Literature DB >> 35507268

Uses and Abuses of the Atomic Displacement Parameters in Structural Biology.

Oliviero Carugo1.   

Abstract

B-factors determined with X-ray crystallographic analyses are commonly used to estimate the flexibility degree of atoms, residues, and molecular moieties in biological macromolecules. In this chapter, the most recent studies and applications of B-factors in protein engineering and structural biology are briefly summarized. Particular emphasis is given to the limitations in using B-factors, in order to prevent inappropriate applications. It is eventually predicted that future applications will involve anisotropically refined B-factors, deep learning, and data produced by cryo-EM.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  B-factor; Protein Data Bank; Protein flexibility; Protein structure; Structural biology; X-ray crystallography

Mesh:

Year:  2022        PMID: 35507268     DOI: 10.1007/978-1-0716-2095-3_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  39 in total

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Authors:  S Longhi; M Czjzek; C Cambillau
Journal:  Curr Opin Struct Biol       Date:  1998-12       Impact factor: 6.809

Review 2.  The benefits of atomic resolution.

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Journal:  Curr Opin Struct Biol       Date:  1997-10       Impact factor: 6.809

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Authors:  O Carugo; P Argos
Journal:  Proteins       Date:  1998-05-01

4.  Ring flips revisited: (13)C relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor.

Authors:  Ulrich Weininger; Kristofer Modig; Mikael Akke
Journal:  Biochemistry       Date:  2014-07-11       Impact factor: 3.162

5.  Relationship of protein flexibility to thermostability.

Authors:  M Vihinen
Journal:  Protein Eng       Date:  1987-12

6.  Solvent content of protein crystals.

Authors:  B W Matthews
Journal:  J Mol Biol       Date:  1968-04-28       Impact factor: 5.469

7.  Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.

Authors:  H Schrauber; F Eisenhaber; P Argos
Journal:  J Mol Biol       Date:  1993-03-20       Impact factor: 5.469

Review 8.  Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability.

Authors:  Zhoutong Sun; Qian Liu; Ge Qu; Yan Feng; Manfred T Reetz
Journal:  Chem Rev       Date:  2019-01-30       Impact factor: 60.622

9.  Protein hydration: Investigation of globular protein crystal structures.

Authors:  Oliviero Carugo
Journal:  Int J Biol Macromol       Date:  2017-02-23       Impact factor: 6.953

10.  TLS from fundamentals to practice.

Authors:  Alexandre Urzhumtsev; Pavel V Afonine; Paul D Adams
Journal:  Crystallogr Rev       Date:  2013-07-01       Impact factor: 2.467

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