Literature DB >> 28808004

Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion.

Marina Katava1, Guillaume Stirnemann1, Marco Zanatta2, Simone Capaccioli3, Maria Pachetti3, K L Ngai3, Fabio Sterpone4, Alessandro Paciaroni5.   

Abstract

Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested. This solvation shell-independent dynamical regime arises from an equivalent sampling of the energy landscape at the respective melting temperatures. Thus, we propose that a threshold for the conformational entropy provided by structural fluctuations of proteins exists, beyond which thermal unfolding is triggered.

Entities:  

Keywords:  Lindemann criterion; cell thermal stability; molecular dynamics simulation; neutron scattering; protein dynamics

Mesh:

Substances:

Year:  2017        PMID: 28808004      PMCID: PMC5584445          DOI: 10.1073/pnas.1707357114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  47 in total

Review 1.  How soft is a protein? A protein dynamics force constant measured by neutron scattering.

Authors:  G Zaccai
Journal:  Science       Date:  2000-06-02       Impact factor: 47.728

2.  Microscopic origins of entropy, heat capacity and the glass transition in proteins.

Authors:  A L Lee; A J Wand
Journal:  Nature       Date:  2001-05-24       Impact factor: 49.962

3.  A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy.

Authors:  Jörg Fitter
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

Review 4.  Protein folding and misfolding.

Authors:  Christopher M Dobson
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

5.  Effect of the environment on the protein dynamical transition: a neutron scattering study.

Authors:  Alessandro Paciaroni; Stefania Cinelli; Giuseppe Onori
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

6.  Hierarchical map of protein unfolding and refolding at thermal equilibrium revealed by wide-angle X-ray scattering.

Authors:  Mitsuhiro Hirai; Masaharu Koizumi; Tomohiro Hayakawa; Hiroshi Takahashi; Satoru Abe; Harutaka Hirai; Keiko Miura; Katsuaki Inoue
Journal:  Biochemistry       Date:  2004-07-20       Impact factor: 3.162

7.  How fast-folding proteins fold.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Ron O Dror; David E Shaw
Journal:  Science       Date:  2011-10-28       Impact factor: 47.728

8.  Evidence of coexistence of change of caged dynamics at T(g) and the dynamic transition at T(d) in solvated proteins.

Authors:  S Capaccioli; K L Ngai; S Ancherbak; A Paciaroni
Journal:  J Phys Chem B       Date:  2012-02-03       Impact factor: 2.991

9.  Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state.

Authors:  Y Zhou; D Vitkup; M Karplus
Journal:  J Mol Biol       Date:  1999-01-29       Impact factor: 5.469

10.  Motional displacements in proteins: The origin of wave-vector-dependent values.

Authors:  Derya Vural; Liang Hong; Jeremy C Smith; Henry R Glyde
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-05-14
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  6 in total

1.  Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins.

Authors:  Derya Vural; Jeremy C Smith; Henry R Glyde
Journal:  Biophys J       Date:  2018-03-24       Impact factor: 4.033

Review 2.  A Minireview on Temperature Dependent Protein Conformational Sampling.

Authors:  Ming Dong
Journal:  Protein J       Date:  2021-06-28       Impact factor: 2.371

3.  Thermal stability of single-domain antibodies estimated by molecular dynamics simulations.

Authors:  Gert-Jan Bekker; Benson Ma; Narutoshi Kamiya
Journal:  Protein Sci       Date:  2018-12-20       Impact factor: 6.725

4.  The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering.

Authors:  Andrew D Hanson; Donald R McCarty; Christopher S Henry; Xiaochen Xian; Jaya Joshi; Jenelle A Patterson; Jorge D García-García; Scott D Fleischmann; Nathan D Tivendale; A Harvey Millar
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-30       Impact factor: 11.205

5.  Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins.

Authors:  Meili Liu; Akshaya K Das; James Lincoff; Sukanya Sasmal; Sara Y Cheng; Robert M Vernon; Julie D Forman-Kay; Teresa Head-Gordon
Journal:  Int J Mol Sci       Date:  2021-03-26       Impact factor: 5.923

6.  Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant.

Authors:  Stepan Timr; Fabio Sterpone
Journal:  Biology (Basel)       Date:  2021-11-27
  6 in total

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