Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics.
We present immunophysical modeling for VCP, SPICE, and three mutants using MD simulations and Poisson-Boltzmann-type electrostatic calculations. VCP and SPICE are homologous viral proteins that control the complement system by imitating, structurally and functionally, natural regulators of complement activation. VCP and SPICE consist of four CCP modules connected with short flexible loops. MD simulations demonstrate that the rather complex modules of VCP/SPICE and their mutants exhibit a high degree of intermodular spatial mobility, which is affected by surface mutations. Electrostatic calculations using snapshots from the MD trajectories demonstrate variable spatial distribution of the electrostatic potentials, which suggests dynamic binding properties. We use covariance analysis to identify correlated modular oscillations. We also use electrostatic similarity indices to cluster proteins with common electrostatic properties. Our results are compared with experimental data to form correlations between the overall positive electrostatic potential of VCP/SPICE with binding and activity. We show how these correlations can be used to predict binding and activity properties. This work is expected to be useful for understanding the function of native CCP-containing regulators of complement activation and receptors and for the design of antiviral therapeutics and complement inhibitors.
Zhang
Li
L
Department of Chemistry, University of California, Riverside, California 92521, USA.
Morikis
Dimitrios
D
D000595:Amino Acid Sequence; D003169:Complement Inactivator Proteins / Q000378:metabolism*; D003165:Complement System Proteins / Q000378:metabolism*; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D011237:Predictive Value of Tests; D017434:Protein Structure, Tertiary; D017365:Spices; D055672:Static Electricity; D013816:Thermodynamics; D014616:Vaccinia virus / Q000737:chemistry / Q000276:immunology*; D012901:Variola virus / Q000737:chemistry / Q000276:immunology*; D014764:Viral Proteins / Q000378:metabolism*
D003169:Complement Inactivator Proteins; D014764:Viral Proteins; C066459:complement-control protein, Vaccinia virus; D003165:Complement System Proteins