Conformation in polypeptide

Angles of Rotation in the Baokbone for Various Conformations in Polypeptides of L-Amino... 

M. Vasquez and H. A. Scheraga, Biopolymers, 27, 41 (1988). Effect of Sequence-Specific Interactions on the Stability of Helical Conformations in Polypeptides. 

Discuss the nature of the amide bond and its influence on conformation in polypeptides and proteins. (In answering this and most of the other questions listed below, a picture is worth a thousand words )... 

Optical rotation and chain conformation in polypeptides and proteins have their common ground in the peptide bond, for it is the spatial disposition of this generic chemical group that gives rise to the principal rotatory characteristics of these snbstances and at the same time defines their secondary structure. Changes in the mutual orientation of peptide groups in the polymeric backbone are thus tantamount to conformational changes, so that the special sensitivity of optical rotatory power to steric form renders it uniquely suited to the study of conformation. 

In view of the progress to date, it is clear that IR and Raman spectroscopy, together with normal-mode analysis, will have a major contribution to make to the detailed study of conformation in polypeptides and proteins. 

The amide VI mode is predominantly CO ob, with a significant CCH3 out-of-plane rock (or) contribution. This, of course, cannot be represented in a CHj point-mass model [5], The natiure of this mode is also significantly dependent on conformation in polypeptide structures [5]. 

Brahms, S., Spach, G., Brack, A. Identification of p, p-tums and unordeied conformations in polypeptide chains by vacuum UV circular dichroism. Proc. Natl. Acad. Sci. 74, 3208-3212... 

Fortunately, it was found that in polypeptide systems the effective dimensionality of conformational spaces is significantly smaller than the dimensionality of the full space, with only a few principal axes contributing to the projection [38-41]. In fact, in many cases a projection quality of 70-90% can be achieved in as few as tliree dimensions [42], opening the way for real 3D visualization of molecular conformational space. Figure 8... 

Figure 13.6 Schematic diagram of Go. from transducin with a bound GTP analog. The polypeptide chain is organized Into two domains a catalytic domain (light red) with a structure similar to Ras, and a helical domain (green) which is an Insert in the loop between al and P2. There are three switch regions (violet) that have different conformations in the different catalytic states of Go.. The GTP analog (brown) Is bound to the catalytic domain in a cleft between the two domains. (Adapted from J. Noel et al.. Nature 366 654-663, 1993.)...

Kubota S, Easman GD (1975) Beta-conformation of polypeptides of valine, isoleucine, and threonine in solution and solid-state - optical and infrared studies. Biopolymers 14 605-631... 

Heparin has been reported to complex with a variety of basic species, including biogenic amines and drugs for reviews, see Refs. 10 and 391. For its possible relevance to the pharmacological properties of heparin and complexed species, mention is made here of complexes with histamine392,393 and anthracycline antibiotics.394 C.d. studies on the interaction of basic homopolypeptides with heparin and other glycosaminogly-cans have shown that heparin is able to induce an ordered, helical conformation in the polypeptide.395 397 Similar, and even more dramatic, effects were observed with mixed basic polypeptides, presumed to represent better models for the biologically relevant interactions with plasma proteins.368... 

It has been suggested recently that PPII helix may be the killer conformation in such diseases (Blanch et al., 2000). This was prompted by the observation, described in Section III,B, of a positive band at 1318 cm-1, not present in the ROA spectrum of the native state, that dominates the ROA spectrum of a destabilized intermediate of human lysozyme (produced by heating to 57°C at pH 2.0) that forms prior to amyloid fibril formation. Elimination of water molecules between extended polypeptide chains with fully hydrated 0=0 and N—H groups to form... 

The IR and VCD for a-helix, /l-sheet, and coil forms have been shown to have distincdy different amide I and II spectra (see Fig. 2 for typical spectra of charged peptides of different conformation in H2O). Similar band shapes have been measured for a variety of polypeptides (Paterlini et al., 1986 Yasui and Keiderling, 1986a,b Baumruk et al.,... 

Before discussing details of their model and others, it is useful to review the two main techniques used to infer the characteristics of chain conformation in unordered polypeptides. One line of evidence came from hydrodynamic experiments—viscosity and sedimentation—from which a statistical end-to-end distance could be estimated and compared with values derived from calculations on polymer chain models (Flory, 1969). The second is based on spectroscopic experiments, in particular CD spectroscopy, from which information is obtained about the local chain conformation rather than global properties such as those derived from hydrodynamics. It is entirely possible for a polypeptide chain to adopt some particular local structure while retaining characteristics of random coils derived from hydrodynamic measurements this was pointed out by Krimm and Tiffany (1974). In support of their proposal, Tiffany and Krimm noted the following points ... 

Kallenbach and co-workers have recently demonstrated via CD spec-tropolarimetry and NMR spectrometry that a seven-residue alanine peptide adopts predominantly the PPII helical conformation in aqueous solution (Shi et al., 2002). Since alanine is nothing but backbone, such a finding indicates that the polypeptide backbone possesses an intrinsic... 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

Configuration mixing model a general approach to organic reactivity, 21,99 Conformations of polypeptides, calculations of, 6,103 Conjugated molecules, reactivity indices, in, 4,73... 

---