Hydrophobic moments of protein structures: spatially profiling the distribution

Proceedings of the National Academy of Sciences of the United States of America
B D Silverman

Abstract

It is generally accepted that globular proteins fold with a hydrophobic core and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing this distribution from the protein interior to exterior has been examined for 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys. A second-order hydrophobic moment has provided a simple measure of the spatial variation. Shapes of the calculated spatial profiles of all native structures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted protein structures and in discriminating between different protein-folding pathways. The spatial profiles of the 14 decoys are clearly distinguished from the profiles of their native structures.

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Citations

Mar 31, 2007·Journal of Molecular Modeling·Michal BrylinskiIrena Roterman
Feb 11, 2016·Education for Primary Care : an Official Publication of the Association of Course Organisers, National Association of GP Tutors, World Organisation of Family Doctors·Jane Stewart
Aug 12, 2003·Proteins·Ruhong ZhouPrasanna Athma
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Nov 24, 2004·Journal of Chemical Information and Computer Sciences·Yizong ChengXiaoyang Qi
Jun 25, 2002·Journal of Theoretical Biology·B David Silverman
Apr 27, 2016·Scientific Reports·Yuanzhao ZhangRuhong Zhou
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Nov 21, 2012·Qualitative Health Research·Renata KokanovicJane Gunn
Jul 16, 2010·Journal of Intellectual Disabilities : JOID·Steve Mee
Nov 25, 2003·Proteins·B David Silverman
Feb 9, 2012·Journal of Health Services Research & Policy·Pauline AllenRossella Verzulli
Mar 12, 2010·International Journal of Palliative Nursing·Deborah Cartlidge, Sue Read
Oct 1, 2003·Proteins·Daniel E PlattIsidore Rigoutsos
Apr 30, 2019·PloS One·Angel Mozo-Villarías, Enrique Querol
Feb 17, 2017·The Journal of Chemical Physics·Adesh KumarParbati Biswas
Mar 7, 2021·International Journal of Molecular Sciences·Aikaterini KefalaMichael Kokkinidis
Jun 17, 2021·European Biophysics Journal : EBJ·Angel Mozo-VillaríasEnrique Querol
May 16, 2012·The Journal of Physical Chemistry. B·Nidhi Rawat, Parbati Biswas

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