Biomolecular crystallography

Protein crystal structures are archived in the Protein Data Bank (PDB) (Bernstein et al. 1977 Berman et al. 2000). About 5 per cent of the approximately 14 000 (December 2000) entries ( 12 500 proteins, peptides, and viruses, 900 nucleic acids, 600 pro-tein/nucleic acid complexes, 20 carbohydrates) contain the qualifier form in the compound name/descriptor field, and most of those refer to polymorphic varieties. In biomolecular crystallography great efforts are expended varying crystallization conditions in the attempts to obtain single crystals suitable for structural investigations... 

Rupp B (2010) Biomolecular crystallography—principles practice and application to structural biology. Garland Sciene, New York... 

Much useful information in crystal structure studies is often passed over by the authors themselves and has to be actively sought and recovered, either from the original publications or from databases. From the very early days, isolated bits of information were collected and used to construct tables of standard distances for various types of covalent bonds and of van der Waals radii for intermolecular contact distances, as collected in Pauling s influential book [41] and elsewhere, as well as standard dimensions for structural fragments that are important in biomolecular crystallography, such as the peptide moiety and the nucleic acid bases. 

Figure 2.43. Comparison between a real monoclinic crystal lattice (a = b c) and the corresponding reciprocal lattice. Dashed lines indicate the unit cell of each lattice. The magnitudes of the reciprocal lattice vectors are not in scale for example, la l = 1/dioo, lc l = 1/dooi, IGioil = dioi, etc. Note that fra-orthogonal unit cells (cubic, tetragonal, orthorhombic), the reciprocal lattice vectras will be aligned parallel to the real lattice vectors. 2009 From Biomolecular Crystallography Principles, Practice, and Application to Structural Biology by Bernard Rupp. Reproduced by permission of Garland Science/ Taylor Francis Group LLC.

Rupp, B. (2009) Biomolecular Crystallography. Principles, Practice and Application to Structural Biology, Garland Science, New York. 

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. 

S S CONTENTS Preface, C. Allen Bush. Methods in Macromo-lecular Crystallography, Andrew J. Howard and Thomas L. Poulos. Circular Dichroism and Conformation of Unordered Polypeptides, Robert W. Woody. Luminescence Studies with Horse Liver Dehydrogenase Information on the Structure, Dynamics, Transitions and Interactions of this Enzyme, Maurice R. Eftink. Surface-Enhanced Resonance Raman Scattering (SERRS) Spectroscopy A Probe of Biomolecular Structure and Bonding at Surfaces, Therese M. Cotton, Jae-Ho Kim and Randall E. Holt. Three-Dimensional Conformations of Complex Carbohydrates, C. Allen Bush and Perse-veranda Cagas. Index. 

A wide variety of experimental methods have provided insight into protein, and in particular enzyme structure, and these structures are in turn the raw materials of much biomolecular modelling. The most important experimental technique for studying protein structure to date has been X-ray crystallography. A well-ordered crystal of the protein is required. Finding appropriate conditions to produce suitable crystals can be challenging, for example... 

Lu, M. and Ma, J., A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography, Proc. Natl. Acad. Sci. U.S.A.,105, 15358 (2008). 

Biophysical tools and techniques have become extremely useful in many areas and fields. They have furthered research in protein crystallography, synthetic biology, and nanobiology, and allowed scientists to discover new pharmaceuticals and to study biomolecular structures and interactions and membrane structure... 

Simulated annealing is widely used to refine biomolecular structures found from X-ray crystallography or NMR. 

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