Literature DB >> 26957601

Energy landscape in protein folding and unfolding.

Francesco Mallamace1, Carmelo Corsaro2, Domenico Mallamace3, Sebastiano Vasi4, Cirino Vasi5, Piero Baglioni6, Sergey V Buldyrev7, Sow-Hsin Chen8, H Eugene Stanley9.   

Abstract

We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.

Entities:  

Keywords:  energy landscape; hydration water; protein folding; proton NMR

Mesh:

Substances:

Year:  2016        PMID: 26957601      PMCID: PMC4812744          DOI: 10.1073/pnas.1524864113

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


  30 in total

1.  The middle way.

Authors:  R B Laughlin; D Pines; J Schmalian; B P Stojkovic; P Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

Review 2.  Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Adv Protein Chem       Date:  2002

3.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

4.  Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.

Authors:  Jacques-Philippe Colletier; Dominique Bourgeois; Benoît Sanson; Didier Fournier; Joel L Sussman; Israel Silman; Martin Weik
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-13       Impact factor: 11.205

5.  Thermodynamic properties of bulk and confined water.

Authors:  Francesco Mallamace; Carmelo Corsaro; Domenico Mallamace; Sebastiano Vasi; Cirino Vasi; H Eugene Stanley
Journal:  J Chem Phys       Date:  2014-11-14       Impact factor: 3.488

6.  How does a protein fold?

Authors:  A Sali; E Shakhnovich; M Karplus
Journal:  Nature       Date:  1994-05-19       Impact factor: 49.962

7.  Water-inserted alpha-helical segments implicate reverse turns as folding intermediates.

Authors:  M Sundaralingam; Y C Sekharudu
Journal:  Science       Date:  1989-06-16       Impact factor: 47.728

8.  The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

Authors:  Scott T R Walsh; Richard P Cheng; Wayne W Wright; Darwin O V Alonso; Valerie Daggett; Jane M Vanderkooi; William F DeGrado
Journal:  Protein Sci       Date:  2003-03       Impact factor: 6.725

9.  Effect of flexibility and cis residues in single-molecule FRET studies of polyproline.

Authors:  Robert B Best; Kusai A Merchant; Irina V Gopich; Benjamin Schuler; Ad Bax; William A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-20       Impact factor: 11.205

10.  Heat capacity effects in protein folding and ligand binding: a re-evaluation of the role of water in biomolecular thermodynamics.

Authors:  Alan Cooper
Journal:  Biophys Chem       Date:  2004-12-24       Impact factor: 2.352

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  8 in total

1.  Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.

Authors:  Rupesh Agarwal; Utsab R Shrestha; Xiang-Qiang Chu; Loukas Petridis; Jeremy C Smith
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2.  Alpha-Synuclein Is a Target of Fic-Mediated Adenylylation/AMPylation: Possible Implications for Parkinson's Disease.

Authors:  Anwesha Sanyal; Sayan Dutta; Ali Camara; Aswathy Chandran; Antonius Koller; Ben G Watson; Ranjan Sengupta; Daniel Ysselstein; Paola Montenegro; Jason Cannon; Jean-Christophe Rochet; Seema Mattoo
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3.  Genuine antiplasticizing effect of water on a glass-former drug.

Authors:  Guadalupe N Ruiz; Michela Romanini; Astrid Hauptmann; Thomas Loerting; Evgenyi Shalaev; Josep Ll Tamarit; Luis C Pardo; Roberto Macovez
Journal:  Sci Rep       Date:  2017-08-07       Impact factor: 4.379

4.  Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation.

Authors:  George P Lisi; Allen A Currier; J Patrick Loria
Journal:  Front Mol Biosci       Date:  2018-02-06

Review 5.  Circuit Topology Analysis of Polymer Folding Reactions.

Authors:  Maziar Heidari; Helmut Schiessel; Alireza Mashaghi
Journal:  ACS Cent Sci       Date:  2020-05-12       Impact factor: 14.553

Review 6.  The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results.

Authors:  Domenico Mallamace; Enza Fazio; Francesco Mallamace; Carmelo Corsaro
Journal:  Int J Mol Sci       Date:  2018-11-30       Impact factor: 5.923

Review 7.  The Current Status of Genes and Genetic Testing in Emergency Medicine: A Narrative Review.

Authors:  Seyed Mohammad Kazem Aghamir; Mehdi Ebrahimi; Fatemeh Khatami
Journal:  Adv J Emerg Med       Date:  2019-08-25

8.  An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.

Authors:  Talia A Shmool; Laura K Martin; Liem Bui-Le; Ignacio Moya-Ramirez; Pavlos Kotidis; Richard P Matthews; Gerhard A Venter; Cleo Kontoravdi; Karen M Polizzi; Jason P Hallett
Journal:  Chem Sci       Date:  2021-06-22       Impact factor: 9.825

  8 in total

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