ABSTRACT
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.
Subject(s)
Amino Acids/chemistry , Proteins/chemistry , Amino Acid Sequence , Animals , Chemical Phenomena , Chemistry, Physical , Models, Chemical , Molecular Sequence Data , Myoglobin/chemistry , Plant Proteins/chemistry , Solubility , Thermodynamics , Water/chemistryABSTRACT
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.
Subject(s)
Antigen-Antibody Complex/chemistry , Models, Chemical , Amino Acid Sequence , Amino Acids/chemistry , Animals , Binding Sites , Chemical Phenomena , Chemistry, Physical , Immunoglobulin Fab Fragments/chemistry , Molecular Sequence Data , Muramidase/chemistry , Muramidase/immunology , ThermodynamicsABSTRACT
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.
Subject(s)
Models, Chemical , Peptide Fragments/chemistry , Protein Conformation , Proteins/chemistry , Amino Acid Sequence , Amino Acids/chemistry , Apoproteins/chemistry , Apoproteins/metabolism , Bence Jones Protein/chemistry , Cytochrome c Group/chemistry , Cytochrome c Group/metabolism , Flavin-Adenine Dinucleotide/chemistry , Flavin-Adenine Dinucleotide/metabolism , Flavodoxin/chemistry , Flavodoxin/metabolism , Heme/chemistry , Heme/metabolism , Mathematical Computing , Molecular Sequence Data , Myoglobin/chemistry , Myoglobin/metabolism , Normal Distribution , Peptide Fragments/metabolism , Plant Proteins/chemistry , Protein Structure, Secondary , Proteins/metabolism , Solvents , Thiosulfate Sulfurtransferase/chemistryABSTRACT
Accessible surface areas of DNA molecules (A- and B-forms) for different probe particle radii were calculated for poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)] sequences. The problem of different forms stability is discussed in connection with accessible surface area characteristics as well as coulombic interaction between base pairs. The coulombic interaction was shown to play an important role in sequence dependent stability of the DNA molecule.
Subject(s)
DNA/chemistry , Water/chemistry , Models, Molecular , Nucleic Acid Conformation , Poly dA-dT/chemistryABSTRACT
Different possibilities of H-bonds formation for formamide-water complexes and dimers of formamide were studied. Potential energy maps were calculated for di-, tri- and tetrapeptides. The maps provide necessary data to explain the relative stability of different oligopeptide conformers and Ramachandran maps for peptides.
Subject(s)
Oligopeptides , Hydrogen Bonding , Models, Molecular , Protein ConformationABSTRACT
The problem of stabilization of oligopeptide alpha-helix conformation is discussed. The stabilizing role of intramolecular H-bonds and coulombic interactions for single molecules was shown. The influence of media results in the competition for formation of inter and intramolecular H-bonds and for coulombic interactions. High competitive media, eg. water, diminishes alpha-helix stability.
