Biomolecular structures, characterization

Nuclear magnetic resonance (NMR) spectroscopy has gained an outstanding role in the characterization of biomolecular structures in solution during the past decade. In the case of metalloproteins in general. 

Since conception over 100 years ago, MS has become an important analytical and research tool with diverse applications ranging from astronomical study of the solar system to materials analysis and process monitoring in chemical, oil and pharmaceutical industries. Use of MS has led to very many scientific breakthroughs including the discovery of isotopes, accurate determination of atomic mass, and the characterization of biomolecular structure. Indeed, MS is now a fundamental technique employed in pharmacology, toxicology and other biological, environmental and biomedical sciences. 

Biomolecules are mostly chiral, therefore chiroptical methods are the first choice among the spectroscopic methods applied to biomolecular structural studies. Characterization of peptides, nucleotides, proteins and nucleic acids by their ECD spectra became a generally used procedure and was repeatedly reviewed [1]. 

Self assemblage of extended biomolecular structures on solid surfaces was verified by the SPM measurements. Supramolecular structures were detected on solid surfaces of practically all samples. Aiming to characterize transferability of the structures from the solution onto solid surface, we performed experiments with sufficiently stable lisozyme fibrils. In these experiments hen egg lysozyme fibrils were immobilized on several types of solid substrates listed in section 2 by deposition of the structures from buffer solution. Typical results of these tests are... 

Laboratones not set up for structural characterization of proteins can find assistance for ammo acid analysis, Edman degradation and mass spectrometry in the Yellow Pages of the Membership Directoiy of the Association of Biomolecular Resource Facilities (ABRF, 9650 Rockville Pike, Bethesda, MD)... 

Chang, D. K., Venkatachalam, C. M., Prasad, K. U., Urry, D. W. (1989). Nuclear overhauser effect and computational characterization of the beta-spiral of the polypentapeptide of elastin. Journal of Biomolecular Structure Dynamics, 6, 851-858. 

In conclusion, laser desorption in combination with molecular beam high-resolution spectroscopic methods has enabled the structural characterization of gas-phase biomolecules of significant size. Moreover, IR-UV ion dip spectroscopy offers information about the number and types of conformers present. Applications to diverse classes of biomolecular systems such as peptides, carbohydrates and nucleobases, are described in the various chapters of this book. 

Biological membranes provide the essential barrier between cells and the organelles of which cells are composed. Cellular membranes are complicated extensive biomolecular sheetlike structures, mostly fonned by lipid molecules held together by cooperative nonco-valent interactions. A membrane is not a static structure, but rather a complex dynamical two-dimensional liquid crystalline fluid mosaic of oriented proteins and lipids. A number of experimental approaches can be used to investigate and characterize biological membranes. However, the complexity of membranes is such that experimental data remain very difficult to interpret at the microscopic level. In recent years, computational studies of membranes based on detailed atomic models, as summarized in Chapter 21, have greatly increased the ability to interpret experimental data, yielding a much-improved picture of the structure and dynamics of lipid bilayers and the relationship of those properties to membrane function [21]. 

The refinement of other analytical methods, such as electrophoresis [34,36], the various techniques of optical spectroscopy [103-105], and nuclear magnetic resonance [201], is supplemented by the recent advances in real-time affinity measurements [152,202], contributing to the understanding of biomolecular reactivity. Taken together, the improvement of analytical methods will eventually allow a comprehensive characterization of the structure, topology, and properties of the nucleic acid-based supramolecular components under consideration for distinctive applications in nanobiotechnology. 

Many applications have been reported in the field of biomolecular NMR spectroscopy which use RDCs for the refinement of three-dimensional structures. The approach is quite powerful and can also be applied to smaller molecules whenever the conformation of a molecule is important, as for example in the case of rational drug design. Traditionally, NMR in liquid crystals is applied on a multitude of small organic compounds to obtain their fully characterized structure. Most examples are measured on all kinds of aromatic systems as reported in refs. 204—212 other recent examples deal with substituted alkanes, aldehydes216,217 or bridged systems like norbomadiene.218 In general, these very detailed studies can be applied to molecules with up to 12 protons. 

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