Biopolymers, folding

It is well known that nature folds macromolecules like proteins, RNA, and DNA into defined stmctures with specific shape and that these shapes are intimately related to their function [14-18]. Tremendous research effort has provided some understanding of how this folding occurs in proteins. In fact, it is now possible to design, from scratch, with great success an unnatural protein sequence which will fold into the predicted secondary stracture [19]. However, many of the fundamental questions of biopolymer folding are not yet solved. Careful study of foldamers, which can be... 

Elastin-like biopolymers fold and assemble, due to the periodicity of repeating sequences[44, 344]... 

Guo Z and Thirumalai D 1995 Kinetics of protein folding nucleation mechanism, time scales and pathways Biopolymers 36 83-103... 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Bruccoleri R E and M Karplus 1987. Prediction of the Folding of Short Polypeptide Segments by Uniform Conformational Sampling. Biopolymers 26 137-168. 

R Bruccoleri, M Karplus. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26 137-168, 1987. 

JD Eloneycutt, D Thirumalai. The nature of folded states of globular proteins. Biopolymers 32 695-709, 1992. 

P. Grassberger, G. T. Barkema, W. Nadler, eds. Monte Carlo Approaeh to Biopolymers and Protein Folding. Singapore World Scientific, 1997. 

The ionic strength dependence of intrinsic viscosity is function of molecular structure and protein folding, ft is well known that the conformational and rheological properties of charged biopolymer solutions are dependent not only upon electrostatic interactions between macromolecules but also upon interactions between biopolymer chains and mobile ions. Due electrostatic interactions the specific viscosity of extremely dilute solutions seems to increase infinitely with decreasing ionic concentration. Variations of the intrinsic viscosity of a charged polyampholite with ionic strength have problems of characterization. 

Determination of protein secondary structure has long been a major application of optical spectroscopic studies of biopolymers (Fasman, 1996 Havel, 1996 Mantsch and Chapman, 1996). These efforts have primarily sought to determine the average fractional amount of overall secondary structure, typically represented as helix and sheet contributions, which comprise the extended, coherent structural elements in well-structured proteins. In some cases further interpretations in terms of turns and specific helix and sheet segment types have developed. Only more limited applications of optical spectra to determination of tertiary structure have appeared, and these normally have used fluorescence or near-UV electronic circular dichroism (ECD) of aromatic residues to sense a change in the fold (Haas, 1995 Woody and Dunker, 1996). 

McPhie, P. (2004). CD studies on films of amyloid proteins and polypeptides Quantitative g-factor analysis indicates a common folding motif. Biopolymers 75, 140-147. 

As discussed in Section 3.1.6.1., natural biopolymers are useful chiral selectors, some of which are readily available they are constructed from chiral subunits (monomers), for instance, from L-amino acids or D-glucose. If synthetic chiral polymers of similar type are to be synthesized, appropriate chiral starting materials and subunits, respectively, must be found. Chiral polymers with, for example, a helical structure as the chiral element, are built using a chiral catalyst as chirality inducing agent in the polymerization step. If the chirality is based on a chiral subunit, the chirality of the polymer is inherent, whereas if the polymer is constructed from chiral starting materials, chiral subunits are formed which lead to chirally substituted synthetic polymers that in addition may order or fold themselves to a supramolecular structure (cf. polysaccharides). 

---