Conformational limitations

The first part of this Section will deal with the biological effects of the inhibition of protein glycosylation, and the consequences for conformation, limited proteolysis, routing, secretion, recognition, and uptake of glycoproteins. The more comprehensive topics, such as the effects on differentiation, the multiplication of enveloped viruses, and cellular phenomena, will also be described. 

Wolf B,- Hanlon S (1975) Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. I. Reference spectra of conformational limits. Biochemistry 14 1648-1660... 

Whitcombe described a hybrid method of imprinting where a covalent bond conformationally limited the template prior to a non-covalent type pre-organisation and subsequent polymerisation [136], It was claimed that this type of approach reduced heterogeneity in the binding site population. 

The conformational limitations that are imposed upon phosphorus in bicyclic systems are illustrated by the surprising conversion of (153) into (154), in which attack occurs at the methyl rather than benzylic carbon, owing to the inability of the benzylic group to become apical in the trigonal-bipyramidal intermediate. 

A description of the molecular stereochemistry is also included in both the structural formula and nomenclature. Each ring junction can exist in either a cis or trans conformation, yielding six centers of asymmetry or chirality (C-5, 8, 9, 10, 13, 14). Hence, 64 stereoisomers are possible for the ring system alone. With the C-17 side-chain forming a seventh site of asymmetry, the theoretical number of stereoisomers increases to 128. However, in practice, the isomeric possibilities are restricted by the overall conformational limitations of the ring system. 

Significant research efforts have been devoted to the free-radical polymerization of hydrophobic monomers [eg, ST, methyl methacrylate (MMA), and butyl acrylate (BA)] in 0/W microemulsions. The anionic surfactant SDS in combination with a short-chain alcohol (eg, C5OH) as the cosurfactant is the most popular stabilization package. However, as more polymer forms with the progress of polymerization, the increase of free energy as a result of the conformational limitation and/or incompatibility between polymer and cosurfactant results in the instability or turbidity of microemulsion polymer (16). When a cationic surfactant. 

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This form is obeyed fairly well above x values of 5-10 dyn/cm in Fig. Ill-15c. Limiting areas or a values of about 22 per molecule result, nearly independent of chain length, as would be expected if the molecules assume a final orientation that is perpendicular to the surface. Larger A values are found for longer-chain surfactants, such as sodium dodecyl sulfate, and this has been attributed to the hydrocarbon tails having a variety of conformations [127]. 

Metzler W J, Hare D R and Pardi A 1989 Limited sampling of conformational space by the distance geometry algorithm implications for structures generated from NMR data Bioohemistry 2S 7045-52... 

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

The previous application — in accord with most MD studies — illustrates the urgent need to further push the limits of MD simulations set by todays computer technology in order to bridge time scale gaps between theory and either experiments or biochemical processes. The latter often involve conformational motions of proteins, which typically occur at the microsecond to millisecond range. Prominent examples for functionally relevant conformatiotial motions... 

Nevertheless, the technique suffers from a severe time scale problem -the trajectories are computed for (at most) a few nanoseconds. This is far too short compared to times required for many processes in biophysics. For example, the ii to T conformational transition in hemoglobin lasts tens of microseconds [1], and the typical time for ion migration through the gramicidin channel is hundreds of nanoseconds. This limits (of course) our ability to make a meaningful comparison to experiments, using MD. 

Limiting Conformational Changes during High Temperature Simulations... 

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