HELIX-CAPPING INTERACTION IN LAMBDA-CRO PROTEIN - A FREE-ENERGY SIMULATION ANALYSIS

The stability mutant Tyr-26-->Asp was studied in the Cro protein from bacteriophage lambda using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 +/- 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1. 4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was fou nd to form a capping interaction with the amino terminus of the third alpha-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing h elix caps-namely, a model of local unsatisfied hydrogen bonds at the h elix termini and the helix macrodipole model. Analysis of the simulati ons shows that the stabilizing effect of this charged helical cap is d ue both to favorable hydrogen bonds with backbone NH groups at the hel ix terminus and to favorable electrostatic interactions (but not hydro gen bonds) with their carbonyls (effectively the next row of local dip oles in the helix). However, electrostatic interactions are weak or ne gligible with backbone dipolar groups in the helix further away from t he terminus. Moreover, the importance of other local electrostatic int eractions with polar side chains near the helix terminus, which are ne glected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix t erminus and other, local preoriented dipolar groups stabilize the heli x cap. These findings suggest that similar interactions with preorient ed dipolar groups may be important for cooperativity in other charge-d ipole interactions and may be employed to advantage for molecular desi gn. (C) 1994 Wiley-Liss, Inc.