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Gaussian neighborhood: A new measure of accessibility for residues of protein molecules
Author(s) -
Nauchitel Vladimir V.,
Somorjai Rajmund L.
Publication year - 1993
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340150107
Subject(s) - flavodoxin , rhodanese , chemistry , residue (chemistry) , myoglobin , monomer , gaussian , crystallography , molecule , protein structure , computational chemistry , biochemistry , enzyme , polymer , organic chemistry , ferredoxin
We introduce a new method for assessing the extent of residue exposure in proteins. For each atom of every residue a Gaussian‐weighted atomic surroundings value (the G‐neighborhood) is calculated. A normalized sum of G‐neighborhood values over all the atoms of a residue is complementary to conventional surface accessibility characteristics. The G‐0neighborhood value of a residue is a sensitive indicator of its location, strongly dependent on the 3D structure of a the protein. Correlations between secondary structures and patterns of G‐neighborhood values for six different protein molecules are discussed. Comparison of the distribution of hydrophobic and charged residues in the 3D structure for the alcohol‐soluble protein crambin and that of five water‐soluble proteins (cytochrome c , flavodoxin, myoglobin, rhodanese, and Bence–Jones protein) shows striking differences in their G‐neighborhood patterns. Contacts between the prosthetic group and the peptide portion of a protein as well as protein interdomain contacts and monomer–monomer contacts are characterized. © 1993 Wiley‐Liss, Inc.