Literature DB >> 27698032

Improved insights into protein thermal stability: from the molecular to the structurome scale.

Fabrizio Pucci1, Marianne Rooman2.   

Abstract

Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability-at the structurome level-contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
© 2016 The Author(s).

Keywords:  amino acid interactions; evolutionary pressure; protein mutations; stability prediction; statistical potentials

Mesh:

Substances:

Year:  2016        PMID: 27698032      PMCID: PMC5052726          DOI: 10.1098/rsta.2016.0141

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  34 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Thermophilic adaptation of proteins.

Authors:  R Sterner; W Liebl
Journal:  Crit Rev Biochem Mol Biol       Date:  2001       Impact factor: 8.250

3.  Elucidation of determinants of protein stability through genome sequence analysis.

Authors:  S Chakravarty; R Varadarajan
Journal:  FEBS Lett       Date:  2000-03-17       Impact factor: 4.124

4.  Factors enhancing protein thermostability.

Authors:  S Kumar; C J Tsai; R Nussinov
Journal:  Protein Eng       Date:  2000-03

5.  Salt bridge stability in monomeric proteins.

Authors:  S Kumar; R Nussinov
Journal:  J Mol Biol       Date:  1999-11-12       Impact factor: 5.469

Review 6.  Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.

Authors:  C Vieille; G J Zeikus
Journal:  Microbiol Mol Biol Rev       Date:  2001-03       Impact factor: 11.056

7.  Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study.

Authors:  Suvobrata Chakravarty; Raghavan Varadarajan
Journal:  Biochemistry       Date:  2002-06-25       Impact factor: 3.162

8.  PISCES: a protein sequence culling server.

Authors:  Guoli Wang; Roland L Dunbrack
Journal:  Bioinformatics       Date:  2003-08-12       Impact factor: 6.937

9.  Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.

Authors:  S Tanaka; H A Scheraga
Journal:  Macromolecules       Date:  1976 Nov-Dec       Impact factor: 5.985

10.  Optimality of the genetic code with respect to protein stability and amino-acid frequencies.

Authors:  D Gilis; S Massar; N J Cerf; M Rooman
Journal:  Genome Biol       Date:  2001-10-24       Impact factor: 13.583

View more
  6 in total

1.  Bridging the gaps at the physics-chemistry-biology interface.

Authors:  P V Coveney; J P Boon; S Succi
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-11-13       Impact factor: 4.226

2.  A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes.

Authors:  Stewart Gault; Peter M Higgins; Charles S Cockell; Kaitlyn Gillies
Journal:  Biosci Rep       Date:  2021-04-30       Impact factor: 3.840

3.  Insights on protein thermal stability: a graph representation of molecular interactions.

Authors:  Mattia Miotto; Pier Paolo Olimpieri; Lorenzo Di Rienzo; Francesco Ambrosetti; Pietro Corsi; Rosalba Lepore; Gian Gaetano Tartaglia; Edoardo Milanetti
Journal:  Bioinformatics       Date:  2019-08-01       Impact factor: 6.937

4.  High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels.

Authors:  Ying-Chen Chao; Melanie Merritt; Devin Schaefferkoetter; Tyler G Evans
Journal:  BMC Evol Biol       Date:  2020-02-13       Impact factor: 3.260

5.  Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting.

Authors:  Erwin Pannecoucke; Maaike Van Trimpont; Johan Desmet; Tim Pieters; Lindy Reunes; Lisa Demoen; Marnik Vuylsteke; Stefan Loverix; Karen Vandenbroucke; Philippe Alard; Paula Henderikx; Sabrina Deroo; Franky Baatz; Eric Lorent; Sophie Thiolloy; Klaartje Somers; Yvonne McGrath; Pieter Van Vlierberghe; Ignace Lasters; Savvas N Savvides
Journal:  Sci Adv       Date:  2021-03-26       Impact factor: 14.136

6.  Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants.

Authors:  Anna Laddach; Joseph Chi Fung Ng; Franca Fraternali
Journal:  PLoS Biol       Date:  2021-04-28       Impact factor: 8.029

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.