D Protein Structure

Site address http//www.rcsb.org/pdb Searchable repository of 3-D protein structure. 

Hoffman, M. New 3-D Protein Structures Revealed, Science. 382 (My 26, 1991). Hoffman. M. New Role Found for a Common Protein MorifY Science, 742 (August 16. 1991). 

For several years we have been involved in a wide-ranging project to develop methods for the representation and searching of the three-dimensional (3-D) protein structures in the Brookhaven Protein Data Bank [28, 29], Our work derives from the graph-theoretic methods that are used for the storage and retrieval of information pertaining to both two-dimensional (2-D) and 3-D small molecules [1, 58]. 

Greiff, D. Protein structure and freeze drying the effects of residual moisture and gases. Cryobiology 1971, 8, 145-152. 

The National Center for Biotechnology Information (NCBI, www.ncbi.nlm.nih.gov), which is responsible for the databases that contain DNA and protein sequences, genome mapping data, and 3-D protein structures. 

Whitford, D. Proteins, Structure and Function, Istedition. JohnWiley Sons, 2005 pp. 56-57. 

Shindyalov, I. N., Bourne, P. E. A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm. Nucl. Acids Res. 2001,29, 228-229. 

Database of 3-D Protein Structure 3-D Protein Structure Comparison and Alignment http //cl.sdsc.edu/ ce.html [297]... 

Gibbons, A., and M. Hoffman. New 3-D Protein Structures Revealed. Sdmce 253, 382-383 (1991). [Fixamples of the use of X-ray crystallography to determine protein structure.]... 

DU, G., PRESTWICH, G.D., Protein structure encodes the ligand binding specificity in pheromone binding proteins. Biochemistry (Mosc). 1995, 34, 8726-8732. 

The number of atoms taken into account in MD nowadays may reach a million. The real problem is not the size of the system, but rather its complexity and the wealth of possible structures, with their too large number to be investigated. Some problems may be simplified by considering a quantum-mechanical part in the details and a classical part described by Newton equations. Another important problem is to predict the 3-D structure of proteins, starting from the available amino acid sequence. Every two years beginning in 1994, CASP (Critical Assessment of techniques for protein Structure Prediction) has been organized in California. CASP is a kind of scientific competition, in which theoretical laboratories (knowing only the amino acid sequence) make blind predictions about 3-D protein structures about to be determined in experimental laboratories. Most of the theoretical methods are based on the similarity of the sequence to a sequence from the Protein Data Bank of the 3-D structures, only some of the methods are related to chemical physics. Fig. 7.17 shows an example of the latter. 

CE Repository of 3-D protein structure alignments http //cl.sdsc.edu/ce.html... 

Sweet (69), Levin et al. (70) and Nishikawa and Ooi (71) all converged on the notion to utilize consensus secondary structures of oligopeptides in the data bank of known three-D protein structures. A window is defined (7 to 12 residues). Each such span in the sequence to be predicted is judged as homologous to several spans in the known tertiary stuctures. The consensus structure of the positions in the known spans allows a prediction for the unknown span. Moving along the sequence one residue at a time, the window process is repeated and the preferred secondary structure at a particular position taken as the prediction. Generally, there is little improvement over older methods. 

FIGURE 30.2 The 3-D protein structure of Fasl derived from green mamba (D. angusticeps) snake venom. Source Image obtained from the public domain at the US National Library of Medicine, Natiorud Center for Biotechnology Information, MMDB. 

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