Molecular forces in protein structure and crystallography

Conformational properties of the pentapeptide fragment [32-36] of the thymic hormone thymopoietin

The conformational energy for the pentapeptide Arg-Lys-Asp-Val-Tyr (TP5) is calculated using empirical potential functions. Calculation of the local interactions for each independent residue gives a local energy term for which the probabilities as a function of phi, psi are plotted on Ramachandran-type maps. The interaction energy between residues is calculated only for these points in the maps with maximum probability. The most probable conformation for TP5 is found to have an extended backbone arrangement having the Arg and Tyr sidechains folded over the backbone. 13C n.m.r. spin lattice relaxation time measurements show no increase in T1 of the alpha-carbons at the first and terminal amino acids. The increase in T1 along the sidechain as found for Lys does not occur for Arg and Tyr. These signs of reduced mobility are consistent with a set of folded conformations in which the Arg and Tyr sidechains have hindered internal rotations. The vicinal NH-C alpha H couplings agree well with those calculated for the most probable conformer. This is not so for the C alpha H-C beta H couplings. These data are consistent with previous n.m.r. and structure activity studies.

Conformational calculations on gastrin C-terminal tetrapeptide

Energy optimizations were performed on some typical conformations of the gastrin C-terminal peptide amide NAc-Trp-Met-Asp-Phe-NH2. Two families of lowest energy conformations were found corresponding to: (a) alpha-helical structures; (b) conformations having beta-structure at the level of Trp residue, and C7-structure at the level of Asp residue. The two aromatic rings were folded on the peptide backbone and ca. 5 A distant from each other (centre to centre). The last family, favoured by energy and population probability, can better account for conformational experimental results and biological activity observations.

Interatomic potential functions and crystal packing1,2

The potential-energy functions which have been employed in the laboratory of the authors for biopolymer calculations have been applied to calculate the minimum-energy conformations of benzene and sulfur dioxide in their crystalline state. The predicted conformations corresponding to the lowest energy agree remarkably well with the crystal structures determined from x-ray diffraction. Although more than one local energy minimum is found to occur in benzene, those corresponding to other than the lowest energy are higher by about 1 kcal/mole and also occur near regions having disallowed contact distances, thus explaining their nonoccurrence. This method appears to have potentiality for application to more complicated systems.