Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures

Mateusz Kogut; Zhou Gong; Chun Tang; Adam Liwo

doi:10.1002/jcc.26736

Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures

J Comput Chem. 2021 Nov 5;42(29):2054-2067. doi: 10.1002/jcc.26736. Epub 2021 Aug 17.

Authors

Mateusz Kogut¹, Zhou Gong², Chun Tang³, Adam Liwo¹

Affiliations

¹ Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
² Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China.
³ College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.

PMID: 34402552
DOI: 10.1002/jcc.26736

Abstract

Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS² G) or suberic acid (BS³ ) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials.

Keywords: chemical cross-link mass spectroscopy; coarse-grained modeling; molecular dynamics; potentials of mean force.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Models, Molecular*
Protein Conformation
Proteins / chemistry*

Substances

Proteins