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Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density

Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecu...

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Detalles Bibliográficos
Autores principales: Baker, Matthew L, Jiang, Wen, Wedemeyer, William J, Rixon, Frazer J, Baker, David, Chiu, Wah
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626159/
https://www.ncbi.nlm.nih.gov/pubmed/17069457
http://dx.doi.org/10.1371/journal.pcbi.0020146
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author Baker, Matthew L
Jiang, Wen
Wedemeyer, William J
Rixon, Frazer J
Baker, David
Chiu, Wah
author_facet Baker, Matthew L
Jiang, Wen
Wedemeyer, William J
Rixon, Frazer J
Baker, David
Chiu, Wah
author_sort Baker, Matthew L
collection PubMed
description Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies.
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spelling pubmed-16261592006-10-27 Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density Baker, Matthew L Jiang, Wen Wedemeyer, William J Rixon, Frazer J Baker, David Chiu, Wah PLoS Comput Biol Research Article Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies. Public Library of Science 2006-10 2006-10-27 /pmc/articles/PMC1626159/ /pubmed/17069457 http://dx.doi.org/10.1371/journal.pcbi.0020146 Text en © 2006 Baker et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Baker, Matthew L
Jiang, Wen
Wedemeyer, William J
Rixon, Frazer J
Baker, David
Chiu, Wah
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title_full Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title_fullStr Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title_full_unstemmed Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title_short Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
title_sort ab initio modeling of the herpesvirus vp26 core domain assessed by cryoem density
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626159/
https://www.ncbi.nlm.nih.gov/pubmed/17069457
http://dx.doi.org/10.1371/journal.pcbi.0020146
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