Computational analysis of variants of the operator binding domain of the bacteriophage ? repressor

Abstract

In a continuing effort to understand the molecular basis of the dimerization-coupled DNA-binding activity of the bacteriophage λ repressor protein, we analyzed results from conformational energy computations on the wild-type λ repressor protein and its mutants. We find that the hydrogen bonds between the peptide carbonyl oxygen of Tyr-85 and the peptide NH group of the residue at position 89 in active mutants are longer and less linear than their corresponding ones in inactive mutants. This is due to the outward tilting of the carbonyl oxygen of Tyr-85 from the helix axis in active mutants, which, in many cases, results in disruption of its i to the i+4 hydrogen bond involving this residue. The helical and hydrogen-bond parameters computed for both classes of mutants were compared with the results obtained by others in the analysis of X-ray-derived crystal structures of α-helices in globular proteins. We find that the packing of α-helices at the dimer interface of active and inactive mutants results in a hydrogen-bonding geometry for the carbonyl group of Tyr-85 that is similar to that found in α-helices with and without CO groups hydrogen-bonded to a solvent molecule, respectively. A rough correlation is also observed between the tolerance for amino acid substitution at position i of helix-5 with the number of close intermonomer contacts involving the residues at position i and i−2. On the basis of these findings, we discuss the mutability of amino acid residues at the dimer interface. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 313–325, 1999