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

In a continuing effort to understand the molecular basis of the dimerizatio n-coupled DNA-binding activity of the bacteriophage lambda repressor protei n, we analyzed results from conformational energy computations on the wild- type lambda repressor protein and its mutants. We find that the hydrogen bo nds 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 outwa rd tilting of the carbonyl oxygen of Tyr-85 from the helix axis in active m utants, which, in many cases, results in disruption of its i to the i + 4 h ydrogen bond involving this residue. The helical and hydrogen-bond paramete rs computed for both classes of mutants were compared with the results obta ined by others in the analysis of X-ray-derived crystal structures of alpha -helices in globular proteins. We find that the packing of alpha-helices at the dimer interface of active and inactive mutants results in a hydrogen-b onding geometry for the carbonyl group of Tyr-85 that is similar to that fo und in alpha-helices with and without CO groups hydrogen-bonded to a solven t molecule, respectively. A rough correlation is also observed between the tolerance for amino acid substitution at position i of helix-5 with the num ber 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. (C) 1999 John Wiley & Sons, Inc.