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Full-Text Articles in Physics
Structural Assessment Of The Effects Of Amino Acid Substitutions On Protein Stability And Protein-Protein Interaction, Shaolei Teng, Liangjiang Wang, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov
Structural Assessment Of The Effects Of Amino Acid Substitutions On Protein Stability And Protein-Protein Interaction, Shaolei Teng, Liangjiang Wang, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov
Publications
A structure-based approach is described for predicting the effects of amino acid substitutions on protein function. Structures were predicted using a homology modelling method. Folding and binding energy differences between wild-type and mutant structures were computed to quantitatively assess the effects of amino acid substitutions on protein stability and protein–protein interaction, respectively. We demonstrated that pathogenic mutations at the interaction interface could affect binding energy and destabilise protein complex, whereas mutations at the non-interface might reduce folding energy and destabilise monomer structure. The results suggest that the structure-based analysis can provide useful information for understanding the molecular mechanisms of diseases.
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Chemistry & Physics Faculty Publications
Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein–protein and protein–peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of ≈0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. …
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Mixed Alkali Halide Dimers, Robert J. Cave, Ian Ono '94
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Mixed Alkali Halide Dimers, Robert J. Cave, Ian Ono '94
All HMC Faculty Publications and Research
Results are presented from ab initio calculations on several mixed alkali halide dimers made up of Li, Na, F, and Cl. All of the dimers are investigated at the restricted Hartree–Fock level to provide ab initio estimates of geometries, vibrational frequencies, and binding energies. The dimer LiNaF2 is then treated using a variety of basis sets at the Hartree–Fock level, as well as at correlated levels (second‐order Møller–Plesset and coupled‐cluster singles and doubles) to examine the sensitivity of the calculations to use of higher levels of theory. The results are then compared to the experimental data available for the LiNaF2 …
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Alkali Halide Dimers, Robert P. Dickey '93, David Maurice '91, Robert J. Cave, Richard J. Mawhorter
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Alkali Halide Dimers, Robert P. Dickey '93, David Maurice '91, Robert J. Cave, Richard J. Mawhorter
All HMC Faculty Publications and Research
Results are presented from ab initio calculations on the symmetrical alkali halide dimers made up of Li, Na, K, F, and Cl. We examine the sensitivity of representative monomer and dimer geometries to the variation of the basis set with and without polarization and diffuse functions. The geometries are then compared with available experimental results. We have also calculated vibrational frequencies at the restricted Hartree–Fock level and examined the changes in geometry brought about by correlation using second‐order Møller–Plesset perturbation theory. It is found that Hartree–Fock theory in a modest basis set with diffuse and polarization functions yields results comparable …