Energetic asymmetry among hydrogen bonds in MHC class II*peptide complexes

Energetic asymmetry among hydrogen bonds in MHC class II*peptide complexes.

Comparison of crystallized MHC class II*peptide complexes has revealed that, in addition to pocket interactions involving the peptide side chains, peptide binding to MHC class II molecules is characterized by a series of hydrogen bonds between genetically conserved amino acid residues in the class II molecule and the main chain of the peptide. Many class II*peptide structures have two sets of s...

Scoring Docked Protein Complexes with Hydrogen Bonds

Finding the structure of proteins and protein-protein complexes is an important problem in the field of computational biology. Determining protein structures can be done successfully with various experimental methods like x-ray crystallography, but determining protein-protein structures experimentally is more difficult. Instead, these structures are frequently predicted computationally. One app...

H2XP:OH2 Complexes: Hydrogen vs. Pnicogen Bonds

A search of the Cambridge Structural Database (CSD) was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out ...

Energetic Effects of Multiple Hydrogen Bonds. Implications for Enzymatic Catalysis

The rate enhancements obtained by enzymes often require greater than 20 kcaVmol of stabilization that is specific to the transition state. Inspection of active sites suggests that enzymes often use multiple interactions with substrate groups undergoing charge rearrangement to help provide this preferential stabilization. We have analyzed the deprotonation, in DMSO, of benzoic acids with one or ...

Class II Complexes Bond Controls the Stability of Peptide-MHC Cutting Edge: A Single, Essential Hydrogen