INVESTIGATION OF DOMAIN MOTIONS IN BACTERIOPHAGE-T4 LYSOZYME

Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises a n important question: are the different conformers in the unit cell ar tifacts of crystal packing forces, or do they represent different solu tion state structures? The objective of this theoretical study is to d etermine whether domain motions and hinge-bending could be simulated i n T4 lysozyme using molecular dynamics. An analysis of a 400 ps molecu lar dynamics simulation of the 164 amino acid enzyme T4 lysozyme is pr esented. Molecular dynamics calculations were computed using the Disco ver software package (Biosym Technologies). All hydrogen atoms were mo deled explicitly with the inclusion of all 152 crystallographic waters at a temperature of 300 K. The native T4 lysozyme molecular dynamics simulation demonstrated hinge-bending in the protein. Relative domain motions between the N-terminal and C-terminal domains were evident. Th e enzyme hinge bending sites resulted from small changes in backbone a tom conformations over several residues rather than rotation about a s ingle bound. Two hinge loci were found in the simulation. One locus co mprises residues 8-14 near the C-terminal of the A helix; the other si te, residues 77-83 near the C-terminal of the C helix. Comparison of s everal snapshot structures from the dynamics trajectory clearly illust rates domain motions between the two lysozyme lobes. Time correlated a tomic motions in the protein were analyzed using a dynamical cross-cor relation map. We found a high degree of correlated atomic motions in e ach of the domains and, to a lesser extent, anticorrelated motions bet ween the two domains. We also found that the hairpin loop in the N-ter minal lobe (residues 19-24) acted as a mobile 'flap' and exhibited hig hly correlated dynamic motions across the cleft of the active site, es pecially with residue 142.