Literature DB >> 24709805

A theoretical view of protein dynamics.

Modesto Orozco1.   

Abstract

Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.

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Year:  2014        PMID: 24709805     DOI: 10.1039/c3cs60474h

Source DB:  PubMed          Journal:  Chem Soc Rev        ISSN: 0306-0012            Impact factor:   54.564


  23 in total

1.  Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins.

Authors:  Mengxiao Liu; Yaewon Kim; Christian Hilty
Journal:  Anal Chem       Date:  2017-08-09       Impact factor: 6.986

Review 2.  Enhanced sampling techniques in molecular dynamics simulations of biological systems.

Authors:  Rafael C Bernardi; Marcelo C R Melo; Klaus Schulten
Journal:  Biochim Biophys Acta       Date:  2014-10-23

3.  Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.

Authors:  Sophie Sacquin-Mora
Journal:  J R Soc Interface       Date:  2019-07-10       Impact factor: 4.118

4.  Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Authors:  Julia Koehler Leman; Andrew R D'Avino; Yash Bhatnagar; Jeffrey J Gray
Journal:  Proteins       Date:  2017-11-08

Review 5.  Learning Strategies in Protein Directed Evolution.

Authors:  Xavier F Cadet; Jean Christophe Gelly; Aster van Noord; Frédéric Cadet; Carlos G Acevedo-Rocha
Journal:  Methods Mol Biol       Date:  2022

6.  Simultaneous Quantitation of Glycoprotein Degradation and Synthesis Rates by Integrating Isotope Labeling, Chemical Enrichment, and Multiplexed Proteomics.

Authors:  Haopeng Xiao; Ronghu Wu
Journal:  Anal Chem       Date:  2017-09-13       Impact factor: 6.986

7.  Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

Authors:  Sean L Seyler; Avishek Kumar; M F Thorpe; Oliver Beckstein
Journal:  PLoS Comput Biol       Date:  2015-10-21       Impact factor: 4.475

8.  Equilibrium molecular thermodynamics from Kirkwood sampling.

Authors:  Sandeep Somani; Yuko Okamoto; Andrew J Ballard; David J Wales
Journal:  J Phys Chem B       Date:  2015-05-12       Impact factor: 2.991

9.  Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

Authors:  Valentina D'Atri; Massimiliano Porrini; Frédéric Rosu; Valérie Gabelica
Journal:  J Mass Spectrom       Date:  2015-05       Impact factor: 1.982

10.  QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

Authors:  João V Ribeiro; Rafael C Bernardi; Till Rudack; John E Stone; James C Phillips; Peter L Freddolino; Klaus Schulten
Journal:  Sci Rep       Date:  2016-05-24       Impact factor: 4.379

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