Hydrophobic clusters in protein structures

Proteins
J Arunachalam, N Gautham

Abstract

Globular proteins fold such that the hydrophobic groups are packed inside forming hydrophobic clusters, and the hydrophilic groups are present on the surface. In this article we analyze clusters of hydrophobic groups of atoms in 781 protein structures selected from the PDB. Our analysis showed that every structure consists of two types of clusters: at least one large cluster that forms the hydrophobic core and probably dictates the protein fold; and numerous smaller clusters, which might be involved in the stabilization of the fold. We also analyzed the preference of the hydrophobic groups in each of the amino acids toward forming hydrophobic clusters. We find that hydrophobic groups from the hydrophilic amino acids also contribute toward cluster formation.

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Citations

Dec 5, 2008·Protein Engineering, Design & Selection : PEDS·Vagmita Pabuwal, Zhijun Li
Dec 20, 2011·The Journal of Physical Chemistry. B·Kamatchi SankaranarayananReinhard Miller
Jan 30, 2015·Protein Science : a Publication of the Protein Society·Khoa PhamJaroslava Miksovska
Oct 27, 2015·BMC Structural Biology·Kazuo FujiwaraMasamichi Ikeguchi
Oct 15, 2019·Journal of Biomolecular Structure & Dynamics·J Dennis PollackDennis K Pearl

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