Side-chain torsions

Several remedies have been suggested for improving the PB based pKa prediction methods. Most of them are based on strategies that combine conformational flexibility with the PB calculation. You and Bashford included multiple conformers by systematically scanning the side chain torsion angles [107], Alexov and Gunner used Monte-Carlo protocol to sample positions of hydroxyl and other polar protons [1], This method, referred to as the multi-conformation continuum electrostatic (MCCE), was later extended to include rotamers for residues that have strong electrostatic... 

Fig. 6 Determination of the 4F-Phg side chain torsion angle from the respective energy profiles for 4F-Phg in the intact molecules GS-3/3 (A) and GS-1/1 (B). An acceptable range for the 4F-Phg torsion angle is between -40° < /i < 40° for GS-3/3, and -40° < Xi < 10° for GS-1/1 shaded regions). These respective ranges were used to calculate the allowed regions in the r/p-maps of Fig. 5A,B...

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. 

Side-Chain Torsions in Poly(methylethylstloxane). Three bond rotations can be considered for the side chains of poly(methylethylsiloxane) (PMES). 

Side-Chain Torsions in Poly(meihylphenykiloxane). Two bond torsions are possible for the side chains in poly(methylphenylsiloxane) (PMPS). 

Exhaustive conformational search is a simple and practical way to explore the entire conformational space available to a peptide (or molecular segment) with fewer than a dozen rotatable bonds. A search is performed by systematically varying each rotatable bond in the peptide. Rotations are made about backbone dihedrals (<]) and v) and/or side chain torsions (%). In our work, bond lengths and angles are held rigid. After each rotation, the molecule is checked for steric overlap. If overlap occurs, the conformer is discarded otherwise it is... 

Interactions between Leu-Phe and Phe-Leu pairs were analyzed using the protocol described above. Side chains were modeled at positions i (residue 8) and i+2 (residue 10), i+3 (residue 11) or i+4 (residue 12). The (i,i+2) pairs serve as a standard state because, in this position, the side chains are on opposite sides of the hehx and cannot interact. Side chain torsions were rotated in increments of 30°. Results are shown in Table I. 

Figure 2. Ball and stick representation of the blocked Ala-Pro-Tyr peptide in extended conformation. The aliphatic carbons are labelled according to the lUPAC definition. The cis and trans methylene protons (compared to the a proton) of proline and tyrosine are indexed 1 and 2 respectively. The main backbone and side chain torsional angles referred to in the text are indicated by arrows.

Our method of clustering based on a-carbon distances and in turn backbone and side chain torsions has demonstrated the existence of possible structural motifs within well defined linker regions. The method is not quite exhaustive to account for data outside the clusters and its limitadons arise due to non-standard way of defining limits of the clusters. Nevertheless, the method does seem to bring out the stmctural differences among various linkers. Our analyses on mainly -a proteins fiom the CATH database (results not shown here) has resulted in two major clusters of three residue linkers between helices (H-L3-H) and few of the helical proteins have same angle of orientation of helices within a cluster. We are yet to extend this observation to the unique data set of protein chains discussed in this paper. 

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