Literature DB >> 30555007

Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.

Catherine R Knoverek1, Gaya K Amarasinghe2, Gregory R Bowman3.   

Abstract

A protein is a dynamic shape-shifter whose function is determined by the set of structures it adopts. Unfortunately, atomically detailed structures are only available for a few conformations of any given protein, and these structures have limited explanatory and predictive power. Here, we provide a brief historical perspective on protein dynamics and introduce recent advances in computational and experimental methods that are providing unprecedented access to protein shape-shifting. Next, we focus on how these tools are revealing the mechanism of allosteric communication and features like cryptic pockets; both of which present new therapeutic opportunities. A major theme is the importance of considering the relative probabilities of different structures and the control one can exert over protein function by modulating this balance.
Copyright © 2018 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  allostery; cryptic pockets; protein dynamics

Mesh:

Substances:

Year:  2018        PMID: 30555007      PMCID: PMC6422738          DOI: 10.1016/j.tibs.2018.11.007

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  63 in total

1.  Site-directed ligand discovery.

Authors:  D A Erlanson; A C Braisted; D R Raphael; M Randal; R M Stroud; E M Gordon; J A Wells
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-15       Impact factor: 11.205

2.  Allosteric inhibition through core disruption.

Authors:  James R Horn; Brian K Shoichet
Journal:  J Mol Biol       Date:  2004-03-05       Impact factor: 5.469

Review 3.  Natural evolution of TEM-1 β-lactamase: experimental reconstruction and clinical relevance.

Authors:  Merijn L M Salverda; J Arjan G M De Visser; Miriam Barlow
Journal:  FEMS Microbiol Rev       Date:  2010-11       Impact factor: 16.408

4.  FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

Authors:  Maxwell I Zimmerman; Gregory R Bowman
Journal:  J Chem Theory Comput       Date:  2015-11-20       Impact factor: 6.006

5.  A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.

Authors:  Katherine A Henzler-Wildman; Ming Lei; Vu Thai; S Jordan Kerns; Martin Karplus; Dorothee Kern
Journal:  Nature       Date:  2007-11-18       Impact factor: 49.962

6.  Discovery of multiple hidden allosteric sites by combining Markov state models and experiments.

Authors:  Gregory R Bowman; Eric R Bolin; Kathryn M Hart; Brendan C Maguire; Susan Marqusee
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-17       Impact factor: 11.205

Review 7.  To milliseconds and beyond: challenges in the simulation of protein folding.

Authors:  Thomas J Lane; Diwakar Shukla; Kyle A Beauchamp; Vijay S Pande
Journal:  Curr Opin Struct Biol       Date:  2012-12-10       Impact factor: 6.809

8.  Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.

Authors:  Zhaoming Su; Chao Wu; Liuqing Shi; Priya Luthra; Grigore D Pintilie; Britney Johnson; Justin R Porter; Peng Ge; Muyuan Chen; Gai Liu; Thomas E Frederick; Jennifer M Binning; Gregory R Bowman; Z Hong Zhou; Christopher F Basler; Michael L Gross; Daisy W Leung; Wah Chiu; Gaya K Amarasinghe
Journal:  Cell       Date:  2018-02-22       Impact factor: 41.582

9.  Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2.

Authors:  Adelajda Zorba; Vanessa Buosi; Steffen Kutter; Nadja Kern; Francesco Pontiggia; Young-Jin Cho; Dorothee Kern
Journal:  Elife       Date:  2014-05-27       Impact factor: 8.140

10.  Hidden alternative structures of proline isomerase essential for catalysis.

Authors:  James S Fraser; Michael W Clarkson; Sheena C Degnan; Renske Erion; Dorothee Kern; Tom Alber
Journal:  Nature       Date:  2009-12-03       Impact factor: 49.962

View more
  14 in total

1.  The dynamic conformational landscape of the protein methyltransferase SETD8.

Authors:  Shi Chen; Rafal P Wiewiora; Fanwang Meng; Nicolas Babault; Anqi Ma; Wenyu Yu; Kun Qian; Hao Hu; Hua Zou; Junyi Wang; Shijie Fan; Gil Blum; Fabio Pittella-Silva; Kyle A Beauchamp; Wolfram Tempel; Hualiang Jiang; Kaixian Chen; Robert J Skene; Yujun George Zheng; Peter J Brown; Jian Jin; Cheng Luo; John D Chodera; Minkui Luo
Journal:  Elife       Date:  2019-05-13       Impact factor: 8.140

Review 2.  Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

Authors:  Antonija Kuzmanic; Gregory R Bowman; Jordi Juarez-Jimenez; Julien Michel; Francesco L Gervasio
Journal:  Acc Chem Res       Date:  2020-03-05       Impact factor: 22.384

3.  Structure-Based Analysis of Cryptic-Site Opening.

Authors:  Zhuyezi Sun; Amanda Elizabeth Wakefield; Istvan Kolossvary; Dmitri Beglov; Sandor Vajda
Journal:  Structure       Date:  2019-12-03       Impact factor: 5.006

4.  Allosteric conformational ensembles have unlimited capacity for integrating information.

Authors:  John W Biddle; Rosa Martinez-Corral; Felix Wong; Jeremy Gunawardena
Journal:  Elife       Date:  2021-06-09       Impact factor: 8.140

Review 5.  New perspectives in cancer drug development: computational advances with an eye to design.

Authors:  Matteo Castelli; Stefano A Serapian; Filippo Marchetti; Alice Triveri; Valentina Pirota; Luca Torielli; Simona Collina; Filippo Doria; Mauro Freccero; Giorgio Colombo
Journal:  RSC Med Chem       Date:  2021-07-07

6.  Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets.

Authors:  Michael D Ward; Maxwell I Zimmerman; Artur Meller; Moses Chung; S J Swamidass; Gregory R Bowman
Journal:  Nat Commun       Date:  2021-05-21       Impact factor: 14.919

7.  Discovery of a hidden transient state in all bromodomain families.

Authors:  Lluís Raich; Katharina Meier; Judith Günther; Clara D Christ; Frank Noé; Simon Olsson
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-26       Impact factor: 12.779

8.  Conformational distributions of isolated myosin motor domains encode their mechanochemical properties.

Authors:  Justin R Porter; Artur Meller; Maxwell I Zimmerman; Michael J Greenberg; Gregory R Bowman
Journal:  Elife       Date:  2020-05-29       Impact factor: 8.140

9.  FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function.

Authors:  Lucia Trisolini; Nicola Gambacorta; Ruggiero Gorgoglione; Michele Montaruli; Luna Laera; Francesco Colella; Mariateresa Volpicella; Anna De Grassi; Ciro Leonardo Pierri
Journal:  J Clin Med       Date:  2019-12-02       Impact factor: 4.241

10.  SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome.

Authors:  Maxwell I Zimmerman; Justin R Porter; Michael D Ward; Sukrit Singh; Neha Vithani; Artur Meller; Upasana L Mallimadugula; Catherine E Kuhn; Jonathan H Borowsky; Rafal P Wiewiora; Matthew F D Hurley; Aoife M Harbison; Carl A Fogarty; Joseph E Coffland; Elisa Fadda; Vincent A Voelz; John D Chodera; Gregory R Bowman
Journal:  Nat Chem       Date:  2021-05-24       Impact factor: 24.427

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.