摘要:

Using a dynamical Gaussian model of solvation, we have developed a phenomenological theory of solvation dynamics. This theory is applied to compute the solvation dynamics correlation function for solutes in various solvents from time-dependent Stokes shift experiments and to compute the peak shift as a function of population period from three-pulse photon-echo experiments. Employing a quantum chemical estimate of the solute’s charge distribution, the Richard-Lee estimate of its van der Waals surface, and the measured frequency dependent dielectric constant of the pure solvent, we found the calculated results agree closely with those determined by experiments. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301540

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The redox potential of an electron transfer protein is an essential property because it determines the driving force in an electron transfer reaction. The protein itself is an important determining factor since the redox potentials of analogs and proteins with the same metal site or of different proteins with the same metal site may differ by on the order of 1V. On the other hand, homologous proteins with the same redox site may have identical redox potentials or may differ by up to 500 mV, although the larger differences generally correspond to significant differences in the backbone fold. Different computational methods for understanding where these differences arise from will be discussed. Particular attention will be placed on how our knowledge of protein structure function relationships influences the techniques that are used. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301541

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions but they have not been parametrized on such complex problems, and therefore it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than103faster using the Surface Generalized Born implicit solvent model as compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301542

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Approaches to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster are reviewed. A rigorous theoretical formulation is given for the solvent boundary potential which takes the influence of the surrounding bulk into account. The solvent boundary potential is the configuration-dependent solvation free energy of an effective cluster comprising of an arbitrary solute and a finite number of explicit solvent molecules embedded inside a hard sphere of variable radius; the hard sphere does not act directly on the solute or the explicit solvent molecules and its radius varies according to the instantaneous configurations. The formulation follows from an exact separation of the multidimensional configurational Boltzmann integral in terms of the solvent molecules nearest to the solute and the remaining bulk solvent molecules. Extensions to non-spherical system are discussed. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301543

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The excess chemical potentials of methane and its four fluorinated derivatives across the water-hexane, water-octanol, water-glycerol 1-monooleate and water-1-palmitoyl 2-oleoyl sn-glycero 3-phosphatidylcholine (POPC) interfaces are calculated using the particle insertion method. In all cases, the polar species exhibit interfacial minima indicating that these molecules tend to accumulate in the interfacial region, while the non-polar molecules exhibit no such minimum. The excess chemical potentials are further partitioned into electrostatic and non-electrostatic terms. For polar molecules, the electrostatic term changes nearly linearly over the distance of approximately 10 Å in the interfacial region and appears to depend only weakly on the nature of the interface. Solute molecules are not oriented isotropically at the interface, but tend to align themselves with the excess electric field created by the anisotropic interfacial environment. Using dipoles in a cavity as models, it is further shown that, in the water-POPC system, the electrostatic term changes with the size of the dipole according to the predictions of linear response theory. This approximation does not work as well for the other interfacial systems investigated. This may be an artifact due to the neglect of long-range effects in those simulations. The non-electrostatic term, dominated by the reversible work of cavity formation, shows interfacially induced structure. In particular, it is responsible for a maximum of the excess chemical potential on the dense, water side of the water-POPC interface. The results of this study provide guidance to developing simple but accurate implicit models of interfacial systems. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301544

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The cellular membrane is both a solvent for approximately 30&percent; of known proteins, as well as a semi-permeable barrier which maintains differences between ionic concentrations inside and outside of the cell. Proper cell function depends heavily on this unique environment, and electrostatic properties are key to understanding the relationship between biomembrane structure and function. Any attempt to model the membrane bilayer requires a careful treatment of electrostatic calculations. We review general models of electrostatics which could be adapted to membrane systems, and examine existing approaches applied specifically to membrane systems. A new model for the bilayer using a lattice of dipoles with spatially varying properties is also presented. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301545

出版商:AIP    

年代:1999

数据来源: AIP