron diffraction. Proc Natl Acad Sci USA 115(38):9569-9573 Clare DK, Siebert CA, Hecksel C, Hagen C, Mordhorst V, Grange M, Ashton AW, Walsh MA, Grünewald K, Saibil HR, Stuart DI, Zhang P (2017) Electron Bio-Imaging Centre (eBIC): the UK national research facility for biological electron microscopy. Acta Crystallogr D Struct Biol 9(1):65 Zhou L, Song J, Kim J, Pei X, Huang C, Boyce M, Mendonca L, Clare D, Siebert A, Allen C, Liberti E, Stuart DI, Pan X, Nellist P, Zhang P, Kirkland A, and Wang P (2020) Low-Dose Phase Retrieval of Biological Specimens using Cryo-Electron Ptychography. Nat Commun 11 (1):2773. |
Start Year | 2018 |
Description | ptychography imaging of biological samples |
Organisation | University of Oxford |
Department | Oxford Hub |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | we contributed the biological system and duidance for low lose imaging |
Collaborator Contribution | ptychography imaging and reconstruction |
Impact | Zhou L, Song J, Kim J, Pei X, Huang C, Boyce M, Mendonca L, Clare D, Siebert A, Allen C, Liberti E, Stuart DI, Pan X, Nellist P, Zhang P, Kirkland A, and Wang P (2020) Low-Dose Phase Retrieval of Biological Specimens using Cryo-Electron Ptychography. Nat Commun 11 (1):2773. |
Start Year | 2019 |
Description | ptychography imaging of biological samples |
Organisation | University of Warwick |
Department | Warwick Evidence |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | we contributed the biological system and duidance for low lose imaging |
Collaborator Contribution | ptychography imaging and reconstruction |
Impact | Zhou L, Song J, Kim J, Pei X, Huang C, Boyce M, Mendonca L, Clare D, Siebert A, Allen C, Liberti E, Stuart DI, Pan X, Nellist P, Zhang P, Kirkland A, and Wang P (2020) Low-Dose Phase Retrieval of Biological Specimens using Cryo-Electron Ptychography. Nat Commun 11 (1):2773. |
Start Year | 2019 |
Description | regulation of bacterial capsule assembly |
Organisation | Rosalind Franklin Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | structure determination by cryoEM |
Collaborator Contribution | Biological funcation, protein preparation |
Impact | Yang Y, Liu J, Clarke BR, Seidel L, Bolla JR, Ward PN, Zhang P, Robinson CV, Whitfield C, Naismith JH. (2021) The molecular basis of regulation of bacterial capsule assembly by Wzc. Nat Commun. 12(1):4349. |
Start Year | 2018 |
Description | structure of the chemosensory array core signalling unit in an E. coli minicell strain |
Organisation | University of Utah |
Country | United States |
Sector | Academic/University |
PI Contribution | We carried out cryoET and subtomogram averaging of E coli core signaling complex. |
Collaborator Contribution | Parkinson's group provided mutatants and performed functional analysis |
Impact | Cassidy CK, Himes BA, Sun D, Ma J, Zhao G, Parkinson JS, Stansfeld PJ, Luthey-Schulten Z and Zhang P* (2020) Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations. Commun Biol. 3(1):24. doi:10.1038/s42003-019-0748-0 |
Start Year | 2019 |
Description | study of bacterial microcompartments |
Organisation | University of Liverpool |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We contributed the cryoET structural analysis. |
Collaborator Contribution | Liu's group contribited biological and functional analysis and mutagenesis. |
Impact | Huokko T, Ni T, Dykes GF, Simpson DM, Brownridge P, Conradi FD, Beynon RJ, Nixon PJ, Mullineaux CW, Zhang P, Liu LN (2021) Probing the biogenesis pathway and dynamics of thylakoid membranes. Nat Commun. 12(1):3475. |
Start Year | 2019 |
Title | CG2AT2 |
Description | An enhance version of our method to convert a coarse-grained system to atomic detail. https://github.com/pstansfeld/cg2at |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Becoming widely used within our research group and those that that are linked to our work. Aims to publish in the near future and induce world-wide usage. |
Title | Free Energy calculation methods for Lipid-Protein Interactions |
Description | We have developed new tools for studying lipid-protein interactions. https://github.com/owenvickery/metadynamics_analysis https://github.com/owenvickery/umbrella_sampling |
Type Of Technology | New/Improved Technique/Technology |
Year Produced | 2019 |
Impact | For further details see: Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations. Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ. J Chem Theory Comput. 2019 Oct 8;15(10):5727-5736. doi: 10.1021/acs.jctc.9b00548. |
URL | https://github.com/owenvickery/metadynamics_analysis |
Title | High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity |
Description | Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA. |
Type Of Technology | Software |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | emClarity allows for high resolution structure determination of proteins and protein complexes within the very native cellular context. This is a protocol paper for any research scientist who wishes to unleash the power of in situ structural biology. |
Title | IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice |
Description | IceBreaker allows users to estimate the relative ice gradient and flatten it by equalizing the local contrast. It allows the differentiation of particles from the background and improves overall particle picking performance. Furthermore, we introduce an additional parameter corresponding to local ice thickness for each particle. Particles with a defined ice thickness can be grouped and filtered based on this parameter during processing. |
Type Of Technology | Software |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | These functionalities are especially valuable for on-the-fly processing to automatically pick as many particles as possible from each micrograph and to select optimal regions for data collection. Finally, estimated ice gradient distributions can be stored separately and used to inspect the quality of prepared samples. |
URL | https://github.com/DiamondLightSource/python-icebreaker |
Title | Lipoprotein Modification Tool |
Description | We have developed a method to automatically modify lipoprotein cysteine residues. |
Type Of Technology | Software |
Year Produced | 2020 |
Impact | This forms part of this paper: Characterising Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations Shanlin Rao, George Bates, Callum Matthews, Owen Vickery, Phillip J. Stansfeld Structure The tool is here: https://github.com/owenvickery/add_acyl_tails_martini_2.2 |
URL | https://www.sciencedirect.com/science/article/pii/S0969212620300125 |
Title | bHimes/emClarity: Test Zenodo |
Description | No description provided. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by cryo-electron tomography (cryo-ET) combined with subtomogram alignment and classification, which in exceptional cases achieves subnanometer resolution, yielding insight into structure-function relationships. However, it remains challenging to apply this approach to specimens that exhibit conformational or compositional heterogeneity or are present in low abundance. To address this, we developed emClarity (https://github.com/bHimes/emClarity/wiki), a GPU-accelerated image-processing package featuring an iterative tomographic tilt-series refinement algorithm that uses subtomograms as fiducial markers and a 3D-sampling-function-compensated, multi-scale principal component analysis classification method. We demonstrate that our approach offers substantial improvement in the resolution of maps and in the separation of different functional states of macromolecular complexes compared with current state-of-the-art software. |
URL | https://zenodo.org/record/4546618 |