Literature DB >> 23933229

Emerging computational approaches for the study of protein allostery.

Galen Collier1, Vanessa Ortiz.   

Abstract

Allosteric regulation of protein function is key in controlling cellular processes so its underlying mechanisms are of primary concern to research in areas spanning protein engineering and drug design. However, due to the complex nature of allosteric mechanisms, a clear and predictive understanding of the relationship between protein structure and allosteric function remains elusive. Well established experimental approaches are available to offer a limited degree of characterization of mechanical properties within proteins, but the analytical capabilities of computational methods are evolving rapidly in their ability to accurately define the subtle and concerted structural dynamics that comprise allostery. This review includes a brief overview of allostery in proteins and an exploration of relevant experimental methods. An explanation of the transition from experimental toward computational methods for allostery is discussed, followed by a review of existing and emerging methods.
Copyright © 2013 Elsevier Inc. All rights reserved.

Keywords:  Allostery; Conformational dynamics; Molecular dynamics; Simulation

Mesh:

Substances:

Year:  2013        PMID: 23933229     DOI: 10.1016/j.abb.2013.07.025

Source DB:  PubMed          Journal:  Arch Biochem Biophys        ISSN: 0003-9861            Impact factor:   4.013


  21 in total

1.  Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.

Authors:  Kristen A Marino; Marta Filizola
Journal:  Methods Mol Biol       Date:  2018

2.  MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations.

Authors:  Andre A S T Ribeiro; Vanessa Ortiz
Journal:  Biophys J       Date:  2015-07-02       Impact factor: 4.033

3.  Identification of Allosteric Effects in Proteins by Elastic Network Models.

Authors:  Guang Hu
Journal:  Methods Mol Biol       Date:  2021

Review 4.  Allosteric communication pipelines in G-protein-coupled receptors.

Authors:  Nagarajan Vaidehi; Supriyo Bhattacharya
Journal:  Curr Opin Pharmacol       Date:  2016-08-04       Impact factor: 5.547

5.  Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

Authors:  Qifang Xu; Qingling Tang; Panagiotis Katsonis; Olivier Lichtarge; David Jones; Samuele Bovo; Giulia Babbi; Pier L Martelli; Rita Casadio; Gyu Rie Lee; Chaok Seok; Aron W Fenton; Roland L Dunbrack
Journal:  Hum Mutat       Date:  2017-05-02       Impact factor: 4.878

6.  Structural modeling of the AhR:ARNT complex in the bHLH-PASA-PASB region elucidates the key determinants of dimerization.

Authors:  Dario Corrada; Michael S Denison; Laura Bonati
Journal:  Mol Biosyst       Date:  2017-05-02

7.  Sparse group selection and analysis of function-related residue for protein-state recognition.

Authors:  Fangyun Bai; Kin Ming Puk; Jin Liu; Hongyu Zhou; Peng Tao; Wenyong Zhou; Shouyi Wang
Journal:  J Comput Chem       Date:  2022-06-03       Impact factor: 3.672

8.  Allosteric Hotspots in the Main Protease of SARS-CoV-2.

Authors:  Léonie Strömich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki
Journal:  J Mol Biol       Date:  2022-07-16       Impact factor: 6.151

Review 9.  Computational approaches to mapping allosteric pathways.

Authors:  Victoria A Feher; Jacob D Durrant; Adam T Van Wart; Rommie E Amaro
Journal:  Curr Opin Struct Biol       Date:  2014-03-22       Impact factor: 6.809

10.  Exploring the putative mechanism of allosteric modulations by mixed-action kappa/mu opioid receptor bitopic modulators.

Authors:  Huiqun Wang; Danni Cao; James C Gillespie; Rolando E Mendez; Dana E Selley; Lee-Yuan Liu-Chen; Yan Zhang
Journal:  Future Med Chem       Date:  2021-02-16       Impact factor: 3.808

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