Microscopic model, protein

Another important result that was obtained recently concerns the evaluation of the contribution to the reorganization energy arising from the polarization of the medium, protein and solvent from a microscopic model including the residual charges and induced dipoles of the protein as well as bound water molecules, a value of about 0.2 eV was calculated for different eleetron transfer processes [97], This weak value results from the apolar character of the medium, and is compatible with the kinetic data which indicate that reorganization energies are small in the reaction center (Sect. 3.2.2)... 

Warshel et al. (1986) calculated protein pX values in solution by using a microscopic model and a reversible charging process. 

C. The Microscopic Model in Protein Electrochemistry Electrochemistry of Protein-Protein Complexes Electrochemistry of Redox Enzymes... 

If Eqs. (5) and (6) describe the physics reasonably well, the pressure shift s should vary in a linear fashion with bum frequency Pb, and there should be a frequency, namely, p ac, where this shift vanishes. At p ag, the hole should broaden, only. We tested these predictions in a series of glasses with a variety of dye probes and found perfect agreement with the model.This encouraged us to apply the technique to proteins. We also stress that the conditions under which Eq. (5) holds can be derived from a microscopic model. Figure 4 shows how a hole burnt into the inhomogeneously broadened absorption spectrum of a protein (meso-porphyrin IX-substituted horseradish peroxidase) deforms under pressure variations up to 1.5 MPa. 

Microscopic Modeling of Polarizable Protein Medium Fixing... 

It has been also indicated experimentally that ectoine enhances the thermodynamic stabilities of their folded (native) structures [24c]. This observation has been explained by the preferential exclusion model, which states that CS molecules are expelled from the protein surface [28,29] and the growth of the preferential exclusion corresponds with the increase of excess chemical potential of the protein [28,29]. In fact, onr previous MD simulation also indicated numerically that ectoine molecnles are preferentially excluded near the CI2 surface [39]. Thus, to understand how CS molecnles interact microscopically with proteins, and whether the addition of CS might indirectly stabilize them irrespective of their molecular properties, the hydration strnctnres have been studied not only for CI2 but also for a smaller... 

The implication here is that proteins, once they bind to their respective electrode sites with (presumably) the correct orientation, may actually transfer electrons very rapidly indeed. The microscopic model [125,126] is in aeeordance with the view, expressed at the beginning of this article—that intrinsically the reactivity of electron-transfer proteins is high, but is tempered by specificity. 

The obvious limitations of the continuum representation of the solvent necessitated the development of microscopic models of the surroundings. Whereas for liquid phases this task is not trivial at all, for structurally well-characterized environments, like proteins [190, 207] or crystals [208] it is possible to calculate the reaction field from the polarizability distribution [209]. Assuming the existence of strongly bound solvent... 

Usually, the mesoscopic, kinetic models are considered to be well suited for predicting dynamic properties of polymer solutions on macroscopic scales. Details of the fast solvent dynamics are in most cases irrelevant for macroscopic properties. Exceptions are polyelectrolytes, where the motion of counterions in the solvent can have a major influence on polymer conformation. Therefore, more microscopic models of polyelectrolytes with explicit counterions are sometimes employed [34] (see also the contribution by M. Muthukumar in this volume). Another exception is the dynamics of individual biopolymers, for example, protein folding, which is modeled with an all atomistic model including an explicit treatment of the (water) solvent molecules [35]. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

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