Literature DB >> 30744993

Allostery in Its Many Disguises: From Theory to Applications.

Shoshana J Wodak1, Emanuele Paci2, Nikolay V Dokholyan3, Igor N Berezovsky4, Amnon Horovitz5, Jing Li6, Vincent J Hilser6, Ivet Bahar7, John Karanicolas8, Gerhard Stock9, Peter Hamm10, Roland H Stote11, Jerome Eberhardt11, Yassmine Chebaro11, Annick Dejaegere11, Marco Cecchini12, Jean-Pierre Changeux13, Peter G Bolhuis14, Jocelyne Vreede14, Pietro Faccioli15, Simone Orioli15, Riccardo Ravasio16, Le Yan17, Carolina Brito18, Matthieu Wyart16, Paraskevi Gkeka19, Ivan Rivalta20, Giulia Palermo21, J Andrew McCammon22, Joanna Panecka-Hofman23, Rebecca C Wade24, Antonella Di Pizio25, Masha Y Niv26, Ruth Nussinov27, Chung-Jung Tsai28, Hyunbum Jang28, Dzmitry Padhorny29, Dima Kozakov29, Tom McLeish30.   

Abstract

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
Copyright © 2019. Published by Elsevier Ltd.

Entities:  

Keywords:  Allostery; allosteric drugs; allosteric material; allosteric switches; elastic network models; energy landscape; molecular dynamics; protein conformational changes; protein function; regulation; signal transduction

Mesh:

Substances:

Year:  2019        PMID: 30744993      PMCID: PMC6688844          DOI: 10.1016/j.str.2019.01.003

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  79 in total

1.  Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP.

Authors:  Melody L Holmquist; Elihu C Ihms; Paul Gollnick; Vicki H Wysocki; Mark P Foster
Journal:  Biochemistry       Date:  2020-06-26       Impact factor: 3.162

Review 2.  Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Authors:  Paraskevi Gkeka; Gabriel Stoltz; Amir Barati Farimani; Zineb Belkacemi; Michele Ceriotti; John D Chodera; Aaron R Dinner; Andrew L Ferguson; Jean-Bernard Maillet; Hervé Minoux; Christine Peter; Fabio Pietrucci; Ana Silveira; Alexandre Tkatchenko; Zofia Trstanova; Rafal Wiewiora; Tony Lelièvre
Journal:  J Chem Theory Comput       Date:  2020-07-16       Impact factor: 6.006

3.  Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction.

Authors:  Michael Schupfner; Kristina Straub; Florian Busch; Rainer Merkl; Reinhard Sterner
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-23       Impact factor: 11.205

4.  Community Network Analysis of Allosteric Proteins.

Authors:  Ivan Rivalta; Victor S Batista
Journal:  Methods Mol Biol       Date:  2021

Review 5.  NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.

Authors:  Kyle W East; Erin Skeens; Jennifer Y Cui; Helen B Belato; Brandon Mitchell; Rohaine Hsu; Victor S Batista; Giulia Palermo; George P Lisi
Journal:  Biophys Rev       Date:  2019-12-14

6.  Establishing the allosteric mechanism in CRISPR-Cas9.

Authors:  Łukasz Nierzwicki; Pablo Ricardo Arantes; Aakash Saha; Giulia Palermo
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2020-10-26

Review 7.  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

8.  Real-time observation of ligand-induced allosteric transitions in a PDZ domain.

Authors:  Olga Bozovic; Claudio Zanobini; Adnan Gulzar; Brankica Jankovic; David Buhrke; Matthias Post; Steffen Wolf; Gerhard Stock; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-05       Impact factor: 11.205

9.  Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding.

Authors:  Stephen Boulton; Katherine Van; Bryan VanSchouwen; Jerry Augustine; Madoka Akimoto; Giuseppe Melacini
Journal:  Biophys J       Date:  2020-08-15       Impact factor: 4.033

10.  Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios.

Authors:  Riccardo Ravasio; Solange Marie Flatt; Le Yan; Stefano Zamuner; Carolina Brito; Matthieu Wyart
Journal:  Biophys J       Date:  2019-10-09       Impact factor: 4.033

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