Motions and Flexibility

FIGURE 8.1 Upper Internal correlation functions for NH vectors in selected residues in a 200 ns simulation of protein GB3 + SPC/E water [13]. Values of Xe show the model-free value for the decay time of these internal correlation functions [14]. Lower Order parameters for NH vectors in binase experimental values from [15], computed values from simulations described in [13]. 

FIGURE 8.2 NH order parameters for ubiquitin (solid circles) and lysozyme (open squares). Upper comparison of MD results from [20] to those computed here from data in [13]. Lower values derived from NMR compared to the MD simulations of [13]. 

FIGURE 8.3 Upper Backbone cartoon for GB3. Lower Comparison of rotamer populations estimated from NMR data [26] with those computed from the ff99SB, TIP4P/EW trajectory reported in [13]. 

FIGURE 8.4 Quantum effects on the order parameters for the NH vectors in the central helix of GB3. 

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In conclusion, the development of an accurate force field and full-scale MD procedure for the study of nucleic acid systems is important to the field since issues of molecular motion and flexibility are expected to be a crucial component in developing a fundamental understanding of the relationship between DNA structure, function, and ligand interactions. An important future methodological direction is to establish the hierarchical link between all-atom MD models and stochastic dynamics, and build the bridges between sequence-structure relationships into molecular genetics and molecular dynamics. 

Locahzed motion can also lead to local variations in correlation times. Folded peptides with unfolded C- or N-terminal residues, for example, will have varying correlation times for the rigid and flexible parts of the molecule, resulting in different cross-relaxation rates. Such effects can usually be distinguished by the Unewidths and intensities of the corresponding diagonal signals, since the autorelaxation rates also depend on the correlation time. 

In general, dendrimers of size G-0 through G-3 have open, asymmetric, and flexible structures with effectively no protected internal areas, due to a large freedom of motion in their branches, and they can readily accommodate additional covalent attachments to their surfaces. See Figures 73-7.5 for illustrations of the two-dimension and three-dimension structure of a... 

The description of protein structure as presented thus far may lead to the conclusion that proteins are static, rigid structures. This is not the case. A protein s constituent atoms are constantly in motion, and groups ranging from individual amino acid side chains to entire domains can be displaced via random motion by anything up to approximately 0.2 nm. A protein s conformation, therefore, displays a limited degree of flexibility, and such movement is termed breathing . 

Since local motions of flexible protein domains can randomize the emission dipoles in a manner that does not reflect the overall tumbling time of the entire protein, and since there is an apparent lack of fluorophores with the appropriate properties for larger analytes, most FPIAs are useful only for determination of relatively low-molecular-weight analytes. Nevertheless, a few studies of larger-molecular-weight analytes have been reported. A competitive assay for human... 

The relationships follow from considerations of Brownian motions and thermal fiuctuations which also infiuence the internal motions in flexible objects. is the translation coefficient of the particle s center of mass where the subscript indicates the z-average over the molar mass distribution. The first bracket in Eq. (12) describes the concentration dependence which often is well represented by a linear dependence... 

Quantum Systems in Chemistry and Physics is a broad area of science in which scientists of different extractions and aims jointly place special emphasis on quantum theory. Several topics were presented in the sessions of the symposia, namely 1 Density matrices and density functionals 2 Electron correlation effects (many-body methods and configuration interactions) 3 Relativistic formulations 4 Valence theory (chemical bonds and bond breaking) 5 Nuclear motion (vibronic effects and flexible molecules) 6 Response theory (properties and spectra atoms and molecules in strong electric and magnetic fields) 7 Condensed matter (crystals, clusters, surfaces and interfaces) 8 Reactive collisions and chemical reactions, and 9 Computational chemistry and physics. 

The flexibility of amorphous polymers is reduced drastically when they are cooled below a characteristic transition temperature called the glass transition temperature (Tg). At temperatures below Tg there is no ready segmental motion and any dimensional changes in the polymer chain are the result of temporary distortions of the primary covalent bonds. Amorphous plastics perform best below Tg but elastomers must be used above the brittle point, or they will act as a glass and be brittle and break when bent. 

Nuclear Motion, Vibronic Effects and Flexible Molecules... 

Nuclear motion, vibronic effects, and flexible molecules (Chair J. Maruani) Response theory—Properties and spectra Atoms and molecules in strong electric and magnetic fields (Chair J. Gerratt)... 

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