Analysis of Conformations

Distance geometry produces a series of random trial structures that do not necessarily have unique conformations many of the randomly generated conformations may in fact be very similar. Several methods have been used with 

Jarvis-Patrick clustering requires a nearest-neighbor list. The rms matrix is treated as an N-dimensional Cartesian coordinate matrix for N conformers 

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Hassel shared the 1969 Nobel Prize in chemistry with Sir Derek Barton of Imperial College (London) Barton demonstrated how Hassel s structural results could be extended to an analysis of conformational effects on chemical reactivity... 

The thermodynamic analysis of conformational and structural transformations in the melt at high pressures34 showed that the free volume and free energy minimum required for hydrostatic compression is attained as a result of the transition of the molecules in the melt into a more extended conformation (gauche —> trans transitions) since the extended molecules ensure a more compact packing of the chains at compression. Chain uncoiling leads to a decrease in their flexibility parameter f with increasing pressure p ... 

The proposal of multiple crystalline forms in native celluloses implies that all native celluloses are compositions of two distinct forms, which has been earlier indicated for Acetobacter and Vallonia celluloses, 8). From the resolution of the NMR spectra an estimate of about 60-70 % of the la form in Acetobacter cellulose and of 60-70 % of the lb form in cotton was obtained. A further detailed analysis of conformational features in celluloses seemed to need X-ray diffractometric and Raman spectroscopic confirmation 19-56). 

Delarue, M. Sanejouand, Y.H., Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases the elastic network model, J. Mol. Biol. 2002, 320, 1011-1024... 

Prediction of the conformational change of the protein under binding is a challenge. New structural parameters based on high resolution X-Ray structures have been presented recently (69). Such studies open the door to a more extended analysis of conformational changes of protein cavity when binding with different ligands. 

A careful analysis of conformational energy maps (Ramachandran plots) revealed that both enantiomers of P-tetralin amino acids were compatible with the right handed a-helical conformation.109 This was an important prerequisite for the development of N- and C-caps since the ( -configuration of the P-tetralin amino acid is needed for N-terminal helix induction, whereas the (R)-enantiomer was used in the C-cap series. The fact that both configurations were compatible with a-helical conformations made these amino acids our first choice as building blocks for... 

The area between enzymatic and chemical catalyses, associated with simulation of biochemical processes by their basic parameters, is accepted as mimetic catalysis. The key aspect of the mimetic catalyst is diversity of enzyme and biomimetic function processes, which principally distinguishes the mimetic model from traditional full simulation. Based on the analysis of conformities and diversities of enzymatic and chemical catalysis, the general aspects of mimetic catalysis are discussed. An idealized model of the biomimetic catalyst and the exclusive role of the membrane in its structural organization are considered. The most important achievements in the branch of catalysis are shown, in particular, new approaches to synthesis and study of biomimetic catalase, peroxidase and monooxidases reactions. 

An analysis of conformational flexibility of pyrimidine ring in related molecules (purine, aminopyrimidine, and unsubstituted pyrimidine (Scheme 21.4)) indicates that the flat character of the potential energy surface around minimum is a general property of pyrimidine ring. A presence of amino group and fused imidazole ring only promotes increase of conformational flexibility of heterocycle. 

An analysis of conformational flexibility of imidazole rings in guanine and adenine indicates that these heterocycles are much more rigid (Table 21.4). 

Smellie, A., Kahn, S.D. and Teig, S., Analysis of conformational coverage. 2. Application of conformational models, J. Chem. Inf. Comput. Sci., 35, 295-304, 1995b. 

Jaumot, J., Escaja, N., Gargallo, R., Gonzalez, C., Pedroso, E., and Tauler, R., Multivariate curve resolution a powerful tool for the analysis of conformational transitions in nucleic acids, Nucl. Acid Res., 30, e92, 2002. http //nar.oxfordjoumals. org/content/vol 30/issue 17/index. 

Use analysis of conformations to determine the relative stabilities of stereoisomeric cyclohexane derivatives. (Problems 6.23, 6.24, and 6.26)... 

Kajiwara H (1991) Application of high-performance capillary electrophoresis to the analysis of conformation and interaction of metal-binding proteins. J Chromatogr 559 345-356. 

Betts MJ, Sternberg MJ. An analysis of conformational changes on protein-protein association implications for predictive docking. Protein Eng. 1999 12 271-283. 

Fig. 24.8. Computational simulation analysis of conformational dynamics in T4 lysozyme enzymatic reaction, (a) Histograms of fopen calculated from a simulated single-molecule conformational change trajectory, assuming a multiple consecutive Poisson rate processes representing multiple ramdom walk steps, (b) Two-dimensional joint probability distributions <5 (tj, Tj+i) of adjacent pair fopen times. The distribution <5(ri, Ti+i) shows clearly a characteristic diagonal feature of memory effect in the topen, reflecting that a long topen time tends to be followed by a long one and a short fopen time tends to be followed by a short one...

Examination of Monte Carlo Approaches for Analysis of Conformational Space. ... 

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