Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

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Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy

Biophysical Journal ◽

10.1016/j.bpj.2017.11.1883 ◽

2018 ◽

Vol 114 (3) ◽

pp. 337a

Author(s):

Vivek Govind Kumar

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Particle ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

The Stability ◽

Dynamics Simulations

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Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy

Journal of Structural Biology ◽

10.1016/j.jsb.2004.02.006 ◽

2004 ◽

Vol 147 (3) ◽

pp. 291-301 ◽

Cited By ~ 27

Author(s):

J.Bernard Heymann ◽

James F. Conway ◽

Alasdair C. Steven

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Protein Complexes ◽

Cryo Electron Microscopy

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Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy

Nature Structural & Molecular Biology ◽

10.1038/nsmb.2711 ◽

2013 ◽

Vol 20 (12) ◽

pp. 1352-1357 ◽

Cited By ~ 128

Author(s):

Alberto Bartesaghi ◽

Alan Merk ◽

Mario J Borgnia ◽

Jacqueline L S Milne ◽

Sriram Subramaniam

Keyword(s):

Electron Microscopy ◽

Envelope Glycoprotein ◽

Cryo Electron Microscopy ◽

Hiv 1

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Networks of HIV-1 envelope glycans maintain antibody epitopes in the face of glycan additions and deletions

10.1101/2020.02.21.959981 ◽

2020 ◽

Cited By ~ 2

Author(s):

Gemma E. Seabright ◽

Christopher A. Cottrell ◽

Marit J. van Gils ◽

Alessio D’addabbo ◽

David J. Harvey ◽

...

Keyword(s):

Electron Microscopy ◽

Neutralizing Antibodies ◽

Broadly Neutralizing Antibodies ◽

Site Specific ◽

Glycan Analysis ◽

Cryo Electron Microscopy ◽

Immunogen Design ◽

The Face ◽

Antibody Epitopes ◽

Hiv 1

SUMMARYNumerous broadly neutralizing antibodies (bnAbs) have been identified that target the glycans of the HIV-1 envelope spike. Neutralization breadth is notable given that glycan processing can be substantially influenced by the presence or absence of neighboring glycans. Here, using a stabilized recombinant envelope trimer, we investigate the degree to which mutations in the glycan network surrounding an epitope impact the fine glycan processing of antibody targets. Using cryo-electron microscopy and site-specific glycan analysis, we reveal the hierarchy of importance of glycans in the formation of the 2G12 bnAb epitope, and show that the epitope is only subtly impacted by variations in the glycan network. In contrast, we show that the PG9 and PG16 glycan-based epitopes at the trimer apex are dependent on the presence of the highly conserved surrounding glycans. Glycan networks underpin the conservation of bnAb epitopes and are an important parameter in immunogen design.

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Author response: Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

10.7554/elife.16105.057 ◽

2016 ◽

Author(s):

Abhishek Singharoy ◽

Ivan Teo ◽

Ryan McGreevy ◽

John E Stone ◽

Jianhua Zhao ◽

...

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Author Response ◽

Cryo Electron Microscopy

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Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

10.1101/2021.10.09.463779 ◽

2021 ◽

Author(s):

Anda Trifan ◽

Defne Gorgun ◽

Zongyi Li ◽

Alexander Brace ◽

Maxim Zvyagin ◽

...

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Finite Element Analysis ◽

Finite Element ◽

Pharmaceutical Compounds ◽

Viral Mrna ◽

Element Analysis ◽

Cryo Electron Microscopy ◽

Optimal Resource ◽

Domain Protein

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

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