Conformation thermodynamics

There are of course, many facets of polymers for which our under-standing is far from complete. Polymers with associating groups bonded to their chains, polymer crystallization, liquid crystalline polymers and charged polymers are examples of areas of active research in polymer physics. These four particular examples are also very pertinent to understanding the functions of important biopolymers, such as DNA, RNA, proteins, and polysaccharides. By learning the fundamentals of chain conformations, thermodynamics, elasticity, and mobility, the readers of this book should be ready to consider these more challenging facets. 

We summarise recent work on computer modelling and simulation of proteins involved in bioenergetic processes and in peptide-membrane interactions. Homology modelling, electrostatic calculations and conformational analysis of a photosynthetic reaction centre protein are described. Bacteriorhodopsin, a light-driven proton pump protein is examined from several aspects, including its hydration and conformational thermodynamics. Finally, we present results on lipid perturbation on interaction with a cyclic decapeptide antibiotic, gramicidin S. 

The experimental structure of bR determined at atomic resolution from cryoelectron microscopy and X-ray crystallography revealed a channel containing the Schiff base of the retinal chromophore (27, 28). Site-directed mutagenesis and vibrational spectroscopy experiments have enabled the identification of polar residues in the channel involved in the proton transfer pathway (29-32). Recent work on bacteriorhodopsin has concentrated on hydration and conformational thermodynamics. 

Force fields were originally developed to simulate the conformational, thermodynamic and kinetic behaviors of small molecules or macromolecules much more efficiently, from a computer resource perspective, than quantum mechanical methods. It was hoped that if the interaction components of the force fields were applied to docking and scoring, the more accurate representation of the physics of protein ligand interactions would result in more accurate predictions of protein ligand binding affinities. 

A molecular dynamics simulation describes the phase space region defined by atomic positions and velocities. Consequently, this method allows the calculation of thermal motion. On close inspection, one obtains information on conformations, thermodynamic properties and dynamic features of surfactant and solvent molecules. A... 

The simulations and theoretical arguments predict that at high Tj, the sequence free energy P, dominates and the sequence tends to be completely random, corresponding to the minimum of Fj. At low Tj, the evolution selects those sequences, which correspond to the low value of the conformation free energy (structure of the core-tail typ>e). In the intermediate regime, there is an interplay between the conformational thermodynamic force and the sequence contribution (evolution pressure). Therefore, the formation of nontrivial stractures and sequences is possible. Even in the absence of attraction between P units, the final sequences remain protein-Uke (i.e., the final copolymer has the core-shell stracture of a globule) and therefore maintain certain information complexity. 

NMR can distinguish nuclei at specific positions in a structure and remains increasingly valuable for the study of chosen loci in nucleic acids under a variety of conditions structural, conformational, thermodynamic and kinetic data can be obtained in principle. 

There are several reasons why molecular modeling and computational chemistry are increasingly being incorporated into the undergraduate curriculum. The use of these techniques has expanded beyond physical chemistry to all fields of chemistry, to calculate molecular conformations, thermodynamic properties, and molecular spectra. Molecular modeling plays a key role in many synthetic studies, especially in the pharmaceutical industry. The price of both hardware and software has decreased so much that most campuses can now afford to have their students do calculations that would have been a major research problem only a few years ago. 

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