Protein structure INDEX

CONTENTS Acknowledgments, Margery G. Ord and Lloyd A. Stocken. Introduction. Biochemistry Before 1900. Early Metabolic Studies Energy Needs and the Composition of the Diet. Carbohydrate Utilization Glycolysis and Related Activities. Aspects of Carbohydrate Oxidation, Electron Transfer, and Oxidative Phosphorylation. Amino Acid Catabolism in Animals. The Utilization of Fatty Acids. The Impact of Isotopes 1925-1965. Biochemistry and the Cell. Concepts of protein Structure and Function. Chronological Summary of Main Events Up to ca. 1960. Principal Metabolic Pathways. Index. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

Anderson NG, Anderson L. The human protein index. Clin Chem 28 739-748, 1982. Blake CCF, Johnson LN. Protein structure. Trends Biochem Sci April 147-151, 1987. Branden C, Tooze J. Introduction to Protein Structure. New York Garland, 1991. 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

F. M. Marassi and S. J. Opella, A solid-state NMR index of helical membrane protein structure and topology. J. Magn. Reson.. 2000,144, 150-155. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

DFprot http //sbg.cib.csic.es/Software/ DFprot/index.html The server provides deformabil-ity/flexibility analysis of a 3D protein structure... 

ModBase http //alto.compbio.ucsf.edu/modbase-cgi/index.cgi Annotated comparative protein structures... 

OATH Protein structure classification http //www.biochem.ucl.ac.uk/bsm/ cath new/index.html... 

D. Tobi and R. Fiber, PROTEINS Structure, Function, and Genetics, 41, 40 (2000). Distance-Dependent, Pair Potential for Protein Folding Results From Linear Optimization. Available http //cbsu.tc.cornell.edu/software/loopp/index.htm and http //ser-loopp.tc. cornell.edu/cbsu/loopp.htm. 

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