RESUMEN
A distance constraint model (DCM) is presented that identifies flexible regions within protein structure consistent with specified thermodynamic condition. The DCM is based on a rigorous free energy decomposition scheme representing structure as fluctuating constraint topologies. Entropy non-additivity is problematic for naive decompositions, limiting the success of heat capacity predictions. The DCM resolves non-additivity by summing over independent entropic components determined by an efficient network-rigidity algorithm. A minimal 3-parameter DCM is demonstrated to accurately reproduce experimental heat capacity curves. Free energy landscapes and quantitative stability-flexibility relationships are obtained in terms of global flexibility. Several connections to experiment are made.
Asunto(s)
Conformación Proteica , Proteínas/química , Estabilidad de Medicamentos , Entropía , Enlace de Hidrógeno , Modelos Moleculares , Estrés Mecánico , TermodinámicaRESUMEN
We discuss here the implementation of the Weighted Ensemble Brownian (WEB) dynamics algorithm of Huber and Kim in the University of Houston Brownian Dynamics (UHBD) suite of programs and its application to bimolecular association problems. WEB dynamics is a biased Brownian dynamics (BD) algorithm that is more efficient than the standard Northrup-Allison-McCammon (NAM) method in cases where reaction events are infrequent because of intervening free energy barriers. Test cases reported here include the Smoluchowski rate for association of spheres, the association of the enzyme copper-zinc superoxide dismutase with superoxide anion, and the binding of the superpotent sweetener N-(p-cyanophenyl)-N'-(diphenylmethyl)-guanidinium acetic acid to a monoclonal antibody fragment, NC6.8. Our results show that the WEB dynamics algorithm is a superior simulation method for enzyme-substrate reaction encounters with large free energy barriers.
Asunto(s)
Algoritmos , Anticuerpos Monoclonales/química , Bioquímica/métodos , Simulación por Computador , Fragmentos de Inmunoglobulinas/química , Superóxido Dismutasa/química , Superóxidos/química , Acetatos/química , Sitios de Unión , Dimerización , Guanidinas/química , Cinética , Modelos Moleculares , Conformación Proteica , Estructura Secundaria de Proteína , Electricidad Estática , Superóxido Dismutasa/metabolismo , Superóxidos/metabolismo , Edulcorantes/química , TermodinámicaRESUMEN
Monoclonal antibody NC6.8 is specific for the superpotent sweetener, N-(p-cyanophenyl)-N'-(diphenylmethyl)-guanidiniumacetic++ + acid. The three-dimensional structure of the complex shows the close proximity of complementary charged residues on the antibody and groups of the hapten. As a result, association is dependent on the pH, dielectric, and ionic strength of the medium. Continuum electrostatics methods are used to calculate the pH-dependent association energetics of NC6.8 with the superpotent sweetener. In addition to providing a titration profile, the calculations quantitatively assess the relative influence of charged groups on the energetics of association. Models of site directed mutants are constructed to probe the influence of each charged interface residue on the pH-dependent energetics of association. Examination of electrostatic contribution to free energy of association in mutant complexes, where the key acidic residues on the antibody are neutralized, shows that charge complementarity at the combining site is an important requirement for hapten binding. Also, based on the pKa values of several combining site tyrosine residues, aromatic pi-stacking and van der Waal's contacts between the antibody and hapten contribute to the specificity of the complex.