Literature DB >> 19202077

Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added.

Franc Avbelj1, Robert L Baldwin.   

Abstract

Recent calorimetric measurements of the solvation enthalpies of some dipeptide analogs confirm our earlier prediction that the principle of group additivity is not valid for the interaction of the peptide group with water. We examine the consequences for understanding the properties of peptide solvation. A major consequence is that the current value of the peptide-solvation enthalpy, which is a basic parameter in analyzing the energetics of protein folding, is seriously wrong. Electrostatic calculations of solvation-free energies provide an estimate of the size and nature of the error. Peptide hydrogen exchange rates provide an experimental approach for testing the accuracy of the solvation-free energies of peptide groups found by electrostatic calculations. These calculations emphasize that ignoring electrostatic interactions with neighboring NHCO groups should be a major source of error. Results in 1972 for peptide hydrogen exchange rates demonstrate that peptide-solvation-free energies are strongly affected by adjoining NHCO groups. In the past, the effect of adjoining peptide groups on the exchange rate of a peptide NH proton was treated as an inductive effect. The effect can be calculated, however, by an electrostatic model with fixed partial charges and a continuum solvent.

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Year:  2009        PMID: 19202077      PMCID: PMC2651266          DOI: 10.1073/pnas.0813018106

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


  20 in total

1.  Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi.

Authors:  Franc Avbelj; Robert L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-22       Impact factor: 11.205

2.  Relationships between amino acid sequence and backbone torsion angle preferences.

Authors:  O Keskin; D Yuret; A Gursoy; M Turkay; B Erman
Journal:  Proteins       Date:  2004-06-01

Review 3.  Energetics of protein folding.

Authors:  Robert L Baldwin
Journal:  J Mol Biol       Date:  2007-06-02       Impact factor: 5.469

4.  Role of backbone solvation in determining thermodynamic beta propensities of the amino acids.

Authors:  Franc Avbelj; Robert L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-22       Impact factor: 11.205

5.  Primary structure effects on peptide group hydrogen exchange.

Authors:  R S Molday; S W Englander; R G Kallen
Journal:  Biochemistry       Date:  1972-01-18       Impact factor: 3.162

6.  Determination of an acidity scale for peptide hydrogens from nuclear magnetic resonance kinetic studies.

Authors:  M Sheinblatt
Journal:  J Am Chem Soc       Date:  1970-04-22       Impact factor: 15.419

7.  Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins.

Authors:  F Avbelj
Journal:  J Mol Biol       Date:  2000-07-28       Impact factor: 5.469

8.  Interaction of the peptide bond with solvent water: a vapor phase analysis.

Authors:  R Wolfenden
Journal:  Biochemistry       Date:  1978-01-10       Impact factor: 3.162

9.  Origin of the neighboring residue effect on peptide backbone conformation.

Authors:  Franc Avbelj; Robert L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-14       Impact factor: 11.205

10.  Water, protein folding, and the genetic code.

Authors:  R V Wolfenden; P M Cullis; C C Southgate
Journal:  Science       Date:  1979-11-02       Impact factor: 47.728

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  10 in total

1.  Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.

Authors:  Mateusz Marianski; J J Dannenberg
Journal:  J Phys Chem B       Date:  2012-01-23       Impact factor: 2.991

2.  Protein hydrogen exchange: testing current models.

Authors:  John J Skinner; Woon K Lim; Sabrina Bédard; Ben E Black; S Walter Englander
Journal:  Protein Sci       Date:  2012-06-11       Impact factor: 6.725

3.  Dry molten globule intermediates and the mechanism of protein unfolding.

Authors:  Robert L Baldwin; Carl Frieden; George D Rose
Journal:  Proteins       Date:  2010-10

4.  Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability.

Authors:  Dheeraj S Tomar; D Asthagiri; Valéry Weber
Journal:  Biophys J       Date:  2013-09-17       Impact factor: 4.033

5.  Properties of hydrophobic free energy found by gas-liquid transfer.

Authors:  Robert L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-14       Impact factor: 11.205

6.  An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins.

Authors:  Li L Duan; Tong Zhu; Ye Mei; Qing G Zhang; Bo Tang; John Z H Zhang
Journal:  J Mol Model       Date:  2013-03-12       Impact factor: 1.810

7.  Assignment of PolyProline II conformation and analysis of sequence--structure relationship.

Authors:  Yohann Mansiaux; Agnel Praveen Joseph; Jean-Christophe Gelly; Alexandre G de Brevern
Journal:  PLoS One       Date:  2011-03-31       Impact factor: 3.240

8.  Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

Authors:  Didier Devaurs; Dinler A Antunes; Malvina Papanastasiou; Mark Moll; Daniel Ricklin; John D Lambris; Lydia E Kavraki
Journal:  Front Mol Biosci       Date:  2017-03-10

9.  Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins.

Authors:  Jianmin Gao; Daryl A Bosco; Evan T Powers; Jeffery W Kelly
Journal:  Nat Struct Mol Biol       Date:  2009-06-14       Impact factor: 15.369

10.  Proline: the distribution, frequency, positioning, and common functional roles of proline and polyproline sequences in the human proteome.

Authors:  Alexander A Morgan; Edward Rubenstein
Journal:  PLoS One       Date:  2013-01-25       Impact factor: 3.240

  10 in total

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