Hydrogen bonds in membrane proteins.
Hydrogen 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, we performed molecular dynamics simulations of these fluctuating hydrogen bonds. This indicated long-range entropy and energy contributions extending far into the liquid environment. The results showed that the binding of a given hydrogen bond is much reduced as a result of these interactions in water, as is required for biological activity and in very good confirmation of known experimental results. The larger water environment directly interacts with the hydrogen bond essentially due to long-range molecular interactions. Such a substantial lowering of the energy of the hydrogen bond in water brings it into the range of activation by many biological processes ( Sheu et al. Chem. Phys. Lett. 2008 , 462 , 1 - 5 ). Thus, the water medium profoundly increases the rate. Furthermore, very large entropic changes are associated with the rupture of hydrogen bonds in water, whereas no such effects are seen for the isolated molecule. Interestingly, such an increase in rates in water is still accompanied by a large negative change in entropy in the extended solvent environment, and this reduces the rate by some 2 orders of magnitude. Recent molecular dynamics experiments in D(2)O substantiate this model and show a large solvent isotope effect. In this work, we used lipids as the environment for the hydrogen bond and discovered that the energy is also reduced from that found in the isolated molecule, but not as far as in water. On the other hand, we found that no entropy penalty exists for breaking the hydrogen bond in lipids, as seen for water. These two effects compensate, even though the energy is some 2 times larger. The entropic penalty is reduced such that the rate is higher than in water despite the higher energy. This is a significant result for understanding the reactivity and dynamics of proteins in lipids. It should be noted that these are very important solvent effects on entropies and free energies that are not usually reflected in statistical thermodynamic computations for reactants and products. The very long-range effect of the solvent makes substantial contributions to kinetic rate constants and is readily evaluated in this kinetic method. To ignore these long-range environmental effects on the entropy can lead to very spurious results when calculating rates of protein mobilities. Hence, the results not only agree very well with the known hydrogen-bond energies directly as a result of various environmental factors, but even correctly predict a phase transition in the lipid.
Sheu
Sheh-Yi
SY
Department of Life Sciences and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan. sysheu@ym.edu.tw
Schlag
Edward W
EW
Selzle
Heinrich L
HL
Yang
Dah-Yen
DY
D006860:Hydrogen Bonding; D007700:Kinetics; D008565:Membrane Proteins / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry
D008565:Membrane Proteins; D014867:Water