Overview conformational model

As it was mentioned in Section 9.4.1, 3D structures generated by DG have to be optimized. For this purpose, MD is a well-suited tool. In addition, MD structure calculations can also be performed if no coarse structural model exists. In both cases, pairwise atom distances obtained from NMR measurements are directly used in the MD computations in order to restrain the degrees of motional freedom of defined atoms (rMD Section 9.4.2.4). To make sure that a calculated molecular conformation is rehable, the time-averaged 3D structure must be stable in a free MD run (fMD Sechon 9.4.2.5J where the distance restraints are removed and the molecule is surrounded by expMcit solvent which was also used in the NMR measurement Before both procedures are described in detail the general preparation of an MD run (Section 9.4.2.1), simulations in vacuo (Section 9.4.2.2) and the handling of distance restraints in a MD calculation (Section 9.4.2.3) are treated. Finally, a short overview of the SA technique as a special M D method is given in Sechon 9.4.2.6. 

The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

A great deal of structural information about G proteins is known from x-ray crystallographic studies, providing insight into GTP-mediated conformational changes in Ga, subunit interactions with effector proteins, and the mechanism of GTP hydrolysis. By contrast, relatively little structural information is known about the interaction between the receptor and G protein and how this interaction leads to GDP release. After an overview of the structure of heptahelical receptors and heterotrimeric G proteins, this chapter will discuss the current models of the receptor-G protein complex and proposed mechanisms for receptor-catalyzed nucleotide exchange. 

Peptides and peptidomimetics represent a class of compounds of its own for 3D structure generation and conformational analysis. Therefore, the programs developed for predicting spatial peptide models are rather restricted in their application to this specific group of molecules. In Sec. 6, approaches to the generation of low-energy conformations of peptide molecules will be briefly described. A detailed overview of... 

Another growing field of interest is carbohydrate chemistry. Because of the conformational diversity of these molecules, there is much to be explored by means of computational chemistry. In Chapter 3, Professor Robert J. Woods provides an overview of the molecular modeling techniques as applied to this ubiquitous class of compounds. Historically, few empirical force fields were... 

We have presented an overview of theories that describe the conformations and solution properties of star-branched PEs. Whereas the principal qualitative results can be obtained on the basis of a simplified box-like cell model, systematic... 

Protein folding studies generally concern liquid-phase phenomena however, HDX reactions can also be conducted in the gas phase (e.g., [84-90] for an overview see [91]). For instance, multiply charged ions of several model proteins reacted with DjO in a vacuum following pseudo-first-order kinetics [85]. It was also observed that removing solvent significantly increased conformational rigidity. In other work, ions of bovine ubiquitin were... 

Two useful review articles on the theory of the kinetics and statistics of reactions of functional groups on polymers have appeared. Both polymer-analogous and intramolecular transformation reactions are influenced by a number of specifically macromolecular effects. These include neighbouring-group effects, configurational and conformational effects, electrostatic and supermolecular effects. The incorporation of all these factors into a general theory of macromolecular reactions is extremely difficult. These reviews provide introductions to the mathematical models as well as state-of-the-art overviews. 

It needs to be mentioned here that many other experimental techniques are available for studying monolayers at the air-water interface. Most frequently, surface potential is measured to evaluate the molecular orientation of amphiphiles at the interface. This method is, however, better suited to the study of small molecules. Polymeric amphiphiles, due to their conformational dynamics, are difficult to analyze and simple dielectric layer models do not apply, or produce large errors. Grazing incidence X-ray diffraction provides information on molecular packing, and spectroscopic methods are used to study molecular interactions and the structural changes of molecules upon compression. Fluorescence microscopy is useful for studying two-dimensional organization of small molecular mass amphiphiles however, it is not applied to polymer monolayers. For a more comprehensive overview of experimental methods used to study monolayers at the air-water interface, the reader is referred to more specialized articles, e.g. [18]. 

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