Biomedical subjects

V V Nauchitel

Publications and source records attributed to V V Nauchitel.

3 recordsLinked to original sources

PubMed1994

Spatial and free energy distribution patterns of amino acid residues in water soluble proteins.

We have calculated, for the 20 common amino acid residues: probability density functions that characterize the residues' tendency to occupy different locations in proteins; a propensity scale for the residues to be exposed or buried; mean force potentials that characterize the residues' free energy dependence on their degree of exposure; the average composition of water soluble proteins, and the composition of their core and surface. The nature of differences between different hydrophobicity-related scales is discussed.

Amino Acid Sequence↗

PubMed1994

Antigen-antibody recognition. Model calculations.

Free energy of antigen-antibody binding has been calculated for HyHEL-5, HyHEL-10, and D1.3 complexes. We also have calculated free energies of binding per residue of L- and H- chains of the antibodies, and those of the antigen (lysozyme). The results of the calculations provide support for the notion that TYR and TRP residues may confer on the CDRs of antibodies an enhanced capacity for binding antigens. It was shown also that the composition of residues that provide major part of the binding free energy differs for antibodies and antigens.

Amino Acid Sequence↗

PubMed1993

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.

Amino Acid Sequence↗