Side-chain influence conformation

Abe et ah have studied the conformational characteristics of a series of poly[oxy(-l-alkylethylenes)]. In the first paper a comparison of the statistical weights of various conformations in poly(propylene oxide), deduced from the solution properties of isotactic and atactic chains, were compared with conformational weights derived from a potential-energy surface, and an anomeric effect identified with a discrepancy between the two. Flexible side-chains influence the main chain in a manner which is expressible in the statistical weight matrices. The dimensions of these chains are strongly influenced by their tacticity. Polymer chains containing both sulphur and oxygen heteroatoms have received the attention of... 

These results exhibit a strong dependency of properties on the alkyl side chain length, which can be explained by variation of the electronic band structure and interaction between the side chains influenced by the dimensions and coplanarity of the conjugated main chain, depending on the alkyl chain length and its conformation. In particular, an unique doping effect of Cso in PAT is observed [502, 503]. 

Furthermore it can be shown that besides the direct influence of hydrophilic and hydrophobic hydration on the conformation, the interaction of charged groups with ions is also strongly influenced by the hydration of the groups involved. Such studies were made largely by using relatively simple poly-a-aminoacids with ionogenic side chains as model substances. 

The non-collective motions include the rotational and translational self-diffusion of molecules as in normal liquids. Molecular reorientations under the influence of a potential of mean torque set up by the neighbours have been described by the small step rotational diffusion model.118 124 The roto-translational diffusion of molecules in uniaxial smectic phases has also been theoretically treated.125,126 This theory has only been tested by a spin relaxation study of a solute in a smectic phase.127 Translational self-diffusion (TD)29 is an intermolecular relaxation mechanism, and is important when proton is used to probe spin relaxation in LC. TD also enters indirectly in the treatment of spin relaxation by DF. Theories for TD in isotropic liquids and cubic solids128 130 have been extended to LC in the nematic (N),131 smectic A (SmA),132 and smectic B (SmB)133 phases. In addition to the overall motion of the molecule, internal bond rotations within the flexible chain(s) of a meso-genic molecule can also cause spin relaxation. The conformational transitions in the side chain are usually much faster than the rotational diffusive motion of the molecular core. 

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

In a very real sense, the structure of the closely bound water molecules around a protein are a part of the protein structure they determine conformation of the exposed side chains, stabilize the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. The properties of the bulk water are critical in stabilizing the folded native form of proteins (e.g., Kuntz and Kauzmann, 1974), but it is only the bound water that we will consider to be an actual part of, rather than an influence on, the protein structure. 

Morphology based on chemical environment can be probed using F NMR spectroscopy because the chemical shifts of F atoms in the side chains are considerably separated from those in the backbone. Conformational dynamics as affected by domain-selective solvent incorporation are reflected in the widths of static F peaks. These conformational motions, in turn, can influence the migration of solvent penetrants. 

The influence of chain length and side-chain modifications of ACTH-derived peptides on active avoidance behaviour in rats will be discussed. H-Met(02)-Glu-His--Phe-D-Lys-Phe-OH (Org 2766) emerged from these studies as an orally active peptide with an increased potency and selectivity of action. Physico-chemical data (from the literature) on the reference peptide ACTH--(4-10) did not point to a preferred conformation in solution, whereas in the crystalline state an antiparallel 3-pleated sheet structure was found. At the receptor site we suggested an a-helical conformation in which the Phe and Met residues are close together. Additional support for this suggestion came from the behavioural activity of [des-Tyr", Met ]enkephalin and of cyclo--(-Phe-Met-cAhx-), eAhx merely serving as a spacer. 

With the support of quantum mechanics this proteolysis study has readily shown that fluorinated amino acid side chains are able to direct enzyme substrate interactions, which can have an influence on proteolytic stability. Depending on the absolute stereochemistry and on the position within the sequence, aTfm amino acids can considerably stabilize peptides against proteolysis. The unique electrostatic properties of carbon-bound fluorine, however, may also induce a contrary effect. The conformational restrictions of C -dialkylation seem to be partly dimin-ishable by the electrostatic consequences of fluorination. With this knowledge. 

Furthermore, in flexible linear peptides the chemical shifts are typical of random structures similar to nonfolded proteins. Deviation from these random shifts sometimes identifies specific conformational preferences. NH-proton chemical shifts depend strongly on external influences (solvent, temperature, concentration, specific sequence). Random coil shifts for these protons correlate less well than chemical shifts of the a-protons or a-carbonsJ19-261 Not only are the shift differences of different heterotopic protons similar, but also those of diastereotopic P-protons. A preferred side-chain conformation is normally only found when there is also a preferred backbone conformation. 

Modification of the peptide backbone, including C -alkyl a-amino acids, a, 3-didehydro a-amino acids, and Na<->C and C° Ca cyclized a-amino acids and dipeptides, may influence the conformational properties of the resulting pseudopeptide molecules while preserving the mandatory side-chain substituents. 

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