Conformational scanning

PLG is believed to exist in a type II p-turn in its bioactive conformation. The random incremental pulse search (RIPS)-MM2 > conformational scanning algorithm was used to predict the manner in which the 5,5- and 5,6-bicyclic thiazolidine lactam ring systems would restrict the tli2 and < )3 torsional angles, two of the angles that define a p-turn. These studies revealed that low energy conformations of both model compounds present torsional values close... 

Aoki, H., Anryu, M. and Ito, S. (2005) Two-dimensional polymers investigated by scanning near-field optical microscopy conformation of single polymer chain in monolayer. Polymer, 46, 5896-5902. 

DG was primarily developed as a mathematical tool for obtaining spahal structures when pairwise distance information is given [118]. The DG method does not use any classical force fields. Thus, the conformational energy of a molecule is neglected and all 3D structures which are compatible with the distance restraints are presented. Nowadays, it is often used in the determination of 3D structures of small and medium-sized organic molecules. Gompared to force field-based methods, DG is a fast computational technique in order to scan the global conformational space. To get optimized structures, DG mostly has to be followed by various molecular dynamic simulation. 

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... 

Other than an effect on backbone solvation, side chains could potentially modulate PPII helix-forming propensities in a number of ways. These include contributions due to side chain conformational entropy and, as discussed previously, side chain-to-backbone hydrogen bonds. Given the extended nature of the PPII conformation, one might expect the side chains to possess significant conformational entropy compared to more compact conformations. The side chain conformational entropy, Y.S ppn (T = 298°K), available to each of the residues simulated in the Ac-Ala-Xaa-Ala-NMe peptides above was estimated using methods outlined in Creamer (2000). In essence, conformational entropy Scan be derived from the distribution of side chain conformations using Boltzmann s equation... 

Bpgh, H.O., Zhu X.Q., Qian, B.-Z. and Gasser, R.B. (1999) Scanning for nucleotide variations in mitochondrial DNA fragments of Schistosoma japonicum by single-strand conformation polymorphism. Parasitology 118, 73-82. 

Cross-linking constrains the conformational flexibility of biopolymers and, as a rule, stabilizes their secondary, tertiary, and quaternary structures against the denaturing effects of high temperatures.29 We used differential scanning calorimetry (DSC) to compare the heat-induced conformational transitions of selected RNase A samples that were characterized in Figure 15.2. A brief introduction to DSC is provided in Section 15.15.1 for those readers unfamiliar with this biophysical method. Trace 1 in Figure 15.3a is the heat absorption... 

One such property, as has been demonstrated (see [26]), is the change in partial heat capacity of the copolymer solution upon the heat-induced conformational transition of macromolecules. Such a change was detected by high-sensitivity differential scanning calorimetry (HS-DCS). The DSC data for the NVCl/NVIAz-copolymers synthesized at initial comonomer ratios of 85 15 and 90 10 (mole/mole) are given as thermograms in Fig. 4. 

On the other hand, the method examines the rotations of contiguous residues about the glycosidic bonds, for example, C-l-O and O-C-4 in a (1 —> 4)-linked polysaccharide. This method scans the entire conformational space available to a polymer. The analysis can thus proceed either with a regular, helical structure, or a random conformation. The method has been used quite extensively in the conformational analysis of polysaccharides.9 26 The steric... 

Zarbiv, R., Grunewald, M Kavanaugh, M. P., and Kanner, B. I. (1998) Cysteine scanning of the surroundings of an alkali-ion binding site of the glutamate transporter GLT-1 reveals a conformationally sensitive residue. J. Biol. Chem. 273,14231-14237. 

---