Literature DB >> 34592682

High throughput and quantitative enzymology in the genomic era.

D A Mokhtari1, M J Appel1, P M Fordyce2, D Herschlag3.   

Abstract

Accurate predictions from models based on physical principles are the ultimate metric of our biophysical understanding. Although there has been stunning progress toward structure prediction, quantitative prediction of enzyme function has remained challenging. Realizing this goal will require large numbers of quantitative measurements of rate and binding constants and the use of these ground-truth data sets to guide the development and testing of these quantitative models. Ground truth data more closely linked to the underlying physical forces are also desired. Here, we describe technological advances that enable both types of ground truth measurements. These advances allow classic models to be tested, provide novel mechanistic insights, and place us on the path toward a predictive understanding of enzyme structure and function.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Year:  2021        PMID: 34592682      PMCID: PMC8648990          DOI: 10.1016/j.sbi.2021.07.010

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


  112 in total

1.  Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

Authors:  V Zoete; O Michielin; M Karplus
Journal:  J Mol Biol       Date:  2002-01-04       Impact factor: 5.469

2.  High-accuracy computation of reaction barriers in enzymes.

Authors:  Frederik Claeyssens; Jeremy N Harvey; Frederick R Manby; Ricardo A Mata; Adrian J Mulholland; Kara E Ranaghan; Martin Schütz; Stephan Thiel; Walter Thiel; Hans-Joachim Werner
Journal:  Angew Chem Int Ed Engl       Date:  2006-10-20       Impact factor: 15.336

3.  How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.

Authors:  Renee Otten; Ricardo A P Pádua; H Adrian Bunzel; Vy Nguyen; Warintra Pitsawong; MacKenzie Patterson; Shuo Sui; Sarah L Perry; Aina E Cohen; Donald Hilvert; Dorothee Kern
Journal:  Science       Date:  2020-11-19       Impact factor: 47.728

4.  Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

Authors:  Medhanjali Dasgupta; Dominik Budday; Saulo H P de Oliveira; Peter Madzelan; Darya Marchany-Rivera; Javier Seravalli; Brandon Hayes; Raymond G Sierra; Sébastien Boutet; Mark S Hunter; Roberto Alonso-Mori; Alexander Batyuk; Jennifer Wierman; Artem Lyubimov; Aaron S Brewster; Nicholas K Sauter; Gregory A Applegate; Virendra K Tiwari; David B Berkowitz; Michael C Thompson; Aina E Cohen; James S Fraser; Michael E Wall; Henry van den Bedem; Mark A Wilson
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-04       Impact factor: 11.205

5.  Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.

Authors:  Gloria Yang; Dave W Anderson; Florian Baier; Elias Dohmen; Nansook Hong; Paul D Carr; Shina Caroline Lynn Kamerlin; Colin J Jackson; Erich Bornberg-Bauer; Nobuhiko Tokuriki
Journal:  Nat Chem Biol       Date:  2019-10-21       Impact factor: 15.040

Review 6.  Molecular dynamics: survey of methods for simulating the activity of proteins.

Authors:  Stewart A Adcock; J Andrew McCammon
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

Authors:  Fanny Sunden; Ariana Peck; Julia Salzman; Susanne Ressl; Daniel Herschlag
Journal:  Elife       Date:  2015-04-22       Impact factor: 8.140

8.  Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded.

Authors:  Emily E Wrenbeck; Laura R Azouz; Timothy A Whitehead
Journal:  Nat Commun       Date:  2017-06-06       Impact factor: 14.919

9.  Ensemble epistasis: thermodynamic origins of nonadditivity between mutations.

Authors:  Anneliese J Morrison; Daria R Wonderlick; Michael J Harms
Journal:  Genetics       Date:  2021-08-26       Impact factor: 4.402

10.  How much of protein sequence space has been explored by life on Earth?

Authors:  David T F Dryden; Andrew R Thomson; John H White
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

View more
  1 in total

1.  Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme.

Authors:  Chi-Yun Lin; Matthew G Romei; Irimpan I Mathews; Steven G Boxer
Journal:  J Am Chem Soc       Date:  2022-02-24       Impact factor: 16.383

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.