Biomolecular structure

One of the approaches to understanding biological phenomena has been to purify an individual chemical component from a living organism and to characterize its chemical structure or biological activity. The most commonly used techniques for purifying biomolecules are chromatographic and electrophoretic methods (Deut-scher, 1990 Heftmann, 1983), and the most facile approaches to characterization of molecular structures are spectroscopic methods (Brown, 1998 McHale, 1999). 

Chromatography (Edward, 1970 Millner, 1999 Poole and Poole, 1991)—in particular, high-performance liquid chromatography (HPTC)—is an ideal technique 

The modes of liquid chromatographic separation can be classified as follows  

Gel-filtration/permeation chromatography The technique is normally used for the separation of biological macromolecules and polymers. It separates compounds on the basis of size. Solutes are eluted in the order of decreasing molecular size. 

Adsorption chromatography The process can be considered as a competition between the solute and solvent molecules for adsorption sites on the solid surface of adsorbent to effect separation. In normal phase or liquid-solid chromatography, relatively nonpolar organic eluents are used with the polar adsorbent to separate solutes in order of increasing polarity. In reverse-phase chromatography, solute retention is mainly due to hydrophobic interactions between the solutes and the hydrophobic surface of adsorbent. Polar mobile phase is used to elute solutes in order of decreasing polarity. 

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Barron L D, Hecht L, Bell A F and WIson G 1996 Raman optical activity an incisive probe of chirality and biomolecular structure and dynamics ICORS 96 XVth Int. Conf. on Raman Spectroscopy ed S A Asher and P B Stein (New York Wley) pp 1212-15... 

B.J. Leimkuhler, S. Reich, and R. D. Skeel. Integration methods for molecular dynamics. In Mathematical approaches to biomolecular structure and dynamics, Seiten 161-185, New York, 1996. Springer. 

T. Schlick. Pursuing Laplace s vision on modern computers. In J. P. Mesirov, K. Schulten, and D. W. Sumners, editors. Mathematical Applications to Biomolecular Structure and Dynamics, volume 82 of IMA Volumes in Mathematics and Its Applications, pages 219-247, New York, New York, 1996. Springer-Verlag. 

Lavery R and H Sklenar 1988. The Definition of Generalized Helicoidal Parameters and of A> Curvature for Irregular Nucleic Acids. Journal of Biomolecular Structure and Dynamics 5 63-91. 

AMU Bonvm, R Boelens, R Kaptem. Determination of biomolecular structures by NMR Use of relaxation matrix calculations. In WF van Gunsteren, PK Weiner, AI Wilkinson, eds. Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications, Vol 2. Leiden ESCOM, 1993, pp 407-440. 

Incorporation of fluorine into a biological substrate opens a spectral window for viewmg biomolecular structure and dynamics in solution With mmimal background mletference, fluonne NMR can provide clear spectral information for fluorme conlainmg macromolecules, in contrast to an indecipherable mass of signals from proton or carbon NMR Whether the fluonnated unit is termed a probe, tag, marker, or reporter group, its function is the same to act as a beacon of spectral information... 

Englander, S. W., and Mayne, L., 1992. Protein folding studied using hydrogen exchange labeling and two-dimensional NMR. Annual Review of Biophysics and Biomolecular Structure 21 243—265. 

Wagner, G., Hyberts, S., and Havel, T, 1992. NMR structure determinadon in solution A cridqne and comparison with X-ray crystallography. Annual Review of Biophysics and Biomolecular Structure 21 167—242. 

John.son, L. N., and Barford, D., 1993. The effects of pho.sphorylation on the. structure and function of proteins. Annual Review of Biophysics and Biomolecular Structure 22 199-232. A review of protein pho.sphorylation and its role in regrdation of enzymatic activity, with particular empha.sis on glycogen pho.sphoryla.se. 

Because the time scale of the Raman scattering event ( 3.3 x 10-14s for a vibration with wavenumber shift 1000 cm-1 excited in the visible) is much shorter than that of the fastest conformational fluctuations in biomolecules, the ROA spectrum is a superposition of snapshot spectra from all the distinct chiral conformers present in the sample. Together with the dependence of ROA on chirality, this leads to an enhanced sensitivity to the dynamic aspects of biomolecular structure. The two-group model provides a qualitative explanation since it predicts ROA intensities that depend on absolute chirality in the form of a sin x dependence... 

