Gaussian neighborhood: a new measure of accessibility for residues of protein molecules.
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-neighborhood 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.
Nauchitel
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Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario.
Somorjai
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D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D001536:Bence Jones Protein / Q000737:chemistry; D003574:Cytochrome c Group / Q000737:chemistry / Q000378:metabolism; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry / Q000378:metabolism; D005418:Flavodoxin / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D008432:Mathematical Computing; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism; D016011:Normal Distribution; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012997:Solvents; D013884:Thiosulfate Sulfurtransferase / Q000737:chemistry
D000596:Amino Acids; D001059:Apoproteins; D003574:Cytochrome c Group; D005418:Flavodoxin; D009211:Myoglobin; D010446:Peptide Fragments; D010940:Plant Proteins; D011506:Proteins; D012997:Solvents; D005182:Flavin-Adenine Dinucleotide; D006418:Heme; C024934:crambin protein, Crambe abyssinica; D001536:Bence Jones Protein; D013884:Thiosulfate Sulfurtransferase