Side-chain torsion dynamics

The results of simulating barnase-barstar association after 100 ps of simple multiple copy MD without ensemble enriching are shown in Figure 9. Whereas contact formation in the simple multiple copy MD simulation has leveled off after the initial 100 ps, ensemble enriching with a linear scoring function is able to shift the ensemble population toward a higher number of established native contacts. Compared to the side-chain torsion dynamics... 

Farmer et al. evaluated the conformations and dynamics of poly(di- -hexylsilane). " - " The lowest energy conformer for a polymer containing eight silicon atoms was a helical arrangement with 30° torsional angles in the silane backbone. The authors also monitored different backbone and side chain torsions during dynamics simulations and concluded that the conformation present in the crystalline solid is controlled by intermolecular effects. 

The specimens were treated according to the method of Nakagami and coworkers [17,18]. Japanese linden Tilia japonica Smik.) was treated with trifluoroacetic acid anhydride and the fatty acids (TFAA method), which included acetic acid, propionic acid, valeric acid, hexanoic acid, decanoic acid, lauric acid, and palmitic acid. Dynamic measurements were made with a torsion pendulum apparatus under a vacuum. An increasing temperature rate was 2°C/min. The amount of introduced side chain per gram of wood is about 4-6 mmol/g [16]. The chemical structure of the treated wood is presented by the formula ... 

Residual dipolar couplings have been used by Mittermaier and Kay187 to probe the torsion angle dynamics of protein side-chains. Using the B1 domain of peptostreptococcal protein L, they show that the residual dipolar couplings can be used to distinguish static from mobile side-chains, and that the motions of most mobile side-chains can be adequately explained by rotamer-jump models. 

By dealing with the evolution of constraints (i.e., Ramachandran basins) rather than the backbone torsional coordinates themselves, the dynamics are judiciously simplified [31]. The algorithm consists of a stochastic simulation of the coarsely resolved dynamics, simplified to the level of time-evolving Ramachandran basin assignments. An operational premise is that steric restrictions imposed by the side chains on the backbone may be subsumed into the basin-hopping dynamics. The side chain constraints define regions in the Ramachandran map that can be explored in order to obtain an optimized pattern of nonbonded interactions. 

Fig. 7.1 Protein building blocks. (A) The polypeptide chain, with a closeup showing the chemical form of the backbone , to which the side chains R , R +i,..., are attached. The (C=0) and (N-H) groups are linked by the peptide bond, which has a partial double bond character, making the (C=0)-(N-H) peptide group stiff and approximately planar. The torsion angles tj) and tfr, around single bonds, are soft. (B) The side chains R , R +i,..., can be any of the twenty common amino acid side chains, shown here labeled by their conventionial three-letter abbreviations (see also text). The horizontal axis corresponds roughly to the polarity of the sidechain the vertical axis corresponds to size. Reprinted from Thomas Simonson (2003) Electrostatics and dynamics of proteins. Reports on progresses in physics, vol 66, pp 737-787 with kind permission of lOP Pubhshing...

Recently, Kameda etal. characterized and compared the Ser side-chain dynamics of B. mori and S.c. ricini silk fibroin using solid-state -H NMR.- - A detailed lineshape analysis has provided quantitative data on the rate of motion and on the fractions of two distinct dynamic populations. In addition, the torsion angle of the Ser C -C/j bond and its orientational distribution was measured in uniformly aligned silk fibers. Figures 16(a) and (b) show the -H NMR spectra of [3,3--H2]Ser-labeled silk fibroin from B. mori and S.c. ricini, respectively. 

It appears that such low-frequency, residue-specific dynamics, leading to completely or partially suppressed peaks in the absence of Mn ion, is well related to the possibility of conformational fluctuations for bR from PM labeled with [l- C]Gly, Ala, Leu, Phe, Trp, etc. caused by the time-dependent deviation from the torsion angles corresponding to the lowest energy minimum of a particular conformation. Naturally, it is conceivable that conformational space allowed for such a fluctuation is strongly related to the presence or absence of bulky side-chains at C the allowed space for such Val or He residues may be limited to a very narrow... 

The range of structures for which local conformational dynamics have been simulated is rather limited at this point. A number of workers have simulated polyethylene-like chains [27, 32, 35, 39, 42, 59, 60, 79]. For this structure, the effect of various torsion potentials have been explored [27,39], Recent work has added side-groups to this model [59]. Qualitatively, higher barriers and the addition of side-groups slow dynamics, as would be expected. Simplified versions of polyisoprene [24] and polybutadiene [61] (structures as shown in Fig. Ic) have so been studied. In this section we compare these simulations with each other and with experiments. 

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