Atom depth in protein structure and function.

Alessandro Pintar, Oliviero Carugo, Sándor Pongor

Journal: Trends in biochemical sciences 2004;28(11):593-7

PMID: 14607089

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Abstract

Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. It can be easily computed from the 3D structure of a protein, thus complementing the information provided by the calculation of the solvent accessible surface area and buried surface area. Depth has been found to be correlated with several molecular, residue and atomic properties, such as average protein domain size, protein stability, free energy of formation of protein complexes, amino acid type hydrophobicity, residue conservation and hydrogen/deuterium amide proton exchange rates.

Address: Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy. [email protected]

DOI: 10.1016/j.tibs.2003.09.004

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MeSH Terms: Algorithms, Amino Acids, Computer Simulation, Humans, Interferon alpha-2, Interferon-alpha, Models, Molecular, Protein Conformation, Protein Subunits, Proteins, Recombinant Proteins, Solvents