Conformational fluctuation

Wennmalm S, Edman L and Rigler R 1997 Conformational fluctuations in single DNA molecules Proc. Natl Acad. Sc/. L/SA94 10 641-6... 

The above-mentioned conformational fluctuations can be easily understood on the basis of the blob model [104-109]. For example, this is illustrated for the transition from I to I. Within the chain swollen by excluded-volume... 

Because the time scale of the Raman scattering event ( 3.3 x 10-14s for a vibration with wavenumber shift 1000 cm-1 excited in the visible) is much shorter than that of the fastest conformational fluctuations in biomolecules, the ROA spectrum is a superposition of snapshot spectra from all the distinct chiral conformers present in the sample. Together with the dependence of ROA on chirality, this leads to an enhanced sensitivity to the dynamic aspects of biomolecular structure. The two-group model provides a qualitative explanation since it predicts ROA intensities that depend on absolute chirality in the form of a sin x dependence... 

Fig. 5. Conformational fluctuations in the mGluRl ATD homodimer. The five forms of the mGluRl ATD homodimer solved as high-resolution X-ray structures. The mGluRl ATD homodimer is either nonliganded or complexed with Glu, with Glu and Gd3+, or with the competitive antagonist (.Vj-methyl-4-carboxyphenylglycine [f.S j-MCPG], The identities of the two ATD lobes (Lobe I and II) are indicated in each of the conformations.

Immobilized enzymes have been found in a considerable number of cases to be markedly more stable to denaturation by heat, denaturing agents, or organic solvents, than the corresponding native enzymes (6). The reasons for this effect are still not fully understood, and it is thus recommended that in the future a thorough analysis be carried out of the conformation, ease of denaturation, and conformational fluctuations of immobilized enzymes. 

It is clear that the wide range of protein phosphorescence lifetimes is due to various specific quenching mechanisms kq) or due to flexibility of the tryptophan site, thereby affecting km. It also follows that phosphorescence will be very sensitive to conformational fluctuations since subtle changes in distance or orientation relative to a specific quenching moiety within the protein will affect the lifetimes dramatically. The phosphorescence emission from protein tryptophan remains relatively unexplored in terms of investigation of dynamic structure-function relationships. 

Currently suggested models for tunneling increasingly invoke protein dynamics . These models envision either a series of conformational fluctuations that lead to a suitable tunnehng configuration ( passive dynamics ) or a more active role... 

Tomschik M, Zheng H, van Holde K, Zlatanova J, Leuba SH (2005) Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc Natl Acad Sci USA 102 3278-3283... 

Leger JE, Robert J, Bourdieu L et al (1998) RecA binding to a single double-stranded DNA molecule a possible role of DNA conformational fluctuations. Proc Natl Acad Sci USA 95 12295-12299... 

Next, we discuss strategies to make maximal use of simple unbiased movesets for conformational sampling of biomacromolecules. We provide an example to illustrate how the inclusion of conformational fluctuations spanning multiple length scales can improve the quality of sampling. We conclude with a discussion of the metrics and guidelines that can be used to optimize a moveset for a given system. 

In the enkephalin studies we began to see how theoretical techniques can be used to generate conformations of related molecules. With the results from GnRH and vasopressin we saw how flexible these molecules are and how the conformational fluctuations and dynamics of these molecules can be studied. We also saw how the relative stabilities of conformations of a molecular fragment can be influenced by conformational constraints of the whole molecule. In the following section we will present some ideas on how these calculations can be incorporated into a conformational based approach to drug design. 

Rosenberg, A. and Somogyi, B. (1986) Conformational fluctuations, thermal stability and hydration of proteins, studies by hydrogen exchange kinetics. n Dynamic of Biochemical systems, edited by S. Damjanovich, T.Keleti and L.Tron, pp. 101-112. Amsterdam Elsevier. 

Conformational fluctuations within the transmembrane aggregate produce the open-closed transitions. 

This limitation has been overcome with a special NDDO-HT parameterization for calculating hole coupling matrix elements in DNA-related systems [72]. As reference data, coupling matrix elements were calculated for a set of 130 structures of WCP dimers with different step parameters at the HF/6-31G level. As discussed below in more detail, electronic couplings between neighboring pairs are extremely sensitive to conformational fluctuations of the DNA structure. For instance, the matrix element between base pairs in... 

The insertion of a protein within a membrane not only stabilizes the optimal conformation for the enzyme activity, but also limits the possible conformations it may undergo. Thus, assuming a mechanism for the enzymatic activity, where the underlying assumption is that the conformational fluctuation controls the chemical reaction, a decrease in the number of degrees of freedom for the enzyme increases its probability for... 

One can envision a conformational fluctuation spectrum with the native state being a mean conformation. Since that mean conformation is only marginally stable, it is... 

The formation of a compact globule in copolymers requires them to have specific conformations, which are reached through local conformational fluctuations. A characteristic collapse time may be defined as for instance the time for which the gyration radius reaches its equilibrium value. This time measures the approach to equilibrium for the system and is related to the mean first passage time. 

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