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Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0

Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems...

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Autores principales: Krieger, James Michael, Sorzano, Carlos Oscar S., Carazo, Jose Maria, Bahar, Ivet
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8972803/
https://www.ncbi.nlm.nih.gov/pubmed/35362464
http://dx.doi.org/10.1107/S2059798322001966
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author Krieger, James Michael
Sorzano, Carlos Oscar S.
Carazo, Jose Maria
Bahar, Ivet
author_facet Krieger, James Michael
Sorzano, Carlos Oscar S.
Carazo, Jose Maria
Bahar, Ivet
author_sort Krieger, James Michael
collection PubMed
description Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth of structural data arising from cryoEM and other structural biology methods, has driven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution.
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spelling pubmed-89728032022-04-28 Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0 Krieger, James Michael Sorzano, Carlos Oscar S. Carazo, Jose Maria Bahar, Ivet Acta Crystallogr D Struct Biol Ccp-EM Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth of structural data arising from cryoEM and other structural biology methods, has driven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution. International Union of Crystallography 2022-03-16 /pmc/articles/PMC8972803/ /pubmed/35362464 http://dx.doi.org/10.1107/S2059798322001966 Text en © James Michael Krieger et al. 2022 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Ccp-EM
Krieger, James Michael
Sorzano, Carlos Oscar S.
Carazo, Jose Maria
Bahar, Ivet
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title_full Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title_fullStr Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title_full_unstemmed Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title_short Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
title_sort protein dynamics developments for the large scale and cryoem: case study of prody 2.0
topic Ccp-EM
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8972803/
https://www.ncbi.nlm.nih.gov/pubmed/35362464
http://dx.doi.org/10.1107/S2059798322001966
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