H-bonds are essential tie points inside protein structures. They undergo dynamic rupture and rebonding processes on the time scale of tens of picoseconds. Proteins can partially rearrange during such ruptures. In previous work, the authors performed mol. dynamics simulations of these fluctuating H-bonds. This indicated long-range entropy and energy contributions extending far into the liq. environment. The results showed that the binding of a given H-bond was much reduced as a result of these interactions in water, as was required for biol. activity and in very good confirmation of known exptl. results. The larger water environment directly interacted with the H-bond essentially due to long-range mol. interactions. Such a substantial lowering of the energy of the H-bond in water brought it into the range of activation by many biol. processes. Thus, the water medium profoundly increases the rate. Furthermore, very large entropic changes were assocd. with the rupture of H-bonds in water, whereas no such effects were seen for the isolated mol. Interestingly, such an increase in rates in water was still accompanied by a large neg. change in entropy in the extended solvent environment, and this reduced the rate by some 2 orders of magnitude. Recent mol. dynamics expts. in D2O substantiated this model and showed a large solvent isotope effect. Here, the authors used lipids as the environment for the H-bond and discovered that the energy was also reduced from that found in the isolated mol., but not as far as in water. On the other hand, it was found that no entropy penalty existed for breaking the H-bond in lipids, as seen for water. These 2 effects compensated, even though the energy was ∼2-fold larger. The entropic penalty was reduced such that the rate was higher than in water despite the higher energy. This was a significant result for understanding the reactivity and dynamics of proteins in lipids. It should be noted that these were very important solvent effects on entropies and free energies that were not usually reflected in statistical thermodn. computations for reactants and products. The very long-range effect of the solvent made substantial contributions to kinetic rate consts. and was readily evaluated in this kinetic method. To ignore these long-range environmental effects on the entropy can lead to very spurious results when calcg. rates of protein mobilities. Hence, the results not only agree very well with the known H-bond energies directly as a result of various environmental factors, but even correctly predict a phase transition in the lipid. [on SciFinder(R)]     «

H-bonds are essential tie points inside protein structures. They undergo dynamic rupture and rebonding processes on the time scale of tens of picoseconds. Proteins can partially rearrange during such ruptures. In previous work, the authors performed mol. dynamics simulations of these fluctuating H-bonds. This indicated long-range entropy and energy contributions extending far into the liq. environment. The results showed that the binding of a given H-bond was much reduced as a result of these in...     »

Proteins Role: BSU (Biological study, unclassified), PRP (Properties), BIOL (Biological study) (membrane models for hydrogen bonds in membrane proteins) Hydrogen bond (models for hydrogen bonds in membrane proteins) Peptides Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PRP (Properties), BIOL (Biological study), PROC (Process) (models of peptide hydrogen bonds in lipid environment) Simulation and Modeling (mol. dynamics of peptide hydrogen bonds in lipid environment) Simulation and Modeling (of peptide hydrogen bonds in lipid environment) Activation entropy Free energy of activation (of rupture of peptide hydrogen bonds in lipid environment) membrane protein hydrogen bond model thermodn mol dynamics simulation     «

Proteins Role: BSU (Biological study, unclassified), PRP (Properties), BIOL (Biological study) (membrane models for hydrogen bonds in membrane proteins) Hydrogen bond (models for hydrogen bonds in membrane proteins) Peptides Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PRP (Properties), BIOL (Biological study), PROC (Process) (models of peptide hydrogen bonds in lipid environment) Simulation and Modeling (mol. dynamics of peptide hydrogen bonds in...     »