In order to study dynamic aspects of biomolecular structure, it is necessary to perform measurements over an appropriate temperature range. This is accomplished by directing dry air downward over the sample cell from the nozzle of a device used to cool protein crystals in X-ray... 

This chapter considers the distribution of spin Hamiltonian parameters and their relation to conformational distribution of biomolecular structure. Distribution of a g-value or g-strain leads to an inhomogeneous broadening of the resonance line. Just like the g-value, also the linewidth, W, in general, turns out to be anisotropic, and this has important consequences for powder patterns, that is, for the shape of EPR spectra from randomly oriented molecules. A statistical theory of g-strain is developed, and it is subsequently found that a special case of this theory (the case of full correlation between strain parameters) turns out to properly describe broadening in bioEPR. The possible cause and nature of strain in paramagnetic proteins is discussed. 

A concept of amphiphilicity, as applied to single monomer units of designed water-soluble polymers, is presented in the third chapter by Okhapkin, Makhaeva, and Khokhlov. The concept is relevant to biomolecular structures and assemblies in aqueous solution. The authors consider the substantial body of information obtained experimentally and theoretically on surface molecular chemical structures, including those that are prospective for surface catalysis. Unusual conformational behaviors of single amphiphilic polymers recently observed in simulations are also discussed in detail. 

The website http //www.annualreviews.org/ offers online searching capability to the entire Annual Reviews series. The Annual Reviews of Biochemistry and Annual Reviews of Biophysics and Biomolecular Structure are of most pertinence to... 

Dickerson RE (1981) In Srinivasan R (ed) Biomolecular structure, conformation, function, evolution vol 1 Pergamon, New York... 

Biomolecular Structure and Research Program, Department of Psychiatry, University of Saskatchewan, Saskatoon, SK, Canada... 

The website http //www.annualreviews.org/ offers online searching capability to the entire Annual Reviews series. Annual Reviews publishes authoritative, analytic reviews in 32 focused disciplines within the Biomedical, Physical, and Social Sciences. The Annual Reviews of Biochemistry and Annual Reviews of Biophysics and Biomolecular Structure are of most pertinence to bioinorganic chemists. This nonprofit, by-subscription, scientific publisher provides free searching of the site and no-cost abstract retrieval. 

Cheng, X., Collins, R.E. and Zhang, X. (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annual Review of Biophysics and Biomolecular Structure, 34, 267-294. 

The interest of the scientific community on small systems has been boosted by the recent advent of micromanipulation techniques and nanotechnologies. These provide adequate scientific instruments that can measure tiny energies in physical systems under nonequilibrium conditions. Most of the excitement comes also from the more or less recent observation that biological matter has successfully exploited the smallness of biomolecular structures (such as complexes made out of nucleic acids and proteins) and the fact that they are embedded in a nonequilibrium environment to become wonderfully complex and efficient at the same time [3, 4]. 

T. Herges, H. Merlitz, and W. Wenzel. Stochastic optimisation methods for biomolecular structure prediction. J. Ass. Lab. Autom., 7 98-104, 2002. 

The tremendous progress in supramolecular chemistry and nanoscience provided intellectual concepts and guidelines to implement biomolecules and nano-objects as functional units for the self-assembly of biomolecular structures, or biomolecule-nanoparticle hybrid systems. Such biomolecular supramolecular complexes or hybrid biomolecular composites are anticipated to reveal properties and functions that emerge from the complexity of the structures. 

The first theme of the book is biomolecular structure. We ll look carefully at the complex structures of proteins, carbohydrates, RNA, DNA, and many other substances. We ll not only examine in-depth their molecular architecture but also study the chemical properties that make life possible. 

C. Chothia, T. Hubbard, S. Brenner, H. Bams, and A. Murzin, Annual Review of Biophysics and Biomolecular Structure 26, 597 (1997). 

We may think of biochemistry as being divided into three main areas biomolecular structure, intermediary me-... 

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