Protein structure relaxation

A larger protein dielectric constant of four was used by Eberini et al. [124] to fit the experimental pKa, in a case where the protein structural relaxation upon protonation was especially large. The need for a larger protein dielectric suggests a breakdown of the linear response assumption for this system. It may be preferable in such a case to simulate an additional point along the reaction pathway, such as the midpoint, rather than shifting to what is effectively a parameter-fitting approach. 

Schmidt, M., Nienhaus, K., Pahl, R., Krasselt, A., Nienhaus, U., Parak, R, and Srajer, V. 2005a. Kinetic analysis of protein structural relaxations—A time-resolved crystallographic study. Proc. Natl. Acad. Set USA 13 11704-9. 

Molecular dynamics simulations of proteins often begin with a known structure (such as an X-ray diffraction structure) that you want to maintain during equilibration. Since the solvent may contain high energy hot spots, equilibration of the protein and solvent at the same time can change the protein conformation. To avoid this, select only the water molecules and run a molecular dynamics equilibration. This relaxes the water while fixing the protein structure. Then deselect the water and equilibrate the whole system. 

Figure 2-7. Origins of the increased O2 binding energy in IPNS when the protein is included in an ONIOM model. (A) A comparison of the optimized geometries from an active-site model (silver) and an ONIOM protein model (dark grey), show that the artificial structural relaxation of the active-site model is more pronounced for the reactant state than for the product state. (B) Contributions to O2 binding from the surrounding protein, evaluated only at the MM level (Adapted from Lundberg and Morokuma [26], Reprinted with permission. Copyright 2007 American Chemical Society.)...

Studies of ferredoxin [152] and a photosynthetic reaction center [151] have analyzed further the protein s dielectric response to electron transfer, and the protein s role in reducing the reorganization free energy so as to accelerate electron transfer [152], Different force fields were compared, including a polarizable and a non-polarizable force field [151]. One very recent study considered the effect of point mutations on the redox potential of the protein azurin [56]. Structural relaxation along the simulated reaction pathway was analyzed in detail. Similar to the Cyt c study above, several slow relaxation channels were found, which limited the ability to obtain very precise free energy estimates. Only semiquantitative values were... 

The next step was to perform a structural relaxation and to compute the CO stretch frequency for each of the chosen protein conformations. Tabelle 3.3 summarizes the results obtained for the main structural data defining the Fe-ligand bonds. As expected,... 

Multidimensional NMR methods, combined with isotope labeling, can provide access to virtually every atom in a molecule, unique for protein structural studies. This not only allows characterization of the structure and interaction of proteins in their native milieu, but also provides unparalleled possibilities to obtain a complete atomic-level resolution picture of protein dynamics in a time range from picoseconds up to seconds, the range where most motions relevant to protein function take place. A significant number of 15N and 13C relaxation studies have been performed on a large number of proteins in the last... 

Gilmanshin R., Williams S., Callender R. H., Woodruff W. H. and Dyer R. B. Fast events in protein folding relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc. Natl. Acad. Sci., USA (1997) 94(8) 3709-3713. 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

As shown above, the intrinsic fluorescence spectra of proteins as well as coenzyme groups and probes shift within very wide ranges depending on their environment. Since the main contribution to spectral shifts is from relaxational properties of the environment, the analysis of relaxation is the necessary first step in establishing correlations of protein structure with fluorescence spectra. Furthermore, the study of relaxation dynamics is a very important approach to the analysis of the fluctuation rates of the electrostatic field in proteins, which is of importance for the understanding of biocatalytic processes and charge transport. Here we will discuss briefly the most illustrative results obtained by the methods of molecular relaxation spectroscopy. 

These data may be explained in terms of the above mechanism of the long-wavelength shift of fluorescence spectra for red-edge excitation. The properties of the environment of the tryptophan residues in the proteins studied are such that during the lifetime of the excited state, structural relaxation of the surrounding dipoles fails to proceed. Studies of the dependence of the... 

A. V. Einkelstein, Proteins structural, thermodynamic and kinetic aspects, in Slow Relaxations arul Nonequilibrium Dynamics (J. L. Barrat and J. Kurchan, eds.) Springer-Verlag, Berlin, 2004, pp. 650-703. 

The 3D homology model of the protein structure is validated as much as possible with experimental data, such as mutagenesis data, NMR spin-relaxation measurements (28-30), active site chemical probe studies (31,32), and predictions of CYP substrate- and/or inhibitor-binding and regioselective metabolism and... 

---