PART 3 Biomolecular structure

This book began as lecture notes for a course on optical spectroscopy that 1 taught for graduate students in biochemistry, chemistry, and our interdisciplinary programs in molecular biophysics and biomolecular structure and design. 1 started expanding the notes partly to try to illuminate the stream of new experimental information on photosynthetic antennas and reaction centers, but mostly just for fun. 1 hope that readers will find the results not only useful, but also as stimulating as 1 have. 

Biological interactions between molecules are stereo-specific the fit in such interactions must be stereo-chemically correct. The three-dimensional structure of biomolecules large and small—the combination of configuration and conformation—is of the utmost importance in their biological interactions reactant with enzyme, hormone with its receptor on a cell surface, antigen with its specific antibody, for example (Fig. 1-22). The study of biomolecular stereochemistry with precise physical methods is an important part of modem research on cell structure and biochemical function. 

Biomolecular recognition is mediated by water motions, and the dynamics of associated water directly determine local structural fluctuation of interacting partners [4, 9, 91]. The time scales of these interactions reflect their flexibility and adaptability. For water at protein surfaces, the studies of melittin and other proteins [45, 46] show water motions on tens of picoseconds. For trapped water in protein crevices or cavities, the dynamics becomes much slower and could extend to nanoseconds [40, 71, 92], These rigid water molecules are often hydrogen bonded to interior residues and become part of the structural integrity of many enzymes [92]. Here, we study local water motions in various environments, from a buried crevice to an exposed surface using site-selected tryptophan but with different protein conformations, to understand the correlation between hydration dynamics and conformational transitions and then relate them to biological function. 

Because of the question as to the way in which the response of biological systems to outside stimulation is brought about, it will also be of particular interest to examine how the structure and function of tnopolymers can be affected by the variation of external parameters. In this regard the effects of the interaction of an electric field with biomolecular systems are of considerable significance, since electric fidds are known to occur in biological cells (especially at membranes) and to take part in regulation processes as well as in information transfer (as reflected, e.g., by nerve pulses). 

One of the typical examples of such biomolecular interfaces is a membrane , a two-dimensional molecular array which forms the boundary of biological cells. These membranes are composed of lipids and proteins. Of these, the lipid molecules which are amphipathic (a molecule consisting of two parts, each of which has an affinity for a different phase), are considered to be responsible for maintaining the two-dimensional molecular structure the protein molecules, which perform a variety of biochemical functions, are often associated with (in/on) these lipid bilayer membranes (Figure 16). 

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