Q | R: QUANTUM-BASED REFINEMENT OF BIOMACROMOLECULES

Biczysko, Malgorzata

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https://hdl.handle.net/2142/116795 Copy

Description

Title

Q | R: QUANTUM-BASED REFINEMENT OF BIOMACROMOLECULES

Author(s)

Biczysko, Malgorzata

Contributor(s)

Afonine, Pavel V; Waller, Mark P; Kruse, Holger ; Moriarty, Nigel W; Xu, Yanting

Issue Date

2022-06-20

Keyword(s)

Structure determination

Abstract

Protein structure determination is largely reliant on crystallography (X-ray, neutron or electron), electron cryo-microscopy (Cryo-EM) or NMR experiments. Refinement is the final step in obtaining accurate three-dimensional atomic model based on experimental data. Since the quality of the data (e.g., resolution) is rarely sufficient to utilize these data alone, this step has traditionally relied on parameterized libraries that describe stereochemistry of the molecules in question. The libraries used in major refinement packages do not describe unusual local arrangements of protein residues in Ramachandran space, novel ligands, or non-covalent interactions such as $\pi$ stacking, halogen, hydrogen or salt bridges. The methods we are developing in the Q$\mid$ R project [1-4], which is our next generation open-source software package (http://github.com/qrefine), combine experimental data with chemical restraints derived from quantum-chemical methods. These procedures allow at present quantum refinement of proteins based on both X-ray crystallography or Cryo-EM experiments. Quantum refinement has shown to significantly improve model geometry, considering both the overall aspects of model and model-to-data fit statistics, as well as specific detailed structural features, in particular the hydrogen bonding. [1] M. Zheng, J. R. Reimers, M. P. Waller, P. V. Afonine, Acta Cryst. D 73, 45 (2017) [2] M. Zheng, N. W. Moriarty, Y. Xu, J. R. Reimers, P. V. Afonine, M. P. Waller, Acta Cryst. D 73, 1020 (2017) [3] M. Zheng, M. Biczysko, Y. Xu, N. W. Moriarty, H. Kruse, A. Urzhumtsev, M. P. Waller, P. V. Afonine, Acta Cryst. D 76, 41-50 (2020) [4] L. Wang, H. Kruse, O. V. Sobolev, N. W. Moriarty, M. P. Waller, P. V. Afonine, M. Biczysko, Acta Cryst. D 76, 1184–1191 (2020)

Publisher

International Symposium on Molecular Spectroscopy

Type of Resource

text

Language

eng

Handle URL

https://hdl.handle.net/2142/116795

Copyright and License Information

Copyright 2022 held by the authors

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