Literature DB >> 29101782

Frustration, function and folding.

Diego U Ferreiro1, Elizabeth A Komives2, Peter G Wolynes3.   

Abstract

Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful catalysis, are examples of basic chemical activities that the great majority of polypeptides do not display, and are thought to be the outcome of the natural history of proteins. Function, a concept genuine to Biology, is at the core of evolution and often conflicts with the physical constraints. Locating the frustration between discrepant goals in a recurrent system leads to fundamental insights about the chances and necessities that shape the encoding of biological information.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29101782      PMCID: PMC6005193          DOI: 10.1016/j.sbi.2017.09.006

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


  46 in total

Review 1.  Using the folding landscapes of proteins to understand protein function.

Authors:  V V Hemanth Giri Rao; Shachi Gosavi
Journal:  Curr Opin Struct Biol       Date:  2016-01-24       Impact factor: 6.809

2.  Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein.

Authors:  Sneha Munshi; Athi N Naganathan
Journal:  Phys Chem Chem Phys       Date:  2015-04-28       Impact factor: 3.676

3.  Evidence for the principle of minimal frustration in the evolution of protein folding landscapes.

Authors:  Franco O Tzul; Daniel Vasilchuk; George I Makhatadze
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-14       Impact factor: 11.205

Review 4.  Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature.

Authors:  Jeffrey I Boucher; Daniel N A Bolon; Dan S Tawfik
Journal:  Protein Sci       Date:  2016-04-06       Impact factor: 6.725

5.  Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Authors:  R Gonzalo Parra; Nicholas P Schafer; Leandro G Radusky; Min-Yeh Tsai; A Brenda Guzovsky; Peter G Wolynes; Diego U Ferreiro
Journal:  Nucleic Acids Res       Date:  2016-04-29       Impact factor: 16.971

6.  Conformational frustration in calmodulin-target recognition.

Authors:  Swarnendu Tripathi; Qian Wang; Pengzhi Zhang; Laurel Hoffman; M Neal Waxham; Margaret S Cheung
Journal:  J Mol Recognit       Date:  2015-01-20       Impact factor: 2.137

7.  Localized structural frustration for evaluating the impact of sequence variants.

Authors:  Sushant Kumar; Declan Clarke; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2016-10-18       Impact factor: 16.971

8.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

9.  Learning To Fold Proteins Using Energy Landscape Theory.

Authors:  N P Schafer; B L Kim; W Zheng; P G Wolynes
Journal:  Isr J Chem       Date:  2014-08       Impact factor: 3.333

10.  Protein stability and dynamics modulation: the case of human frataxin.

Authors:  Ernesto A Roman; Santiago E Faraj; Mariana Gallo; Andres G Salvay; Diego U Ferreiro; Javier Santos
Journal:  PLoS One       Date:  2012-09-25       Impact factor: 3.240

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  22 in total

1.  On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences.

Authors:  Pablo Turjanski; Diego U Ferreiro
Journal:  J Phys Chem B       Date:  2018-10-08       Impact factor: 2.991

2.  Funneled energy landscape unifies principles of protein binding and evolution.

Authors:  Zhiqiang Yan; Jin Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-16       Impact factor: 11.205

3.  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

4.  Stability of an aggregation-prone partially folded state of human profilin-1 correlates with aggregation propensity.

Authors:  Edoardo Del Poggetto; Angelo Toto; Chiara Aloise; Francesco Di Piro; Ludovica Gori; Francesco Malatesta; Stefano Gianni; Fabrizio Chiti; Francesco Bemporad
Journal:  J Biol Chem       Date:  2018-05-14       Impact factor: 5.157

5.  Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.

Authors:  Jason Bertram; Joanna Masel
Journal:  Genetics       Date:  2020-02-27       Impact factor: 4.562

6.  Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.

Authors:  Vinícius G Contessoto; Vinícius M de Oliveira; Vitor B P Leite
Journal:  Methods Mol Biol       Date:  2022

7.  Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation.

Authors:  Yuan-Wei Ma; Tong-You Lin; Min-Yeh Tsai
Journal:  Front Mol Biosci       Date:  2021-08-06

8.  Evolution and folding of repeat proteins.

Authors:  Ezequiel A Galpern; Jacopo Marchi; Thierry Mora; Aleksandra M Walczak; Diego U Ferreiro
Journal:  Proc Natl Acad Sci U S A       Date:  2022-07-29       Impact factor: 12.779

9.  Physical foundations of biological complexity.

Authors:  Yuri I Wolf; Mikhail I Katsnelson; Eugene V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-27       Impact factor: 11.205

Review 10.  Assistance for Folding of Disease-Causing Plasma Membrane Proteins.

Authors:  Karina Juarez-Navarro; Victor M Ayala-Garcia; Estela Ruiz-Baca; Ivan Meneses-Morales; Jose Luis Rios-Banuelos; Angelica Lopez-Rodriguez
Journal:  Biomolecules       Date:  2020-05-07
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