Structural plasticity and conformational transitions of biological macromolecules: HIV gp120

Activities of many biological macromolecules involve dynamic processes ranging from local fluctuations of individual atoms to large conformational transitions covering extensive amplitudes, time scales and energies. Structures are often known in atomic detail for stably defined states but static pictures of macromolecules are not sufficient alone to explain molecular function. Therefore, it is of interest to explore the macromolecular dynamics by computation.;The course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Calpha atoms in protein molecules. This force field, called the virtual atom molecular mechanics (VAMM) potential is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting VAMM force field is applied to energy minimization and normal mode analysis for several proteins. We find robust convergence in minimizations to low energies and small energy gradients without significant structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high resolution crystal structures. These findings suggest that VAMM is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.;In order to address large scale conformational transitions, we have described an algorithm based on the VAMM potential. We validate this algorithm in comparison to control algorithms based on simple harmonic and bond-restrained harmonic potentials, which we do through applications to a transition between open and closed states of adenylate kinase (ADK). Normal modes are computed for each state, and that mode from each showing the greatest involvement into the direction toward the other state defines the first moves through a succession of intermediates until convergence to within a defined limit, here a root-mean-square deviation of 1A. Periodic energy minimizations and re-definitions of secondary structure facilitate convergence. Validations show that the VAMM algorithm is highly effective, and the transition pathways examined for ADK are compatible with other structural and biophysical information.;After developing and testing the VAMM-based methods, we have analyzed the structural plasticity and conformational transitions of gp120 with conventional and novel computational tools. HIV envelope glycoprotein gp120 binds sequentially to CD4 and a chemokine receptor in order to mediate the entry of the virus into host cells. The structures of gp120 and thermodynamic data suggest conformational change in gp120 upon CD4 binding. Thermodynamic analysis of antibody binding to gp120 also suggests that gp120 exploits conformational variability to evade immune responses. To better understand the nature of these conformational changes, three major questions are addressed, (i) what is the nature of the conformational plasticity of gp120 around the local minima of known crystal structures and what is the effect of ligand binding on the conformational plasticity? (ii) What is the nature of the structural plasticity in the Phe43 cavity, which is the most critical site of gp120 for CD4 binding and conformational changes? (iii) What are the nature of gp120 dynamics away from its known crystallographic states and the mechanism of its conformational transitions? The results indicate a series of hinge residues at the inner/outer domain interface that coordinate the interdomain motions, reorganizations of the gp120 bridging sheet, the stabilization and synchronization of conserved residues around the Phe43 cavity upon receptor binding and a multi-phased conformational transition along which several different conformational states are sampled.;Based on the current stage of development, we envision a future perspective for VAMM-based methodologies. This includes applications to other biological problems expansion of the scope of the VAMM force field, and further advances application algorithms.