Literature DB >> 31785465

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Yan Zhang1, Pemra Doruker1, Burak Kaynak1, She Zhang1, James Krieger1, Hongchun Li2, Ivet Bahar3.   

Abstract

Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs. These observations brought into light evolutionary adaptation mechanisms that help maintain, optimize or regulate allosteric behavior as the evolution from bacterial to higher organisms introduces sequential heterogeneities and structural complexities.
Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

Entities:  

Year:  2019        PMID: 31785465      PMCID: PMC7250723          DOI: 10.1016/j.sbi.2019.11.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  66 in total

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Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

2.  Switching of the folding-energy landscape governs the allosteric activation of protein kinase A.

Authors:  Jeneffer P England; Yuxin Hao; Lihui Bai; Virginia Glick; H Courtney Hodges; Susan S Taylor; Rodrigo A Maillard
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-23       Impact factor: 11.205

3.  Ca2+ allostery in PTH-receptor signaling.

Authors:  Alex D White; Fei Fang; Frédéric G Jean-Alphonse; Lisa J Clark; Hyun-Jung An; Hongda Liu; Yang Zhao; Shelley L Reynolds; Sihoon Lee; Kunhong Xiao; Ieva Sutkeviciute; Jean-Pierre Vilardaga
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-04       Impact factor: 11.205

Review 4.  Design of proteins from smaller fragments-learning from evolution.

Authors:  Birte Höcker
Journal:  Curr Opin Struct Biol       Date:  2014-05-25       Impact factor: 6.809

Review 5.  Structure-based prediction of protein allostery.

Authors:  Joe G Greener; Michael Je Sternberg
Journal:  Curr Opin Struct Biol       Date:  2017-11-05       Impact factor: 6.809

6.  Allosteric Modulation of Grb2 Recruitment to the Intrinsically Disordered Scaffold Protein, LAT, by Remote Site Phosphorylation.

Authors:  William Y C Huang; Jonathon A Ditlev; Han-Kuei Chiang; Michael K Rosen; Jay T Groves
Journal:  J Am Chem Soc       Date:  2017-11-28       Impact factor: 15.419

7.  Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

Authors:  Tina Perica; Yasushi Kondo; Sandhya P Tiwari; Stephen H McLaughlin; Katherine R Kemplen; Xiuwei Zhang; Annette Steward; Nathalie Reuter; Jane Clarke; Sarah A Teichmann
Journal:  Science       Date:  2014-12-19       Impact factor: 47.728

8.  Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation.

Authors:  Yaozong Li; Kwangho Nam
Journal:  Chem Sci       Date:  2017-03-20       Impact factor: 9.825

9.  Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.

Authors:  Zeynep Kurkcuoglu; Alexandre M J J Bonvin
Journal:  Proteins       Date:  2019-09-03

Review 10.  The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases.

Authors:  Neel H Shah; Jeanine F Amacher; Laura M Nocka; John Kuriyan
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  21 in total

Review 1.  Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.

Authors:  Dimitri Loutchko; Holger Flechsig
Journal:  Biophys Rev       Date:  2020-03-20

Review 2.  Adaptability and specificity: how do proteins balance opposing needs to achieve function?

Authors:  Bentley Wingert; James Krieger; Hongchun Li; Ivet Bahar
Journal:  Curr Opin Struct Biol       Date:  2020-10-11       Impact factor: 6.809

3.  Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase.

Authors:  Karolina Michalska; Changsoo Chang; Natalia I Maltseva; Robert Jedrzejczak; Gregory T Robertson; Fabian Gusovsky; Patrick McCarren; Stuart L Schreiber; Partha P Nag; Andrzej Joachimiak
Journal:  Protein Sci       Date:  2020-01-20       Impact factor: 6.725

Review 4.  Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

Authors:  James M Krieger; Pemra Doruker; Ana Ligia Scott; David Perahia; Ivet Bahar
Journal:  Curr Opin Struct Biol       Date:  2020-07-01       Impact factor: 6.809

Review 5.  Allostery, and how to define and measure signal transduction.

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Journal:  Biophys Chem       Date:  2022-01-29       Impact factor: 2.352

6.  Oncogenic mutations on Rac1 affect global intrinsic dynamics underlying GTP and PAK1 binding.

Authors:  Saliha Ece Acuner; Fidan Sumbul; Hamdi Torun; Turkan Haliloglu
Journal:  Biophys J       Date:  2021-01-28       Impact factor: 4.033

7.  Allostery and Epistasis: Emergent Properties of Anisotropic Networks.

Authors:  Paul Campitelli; S Banu Ozkan
Journal:  Entropy (Basel)       Date:  2020-06-16       Impact factor: 2.524

8.  Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators.

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Journal:  Acta Pharm Sin B       Date:  2020-09-19       Impact factor: 11.413

Review 9.  Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics.

Authors:  Yun Wang; Guanyu Wang; Nicolas Moitessier; Anthony K Mittermaier
Journal:  Front Mol Biosci       Date:  2020-10-19

Review 10.  Enabling protein-hosted organocatalytic transformations.

Authors:  Alexander R Nödling; Nicolò Santi; Thomas L Williams; Yu-Hsuan Tsai; Louis Y P Luk
Journal:  RSC Adv       Date:  2020-04-23       Impact factor: 4.036

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