The neighboring residue effect appears in denatured proteins and also in the "coil library" of PDB structures of residues. When a neighboring residue (i-1 or i+1) belongs to class L (aromatic and ß-branched amino acids, FHITVWY) rather than class S (all others), then the backbone angle ? of residue i is more negative for all amino acids. Calculated values of peptide solvation predict basic properties of the neighboring residue effect. Moreover, values for the "blocking effect" of side chains on the hydrogen exchange rates of peptide NH protons are correlated with ESF values.
COBISS.SI-ID: 3072026
The chemical shifts of certain atomic nuclei in proteins (1H?, 13C?, and 13Cß) depend sensitively on whether or not the amino acid residue is part of a secondary structure (CSI method). We report that the chemical shift contributions arising from secondary structure depend strongly on the extent of exposure to solvent. The effect prevents accurate determination of secondary structure for solvent exposed residues. These results indicate that secondary structure shifts are produced by the electric field of the protein, which is screened by water dipoles at residues in contact with solvent.
COBISS.SI-ID: 3151898
The preferences of amino acid residues for the ?, ? backbone angles vary strikingly among the amino acids in proteins. Identification of the physical reasons for the conformational preferences is very important for understanding folding. We show that the intrinsic backbone preferences of residues are already determined at the dipeptide level. This behavior of dipeptides is in accord with our electrostatic screening model of conformational preferences (ESM). Other theoretical models of conformational preferences fail to explain the experimental data of dipeptides.
COBISS.SI-ID: 3425306
To understand folding of proteins it is important to characterize the structures of denatured proteins. In this study the coil library of residues is being used to model denatured proteins. Monte Carlo simulations of backbone conformations in denatured proteins are used to test two physics-based models: the random coil model of Brant and Flory and an electrostatic screening model (ESM) that includes electrostatic solvation. We show that the ESM is more successful in predicting the g(?) distributions than the random coil model.
COBISS.SI-ID: 2807322
We studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the 3JHN?, which is the indicator for the preference for the dihedral angle ?. We show that alanine dipeptide adopts predominantly a PII conformation. The population of the ß conformation increases in valine dipeptide. The populations of the ?R conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.
COBISS.SI-ID: 3877146