Hydrophobicity of amino acid subgroups in proteins

Glenn J. Lesser; George D. Rose

doi:10.1002/prot.340080104

journal article Jan 01, 1990

Hydrophobicity of amino acid subgroups in proteins

Glenn J. Lesser George D. Rose

Proteins: Structure, Function, and Bioinformatics Vol. 8 No. 1 pp. 6-13 · Wiley

View at Publisher Save 10.1002/prot.340080104

Abstract

AbstractProtein folding studies often utilize areas and volumes to assess the hydrophobic contribution to conformational free energy (Richards, F. M. Annu. Rev. Biophys. Bioeng. 6:151–176, 1977). We have calculated the mean area buried upon folding for every chemical group in each residue within a set of X‐ray elucidated proteins. These measurements, together with a standard state cavity size for each group, are documented in a table. It is observed that, on average, each type of group buries a constant fraction of its standard state area. The mean area buried by most, though not all, groups can be closely approximated by summing contributions from three characteristic parameters corresponding to three atom types: (1) carbon or sulfur, which turn out to be 86% buried, on average; (2) neutral oxygen or nitrogen, which are 40% buried, on average; and (3) charged oxygen or nitrogen, which are 32% buried, on average.

Topics

No keywords indexed for this article. Browse by subject →

References

30

[1]

Some Factors in the Interpretation of Protein Denaturation

W. Kauzmann

Advances in Protein Chemistry 10.1016/s0065-3233(08)60608-7

[2]

10.1073/pnas.83.21.8069

[3]

10.1016/s0065-3233(08)60063-7

[4]

PROTEINS, AMINO ACIDS AND PEPTIDES as Ions and Dipolar Ions

Edwin J. Cohn, John T. Edsall, John G. Kirkwood et al.

The American Journal of the Medical Sciences 1943 10.1097/00000441-194306000-00035

[5]

The Solubility of Amino Acids and Two Glycine Peptides in Aqueous Ethanol and Dioxane Solutions

Yasuhiko Nozaki, Charles Tanford

Journal of Biological Chemistry 10.1016/s0021-9258(19)77210-x

[6]

Affinities of amino acid side chains for solvent water

R. Wolfenden, L. Andersson, P. M. Cullis et al.

Biochemistry 10.1021/bi00507a030

[7]

Fauchère J.‐L. "Hydrophobic parameters π for amino acid side chains from partitioning of N‐acetyl‐amino‐acid amides" Eur. J. Med. Chem.‐Chem. Ther. (1983)

[8]

10.1021/bi00405a042

[9]

10.1016/0022-2836(76)90191-1

[10]

10.1038/277491a0

[11]

The interpretation of protein structures: Estimation of static accessibility

B. Lee, F.M. Richards

Journal of Molecular Biology 10.1016/0022-2836(71)90324-x

[12]

Hydrophobicity of Amino Acid Residues in Globular Proteins

George D. Rose, Ari R. Geselowitz, Glenn J. Lesser et al.

Science 10.1126/science.4023714

[13]

AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE

Frederic M. Richards

Annual Review of Biophysics and Bioengineering 10.1146/annurev.bb.06.060177.001055

[14]

10.1016/s0006-3495(85)83877-7

[15]

Eisenberg D. Solvation energy in protein folding and binding (1986)

[16]

10.1002/prot.340020207

[17]

Distribution of accessible surfaces of amino acids in globular proteins

Charles Lawrence, Ivan Auger, Carmen Mannella

Proteins: Structure, Function, and Bioinformatics 10.1002/prot.340020208

[18]

10.1016/0022-2836(88)90540-2

[19]

10.1002/prot.340020202

[20]

The protein data bank: A computer-based archival file for macromolecular structures

Frances C. Bernstein, Thomas F. Koetzle, Graheme J.B. Williams et al.

Journal of Molecular Biology 10.1016/s0022-2836(77)80200-3

[21]

10.1038/254304a0

[22]

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

A. Shrake, J.A. Rupley

Journal of Molecular Biology 10.1016/0022-2836(73)90011-9

[23]

International Mathematical Subroutine Library 7500 Bellaire Blvd. Houston Texas 77036.

[24]

Miller S. Interior and surface of monomeric proteins (1987)

[25]

Snedecor G. W. (1978)

[26]

Stability of Protein Structure and Hydrophobic Interaction

Peter L. Privalov, Stanley J. Gill

Advances in Protein Chemistry 10.1016/s0065-3233(08)60377-0

[27]

10.1073/pnas.87.3.946

[28]

10.1073/pnas.86.21.8382

[29]

10.1016/0022-2836(82)90515-0

[30]

10.1063/1.440540

Cited By

129

Forces stabilizing proteins

C. Nick Pace, J. Martin Scholtz · 2014

FEBS Letters

Contribution of hydrogen bonds to protein stability

C. Nick Pace, Hailong Fu · 2014

Protein Science

Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding

Yuichi Harano · 2012

Entropy

Measuring and Increasing Protein Solubility

Saul R. Trevino, J.Martin Scholtz · 2008

Journal of Pharmaceutical Sciences

BPPred: A Web‐based computational tool for predicting biophysical parameters of proteins

Christian D. Geierhaas, Adrian A. Nickson · 2007

Protein Science

Hydrophobic Surface Burial Is the Major Stability Determinant of a Flat, Single-layer β-Sheet

Shude Yan, Grzegorz Gawlak · 2007

Journal of Molecular Biology

Advances in protein structure prediction and de novo protein design: A review

Christodoulos A. Floudas, H.K. Fung · 2006

Chemical Engineering Science

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties

Xianfeng Li, Sergio A. Hassan · 2005

Proteins: Structure, Function, and...

Correlation between sequence hydrophobicity and surface‐exposure pattern of database proteins

Susanne Moelbert, Eldon Emberly · 2004

Protein Science

Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium

Sergio A. Hassan · 2004

The Journal of Physical Chemistry B

Protein structure, stability and solubility in water and other solvents

C. Nick Pace, Saul Treviño · 2004

Philosophical Transactions of the R...

Prudent Modeling of Core Polar Residues in Computational Protein Design

Daniel N. Bolon, Joshua S. Marcus · 2003

Journal of Molecular Biology

Energetics of Protein Structure

· 1995

Advances in Protein Chemistry

Protein-protein interactions: A review of protein dimer structures

Susan Jones, Janet M. Thornton · 1995

Progress in Biophysics and Molecula...

How to measure and predict the molar absorption coefficient of a protein

C. Nick Pace, Felix Vajdos · 1995

Protein Science

Metrics

129

Citations

30

References

Details

Published: Jan 01, 1990
Vol/Issue: 8(1)
Pages: 6-13
License: View

Authors

G

Glenn J. Lesser

Department of Biological Chemistry, The Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey 17033

G

George D. Rose

Cite This Article

Glenn J. Lesser, George D. Rose (1990). Hydrophobicity of amino acid subgroups in proteins. Proteins: Structure, Function, and Bioinformatics, 8(1), 6-13. https://doi.org/10.1002/prot.340080104

Hydrophobicity of amino acid subgroups in proteins

You May Also Like