Biopolymers, molecular structures

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. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

All these advances have resulted not only in increases in resolution but have also alleviated the detection problems to a considerable extent. As a result, the last decade has seen a dramatic growth in 15N- and 170-NMR spectroscopy as a versatile method for studying molecular structure, both in isotropic (liquid) and anisotropic (solid) phases. Studies at a natural abundance level of the nucleides are now commonplace. The scope of chemical applications extends from inorganic, organometallic and organic chemistry to biochemistry and molecular biology, and includes the study of reactive intermediates, biopolymers and enzyme-inhibitor complexes. 

Chitosan Chitosan has a molecular structure similar to cellulose. This material is produced from chitin, which is widely found in the exoskeleton of shellfish and crustaceans. Chitin is the second most abundant natural biopolymer after cellulose. Chitosan is a good adsorbent for all heavy metals. It has been estimated that chitosan can be produced from shellfish and crustaceans at a market price of 15.43 /kg. 

Fluorescence techniques have been demonstrated in recent reviews 1( to be powerful methods for obtaining detailed information on the molecular structure of biopolymers and synthetic polymers. The objective of the present review is to concentrate on two aspects of the photophysics of synthetic polymers — excimer formation and singlet exciton migration. Both topics have been considered recently 11 but in less detail. 

Brought to perfection, the selectivity of interaction between macromolecules, i.e., their ability to recognize a certain partner, makes the basis for forming composite molecular structures, which play a decisive role in living organisms. This ability may be assumed to have developed in the evolutionary process and, hence, it might be characteristic not only of biopolymers and their synthetic analogues but of simple macromolecules as well. 

Many of the same models and techniques have been used to study the transitions in these two types of biopolymers, and we will present some common background information first. Then we will specialize and present the results of important thermodynamic studies in proteins and nucleic acids separately. However, common to both reports is the observation that the application of thermodynamic measurements and a thermodynamic analysis to carefully but widely chosen systems allows one to gain insights into structural details that complement molecular structure determinations obtained from instrumental techniques such as spectroscopy and X-ray crystallography. 

Lowdin, P. O., Technical Note No. 85, Uppsala Quantum Chemistry Group 1962 Proc. Bombay Symf., Molecular Structure and Spectroscopy, September 1962 Rev. Mod. Phys. 35, (1963) Proc. Stanford Symp., Quantum Aspects of Polypeptides and Polynucleotides (1963) Biopolymers Symp. 1, 161 (1964). 

Once the ROA measurement of biopolymers became possible, due to the development of backscattering [22,23], the power of empirical rules relating observed ROA to molecular structure became evident [24,25], In the case of biopolymers, the absolute... 

The situation is different for aqueous species of humic substances, the organic matter in soil that is not identifiable as unaltered or partially altered biomass or as conventional biomolecules.21 Humic substances comprise organic compounds that are not synthesized directly to sustain the life cycles of the soil biomass. More specifically, they comprise polymeric molecules produced through microbial action that differ from biopolymers because of their molecular structure and their long-term persistence in soil. This definition of humic substances implies no particular set of organic compounds, range of relative molecular mass, or mode of chemical reactivity. What is essential is dissimilarity to conventional biomolecular structures and biologically refractory behavior. 

NMR methods have also been used extensively to determine the configuration and conformation of both moderate-size molecules and synthetic polymers, whose primary molecular structure is already known. During the past decade high resolution NMR, particularly employing 2D and 3D methods, has become one of only two methods (x-ray crystallography is the other) that can be used to determine precise three-dimensional structures of biopolymers—proteins, nucleic acids, and their cocomplexes—and NMR alone provides the structure in solution, rather than in the solid state. 

There are now a very large number of books aimed at techniques for studying molecular structure, both in small molecules and in polymers and biopolymers. 

In order to invest ate the relationship between the structure and reactivity of model compounds for biopolymers, the structure of cyclic peptides as models for biopolymers must be made dear. The molecular conformation is determined by the bond length, bond angle, and internal rotation an e. With the bond length and bond an e the values for ordinary amides such as N-mefhylacetamide are usually adopted 16,... 

Okuyama K, Xu X, Iguchi M, Noguchi K. Revision of collagen molecular structure. Biopolymers 2006 84 181-191. 

We used the crosslinked chitosan fiber (hereafter called ChF) in this experimental study. ChF was fabricated by Fuji Spinning Co., Japan. Fig.l shows the unit molecular structure of chitosan which was transformed from chitin by deacetylation. Chitin is a natural biopolymer which is contained in the shell of arthropods. Chitosan was crosslinked to make an adsorbent with acid, alkaline, and chemical proofs. The fabrication method of ChF was presented elsewhere.[S,6]. 

The recent history of chemistry shows that problems which traditionally were part of chemistry are increasingly dealt with, even taken over, by other branches of science an important example being elucidation of molecular structure. The perhaps most chemical activity of chemists is synthesis of molecules, and quite probably it s going to be synthesis that experimental chemistry will have to offer as its specific contribution to research in the natural sciences of the future. However, not even synthesis is a secure preserve of experimental chemistry large biopolymers are made by bio technologists. 

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