Structural fluctuations

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

As in classical simulations of biomolecules, there are two general frameworks for setting up QM/MM simulations for a biological system periodic boundary condition (PBC) and finite-size boundary condition (FBC). When the system of interest is small ( 200-300 amino acids), PBC is well suited because the entire system can be completely solvated and therefore structural fluctuations ranging from the residue level to domain scale can potentially be treated at equal footing, within the limit... 

Zhang Y, Kua J, McCammon JA (2003) Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 107 ... 

M molar mass), where I and III are the tricritical or -regions. Here, the chain molecules exhibit an unperturbed random coil confirmation. In contrast, I and II are the critical or good solvent regimes, which are characterized by structural fluctuations in direction of an expanded coil conformation. According to the underlying concept of critical phenomena, the phase boundaries have to be considered as a continuous crossover and not as discontinuous transitions. 

Micelles are extremely dynamic aggregates. Ultrasonic, temperature and pressure jump techniques have been employed to study various equilibrium constants. Rates of uptake of monomers into micellar aggregates are close to diffusion-controlled306. The residence times of the individual surfactant molecules in the aggregate are typically in the order of 1-10 microseconds307, whereas the lifetime of the micellar entity is about 1-100 miliseconds307. Factors that lower the critical micelle concentration usually increase the lifetimes of the micelles as well as the residence times of the surfactant molecules in the micelle. Due to these dynamics, the size and shape of micelles are subject to appreciable structural fluctuations. 

J. R. Lakowicz and G. Weber, Quenching of fluorescence by oxygen A probe for structural fluctuation in macromolecules, Biochemistry 12, 4161 1170(1973). 

Many lines of evidence suggest that proteins undergo structural fluctuations.(62 ) A question is how a molecule in solution can interact with a... 

In this model, whether kq is a function of the solvent viscosity depends upon the relative magnitudes of Mint) and Mext). If Mint) Mext),then kq will depend upon viscosity if Mint) > Mext), the structural fluctuations in the protein allowing penetration of the quencher determine the magnitude of M and change in bulk viscosity may not affect this rate. Simulation of protein penetration behavior suggests that the penetration rate should be extremely sensitive to the size and charge of the quencher.(65)... 

J. R. Lakowicz, Fluorescence studies of structural fluctuations in macromolecules as observed by the time, lifetime and frequency domains, Methods Enzymol. 131, 518-567 (1986). 

Tristram-Nagle S, Nagle JF. Lipid bilayers thermodynamics, structure, fluctuations, and interactions. Chem Phys Lipids 2004 127(1) 3. 

Parak, R G. 2003. Proteins in action The physics of structural fluctuations and conformational changes. Curr. Opin. Struct. Biol. 13 552-57. 

If one traces a longer stretch of a DNA molecule in solution, a clear divergence from linearity becomes evident. Tliermally induced structural fluctuations allow a bending of DNA, which is why long DNA molecules are described as a random cod. This bending of the DNA occurs in molecules with a length of more than approx. 200 bp. 

Table 4 Sensitivity of the hole coupling matrix element Vda (in eV) between the two guanine units to structural fluctuations of the WCP dimer [(GC),(GC) as calculated by the FCD scheme. Also shown is the difference Aq of donor and acceptor charges (in e) ...

Recently, the effects of static and dynamic structural fluctuations on the electron hole mobility in DNA were studied using a time-dependent self-consistent field method [33]. The motion of holes was coupled to fluctuations of two step parameters of a duplex, rise and twist (Fig. 1), namely the distances and the dihedral angles between base pairs, respectively. The hole mobility in an ideally ordered poly(G)-poly(C) duplex was found to be decreased by two orders of magnitude due to twisting of base pairs and static energy disorder. A hole mobility of 0.1 cm V s was predicted for a homogeneous system the mobility of natural duplexes is expected to be much lower [33]. In this context, one can mention several theoretical studies, based on band structure approaches, to estimate the electrical conductivity of DNA [85-87]. 

Because experimental study of the structure of crystal/liquid interfaces has been difficult due to the buried nature of the interface and rapid structural fluctuations in the liquid, it has been investigated by computer simulation and theory. Figure B.3 provides several views of crystal/liquid (or amorphous phase) interfaces, which must be classified as diffuse interfaces because the phases adjoining the interface are perturbed significantly over distances of several atomic layers. 

Figure 18.11 Protection of backbone >NH protons in strands of (3 sheet against exchange with solvent D20. Surface >NH groups exchange at the same high rate as do those in small peptides, but the buried ones exchange slowly, being limited by the rate of structural fluctuations that expose them.

The mechanism of exchange may be probed by the effects of denaturant,50 pH, and mutation51 on kex. Use of mutation is particularly powerful for determining how much structural fluctuation is required for exchange to take place.52 Suppose, as is common, that exchange is occurring at the EX2 limit. Then we can calculate the free energy between the open and closed states from equation 18.29, as follows ... 

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