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Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography

A molecular dynamics (MD)-based pipeline has been designed and implemented to emulate the entire process of collecting diffraction photographs and calculating crystallographic structures of proteins from them. Using a structure of lysozyme solved in-house, a supercell comprising 125 (5 × 5 × 5) crys...

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Autores principales: Liu, Ning, Mikhailovskii, Oleg, Skrynnikov, Nikolai R., Xue, Yi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812212/
https://www.ncbi.nlm.nih.gov/pubmed/36598499
http://dx.doi.org/10.1107/S2052252522011198
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author Liu, Ning
Mikhailovskii, Oleg
Skrynnikov, Nikolai R.
Xue, Yi
author_facet Liu, Ning
Mikhailovskii, Oleg
Skrynnikov, Nikolai R.
Xue, Yi
author_sort Liu, Ning
collection PubMed
description A molecular dynamics (MD)-based pipeline has been designed and implemented to emulate the entire process of collecting diffraction photographs and calculating crystallographic structures of proteins from them. Using a structure of lysozyme solved in-house, a supercell comprising 125 (5 × 5 × 5) crystal unit cells containing a total of 1000 protein molecules and explicit interstitial solvent was constructed. For this system, two 300 ns MD trajectories at 298 and 250 K were recorded. A series of snapshots from these trajectories were then used to simulate a fully realistic set of diffraction photographs, which were further fed into the standard pipeline for structure determination. The resulting structures show very good agreement with the underlying MD model not only in terms of coordinates but also in terms of B factors; they are also consistent with the original experimental structure. The developed methodology should find a range of applications, such as optimizing refinement protocols to solve crystal structures and extracting dynamics information from diffraction data or diffuse scattering.
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spelling pubmed-98122122023-01-09 Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography Liu, Ning Mikhailovskii, Oleg Skrynnikov, Nikolai R. Xue, Yi IUCrJ Research Letters A molecular dynamics (MD)-based pipeline has been designed and implemented to emulate the entire process of collecting diffraction photographs and calculating crystallographic structures of proteins from them. Using a structure of lysozyme solved in-house, a supercell comprising 125 (5 × 5 × 5) crystal unit cells containing a total of 1000 protein molecules and explicit interstitial solvent was constructed. For this system, two 300 ns MD trajectories at 298 and 250 K were recorded. A series of snapshots from these trajectories were then used to simulate a fully realistic set of diffraction photographs, which were further fed into the standard pipeline for structure determination. The resulting structures show very good agreement with the underlying MD model not only in terms of coordinates but also in terms of B factors; they are also consistent with the original experimental structure. The developed methodology should find a range of applications, such as optimizing refinement protocols to solve crystal structures and extracting dynamics information from diffraction data or diffuse scattering. International Union of Crystallography 2023-01-01 /pmc/articles/PMC9812212/ /pubmed/36598499 http://dx.doi.org/10.1107/S2052252522011198 Text en © Ning Liu et al. 2023 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 Research Letters
Liu, Ning
Mikhailovskii, Oleg
Skrynnikov, Nikolai R.
Xue, Yi
Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title_full Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title_fullStr Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title_full_unstemmed Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title_short Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
title_sort simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
topic Research Letters
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812212/
https://www.ncbi.nlm.nih.gov/pubmed/36598499
http://dx.doi.org/10.1107/S2052252522011198
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