Phyre and PhyreRisk – Integrating genetic variant data with experimental and predicted protein structures and their complexes

Kelley, Lawrence A.; David, Alessia; Ittisoponpisan, Sirawit; Mezulis, Stefans; Ofoegbu, Tochukwu C.; Chakravarty, Devlina; Kundrotas, Petras J.; Vakser, Ilya A.; Sternberg, Michael J. E.

doi:10.29007/k83b

Cited by 3 publications

(2 citation statements)

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“…For proteins E1, E2, E3 and CP, homology models were first generated from the MAYV primary sequence using Phyre protein structure prediction server (Kelley et al 2018).…”

Section: Model Building and Refinementmentioning

confidence: 99%

“…These models were fit into the respective density from the single MAYV protomer after NCS averaging using UCSF Chimera and refined in real space using Phenix software taking into account stereochemical and secondary structure restraints (Kelley et al 2018;Pettersen et al 2004). Further, an iterative process of manual editing of the polypeptide backbone and rotamer placements using COOT and further Phenix real space refinements was performed until the refinement statistics and visual fit of atoms showed no clear improvement.…”

Section: Model Building and Refinementmentioning

confidence: 99%

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Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation

Chmielewski¹,

Kaelber

Jin

et al. 2021

Preprint

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Mayaro virus (MAYV) is an arthritis-inducing alphavirus circulating in the Americas, with potential to rapidly emerge in new geographical regions and populated environments. Intraparticle heterogeneity has typically limited atomic resolution structures of alphavirus virions, while imposing icosahedral symmetry in data processing prevents characterization of non-icosahedral features. Here, we report a near-atomic resolution cryo-EM structure of the MAYV E1-E2-E3-CP subunit by addressing deviations from icosahedral symmetry within each virus particle. We identified amino acid contacts at E1 protein interfaces forming the icosahedral lattice and investigated their effect on MAYV growth through site-directed mutagenesis. Further, mutation of a short stretch of conserved residues in E2 subdomain D, near an unidentified “pocket factor” including E2Y358, significantly reduced MAYV growth and provides strong evidence that this unknown factor influences assembly. Further, a symmetry-free reconstruction revealed the MAYV virion is not strictly icosahedral, suggesting defects in global symmetry may be a feature of the virus particle budding process. Our study provides insights into alphavirus assembly and suggests a common path in the formation of spherical, enveloped viruses, leading to particle imperfections.

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“…For proteins E1, E2, E3 and CP, homology models were first generated from the MAYV primary sequence using Phyre protein structure prediction server (Kelley et al 2018).…”

Section: Model Building and Refinementmentioning

confidence: 99%

Section: Model Building and Refinementmentioning

confidence: 99%

Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation

Chmielewski¹,

Kaelber

Jin

et al. 2021

Preprint

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Automatic Generation of Test-cases of Increasing Complexity for Autonomous Vehicles at Intersections

Karimi

Duggirala

2022

2022 ACM/IEEE 13th International Conference on Cyber-Physical Systems (ICCPS)

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Comment: Will Competition-Winning Methods for Causal Inference Also Succeed in Practice?

Zhao¹,

Keele²,

Small³

2019

Statist. Sci.

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First, we would like to congratulate the authors for successfully hosting the causal inference data competition (referred to as Competition henceforth) and contributing a unique and thought-provoking article to the literature. The authors have provided a comprehensive and timely platform to evaluate the ever-growing number of methods used for covariate adjustment in observational studies. In our comment, we don't generally question the results of the competition, but we do wish to emphasize several other key elements about the role statistics plays in causal inference and observational studies.

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Phyre and PhyreRisk – Integrating genetic variant data with experimental and predicted protein structures and their complexes

Cited by 3 publications

References 0 publications

Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation

Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation

Automatic Generation of Test-cases of Increasing Complexity for Autonomous Vehicles at Intersections

Comment: Will Competition-Winning Methods for Causal Inference Also Succeed in Practice?

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