Side-chain mobility

Side-chain mobility is of particular interest because groups responsible for protein function are in many cases located in side chains rather than in the backbone. Gaining an insight into side-chain dynamics, therefore, could be necessary for understanding the relationship between protein dynamics and function. In contrast to protein backbone dy-... 

S. Tazuke, R. Kun Guo, and R. Hayashe, How does the polymer main chain influence the side-chain mobility A fluorescence probe study by means of twisted intramolecular charge-transfer phenomena, Macromolecules 21, 1046 (1988). 

The variation of the temperature interval of structure formation is also accounted for by the effect of side chain mobility on mesophase nucleation. The solutions of cholesterol-containing polymers with longer spacer groups have to be cooled further for mesophase nuclei to be formed. For instance, in a series of PChMO-n polymers the interval of structure formation is for PChMO-14 — 308-313 K, for PChMO-lO — 323-333 K and for PChMO-5 the internal structure is formed at even higher temperatures 187). 

Yet another substitution that restricts the conformational freedom of amino acids is the introduction of a double bond at the Ca and atoms. In addition to the obvious effect that a, /3-unsaturation has on the side-chain mobility, this modification also affects the conformation of the backbone. The effects of Ca-Cp unsaturation have been explored experi-... 

A convenient way to get information about the dynamics of polymers is to measure Ti, Tip and T2 by H pulse NMR. Figure 7.15 shows the side chain length-dependence of the H T2 value measured at 80°C for the side chain of poly(y-n-alkyl L-glutamate)s [26]. As seen from this figure, T2 is almost constant for n = 5-9 and suddenly becomes double for n = 10. It is easy to find the discontinuity between n = 9 and n = 10. Based on BPP theory, T2 increases as the correlation time for the motion decreases. A sudden increment of T2 means that there is a large difference in the side chain mobility between n 9 and n 10. These polymers become a thermotropic liquid crystal if the number of carbon atoms in the alkyl side chain is more than... 

Proteins, with a specific function and isolated from a single source, usually have a homogeneous population of molecules all with the same unique amino acid sequence. Yet with 20 different amino acids possible at each position in a polypeptide chain of n residues, 20 different primary structures are theoretically possible. Furthermore, the great majority of all molecules of a natural protein may exist in a unique conformation despite the degrees of freedom formally permitted by rotation about the peptide backbone (motility) and side chains (mobility). For example, with only 3 conformations defined per residue, a polypeptide chain of 210 residues would have a theoretical possibility of existing in 10 °° different conformations. 

From EPR experiments with spin labels, four primary parameters are obtained (1) side chain mobility, (2) distances to other paramagnetic centers, e.g., a second spin label or a metal ion within the very same or another molecule, (3) solvent... 

J. Clauss, K. Schmidt-Rohr, A. Adam, C. Boeffel, H.W. Spiess, Stiff macromolecules with aliphatic side chains side chain mobility, conformation, and organization from 2D solid-state NMR spectroscopy. Macromolecules 25 (1992) 5208—5214. 

The strategy used to suppress thermal undoping is to avoid the side-chain interactions by separating the side-chains from one another, or from the main chains, while maintaining enough space around the main chain for the dopants. Thermochromism and solvatochromism exhibited by these materials are also related to side-chain mobility [27,81]. 

The treatment of receptor flexibility is likely to be an area of increased research activity in the near future. It is already being considered in the related area of ligand docking into receptors. 4,i45 -pije incorporation of limited side chain mobility should be straightforward in de novo design methods that are controlled by force fields and also in interaction-site-based methodologies, where methods similar to those adopted by Jones et al. s could be used. 

The effect on chiroptical and thermal properties due to the presence of achiral comonomers into polymer and its characterization in terms of side-chain mobility and grown hindrance was studied. The monomer (S)-MPAAP with triphenylmethyl methacrylate (TrMA) and an inactive fert-butyl methacrylate (fert-BMA) in different concentrations followed by radical copolymerization reaction. At different concentration of (S)-MPAAP co-units, the structures of the synthesized compounds poly [(S)-MPAAP-co- TrMA]s and poly[(5)-MPAAP-co-fcrf-BMA]s were investigated... 

Side-chain mobility is analysed mainly by assuming a rapid equilibrium between three staggered conformations. The populations of the conformations can then be derived from the homonuclear and heteronuclear coupling constants using Pachler s equation. The observed coupling then results as the average over all three rotamers, /, weighted with their respective population Pi,... 

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