Academic literature on the topic 'NMR Biomolecular structure Interactions and Dynamic'

Hydrogen bonding properties of water molecules, which are confined in microcavities of biological interfaces, are significantly different from those of bulk water and drive most of the complex biological processes. While NMR, X-ray and UV–vis-IR spectroscopic techniques have been found inadequate for describing the dynamics of the thick (20–40 Å) sheath of hydration layer around biomolecules, recently developed THz spectroscopy has emerged as a powerful technique to directly probe the collective dynamics of hydrogen bonds in the hydration layer, which control all important functions of the biomolecules in life. Both laser and accelerator-based THz sources are intense enough to penetrate up to about 100 μm thick water samples, which makes THz transmission and/or dielectric relaxation measurements possible in aqueous solutions. These measurements provide valuable information about the rattling and rotational motions of hydrated ions, making, breaking and rearrangement of hydrogen bonds in hydration layer as well as hydrophilic and hydrophobic interactions between biomolecule and water. THz spectroscopy has also been successfully applied to study the effect of modulation of the physical conditions, like temperature, pH, concentration of proteins and chemical additives, on the structure and dynamics of hydration layer. THz spectroscopy has also been applied to study the processes of denaturation, unfolding and aggregation of biomolecules.

The biological functions of proteins all depend on their highly specific interactions with other molecules, and the understanding of the molecular basis of the specificity of these interactions is an important part of the effort to understand protein structure-function relationships. NMR spectroscopy can provide information on many different aspects of protein-ligand interactions, ranging from the determination of the complete structure of a protein-ligand complex to focussing on selected features of the interactions between the ligand and protein by using “reporter groups” on the ligand or the protein. It has two particular advantages: the ability to study the complex in solution, and the ability to provide not only structural, but also dynamic, kinetic and thermodynamic information on ligand binding. Early analyses of ligand binding (Jardetzky and Roberts, 1981) focused on measurements of relaxation times, chemical shifts and coupling constants, which gave relatively limited, although valuable, structural information. More recently, it has become possible to obtain much more detailed information, due to the extensive use of nuclear Overhauser effect measurements and isotope-labeled proteins and ligands; a number of reviews of this area are available (Feeney and Birdsall, 1993; Lian et al, 1994; Wand and Short, 1994; Petros and Fesik, 1994; Wemmer and Williams, 1994). In this article, we describe some recent work from our laboratory which illustrates the use of NMR spectroscopy to obtain structural and mechanistic information on relatively large enzyme-substrate and proteinprotein complexes. A number of species of pathogenic bacteria, notably Streptococci and Staphylococci, have proteins on their surface that bind immurioglobulins (reviewed in Boyle (1990)). Protein A from S. aureus and protein G from species of Streptococci are widely used as imrnunological tools and are the most extensively studied of these antibody-binding proteins. A detailed understanding of the binding mechanisms of these proteins is important, not only for providing us with the structural basis for their functions, but also as a contribution toward understanding the general rules of protein-protein interactions.

Fluorescence spectrometry is the most extensively used optical spectroscopic method in analytical measurement and scientific investigation. During the past five years more than 60000 scientific articles have been published in which fluorescence spectroscopy has been used. The large number of applications ranges from the analytical determination of trace metals in the environment to pH measurements in whole cells under physiological conditions. In the scientific research laboratory, fluorescence spectroscopy is being used or applied to study the fundamental physical processes of molecules; structure-function relationships and interactions of biomolecules such as proteins and nucleic acids; structures and activity within whole cells using such instrumentation as confocal microscopy; and DNA sequencing in genomic characterization. In analytical applications the use of fluorescence is dominant in clinical laboratories where fluorescence immunoassays have largely replaced radioimmunoassay techniques. There are two main reasons for this extensive use of fluorescence spectroscopy. Foremost is the high level of sensitivity and wide dynamic range that can be achieved. There are a large number of laboratories that have reported single molecule detection. Secondly, the instrumentation required is convenient and for most purposes can be purchased at a modest cost. While improvements and advances continue to be reported fluorescence instrumentation has reached a high level of maturity. A review of the physical principles of the fluorescence phenomenon permits one to understand the origins of the information content that fluorescence measurements can provide. A molecule absorbs electromagnetic radiation through a quantum mechanical process where the molecule is transformed from a ‘ground’ state to an ‘excited’ state. The energy of the absorbed photon of light corresponds to the energy difference between these two states. In the case of light in the ultraviolet and visible spectral range of 200 nm to 800 nm that corresponds to energies of 143 to 35.8 kcal mol-1. The absorption of light results in an electronic transition in the atom or molecule. In atoms this involves the promotion of an electron from an outer shell orbital to an empty orbital of higher energy.

Pressure-tuning vibrational spectroscopy was first introduced to the study of structural and dynamic properties in biological systems from our laboratory about one decade ago. One of our efforts has been the search for spectral features and their pressure dependencies related to the structural and dynamic properties in biological systems. Pressure-induced correlation field splitting of the vibrational modes of methylene chains is one of the parameters that has been applied to monitor various structural and dynamic properties of a wide range of aqueous lipid bilayers and biomembranes in our laboratory. Correlation field splitting of the vibrational modes of the methylene chains in lipid bilayers is the result of vibrational coupling interactions among the ordered methylene chains with different site symmetry in the two-dimensional matrix. However, the basic theory and the characteristics of these interchain interactions in lipid bilayers still needed to be established. It was unknown whether the interchain interactions that result in the correlation field splitting take place within each lipid molecule or between neighboring molecules in the lamellar bilayers. The relative contributions of 'intramolecular and intermolecular interchain interactions to the correlation field splitting, and the effects of the long-range interchain interactions and interdigitation on the correlation field splitting, were also unknown. These problems have been resolved recently and are addressed in this chapter. Our laboratory has pioneered the study of structural and dynamic properties of biological systems by means of pressure-tuning vibrational spectroscopy (Wong et al., 1982). It is now well recognized that this spectroscopic technique is one of the most powerful physical methods for the study of biological and biomedical phenomena at the molecular level with enhanced resolution (Wong, 1984, 1987a, 1987b, 1987c, 1993). The biological systems we have studied by this method include not only various aqueous biomolecular assemblies but also whole cells and intact biological tissues (Rigas et al, 1990; Wong, 1984, 1987b, 1987c, 1993; Wong et al., 1991a, 1991b, 1993). We have found that the pressure-induced changes in many spectral features and parameters in both FTIR and Raman spectra of biological systems result from modifications in structure and dynamics at the molecular level.