Sequence structure

CATH, FSSP Sequence-structure classification databases... 

KK Koretke, Z Luthey-Schulten, PG Wolynes. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci 5 1043-1059, 1996. 

G Vriend, C Sander, PFW Stouten. A novel search method for protein sequence-structure relations using property profiles. Protein Eng 7 23-29, 1994. 

C Bystroff, D Baker. Prediction of local structure m proteins using a library of sequence-structure motifs. J Mol Biol 281 565-577, 1998. 

To gain the most predictive utility as well as conceptual understanding from the sequence and structure data available, careful statistical analysis will be required. The statistical methods needed must be robust to the variation in amounts and quality of data in different protein families and for structural features. They must be updatable as new data become available. And they should help us generate as much understanding of the determinants of protein sequence, structure, dynamics, and functional relationships as possible. 

RH Lathi op, IR Rogers Ir, TE Smith, IV White. A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bull Math Biol 60 1039-1071, 1998. 

PE Leopold, M Montal, JN Onuchic. Protein folding funnels A kinetic approach to the sequence-structure relationship. Pi oc Natl Acad Sci USA 89 8721-8725, 1992. 

Barnes, C. J., Dalgleish, G., Jared, G., Swift, K. G. and Tate, S. 1997 Assembly Sequence Structures in Design for Assembly. In Proceedings IEEE International Symposium on Assembly and Task Planning, Marina del Rey, California, 164-169. 

Park, C.H., Tulinsky, A. Three-dimensional sfructure of the Kringle sequence structure of profhrombin fragment 1. Biochemistry 25 3977-3982, 1986. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

The constantly increasing amount of data coming from high throughput experimental methods, from genome sequences, from functional- and structural genomics has given a rise to a need for computer-assisted methods to elucidate sequence-structure-function relationships. 

There are two different dimensions, breadth and depth, used to reveal sequence-structure -functional relationships by computational methods [1]. 

Swiss-Prot ia a curated databank of information on protein sequence, structure and function. It can be found under http //www.ebi.ac.uk/swissprot/. 

Hayash C.I., Shipley N., and Lewis R., Hypotheses that correlate the sequence, structure, and mechanical properties of spider silk proteins, Int. J. Biol. Macromol., 24, 271, 1999. 

Improve Understanding of Peptoid Sequence/Structure Relationships... 

Efforts to investigate the questions posed here will lead to more useful peptoid designs while simultaneously leading to a better fundamental understanding of molecular recognition and sequence/structure/function relationships in non-natural, sequence-specific peptidomimetic ohgomers. 

Keddie, E.M., Higazi, T. and Unnasch, T.R. (1998) The mitochondrial genome of Onchocerca volvulus, sequence, structure and phylogenetic analysis. Molecuhr and BiochemicalParasitohgy 95, 111—127. 

Two of the most widely spread and well-studied enterotoxigenic forms of bacterial diarrhea are ETEC and Vibrio cholerae. The toxins they produce, labile toxin (LT) and cholera toxin (CT) respectively, are very similar in primary sequence, structure, and mechanism of action [72]. They are homologous multi-subunit proteins in which the non-toxic B subunit mediates GMj ganglioside binding, and thus are candidates for vaccines that can neutralize toxin activity. 

These families are defined by individual members, which are related to each other by common primary sequences, structural motifs and binding properties (e.g. Fig. 7-1). In spite of differences in the biochemistry and function of each CAM, we can make certain generalizations about how they function in nervous tissue. First, CAMs act at... 

An understanding of the relationships between sequence, structure, and function of /l-solenoid proteins also opens the way for successful de novo molecular design of such molecules, with applications in nanotechnology or biomaterial studies. For example, these structures may allow the assembly of rigid and regular nanoscale lattices and display platforms (Hyman et aL, 2002) that are also durable in their resistance to high temperature, proteases, and other extreme conditions. 

Kajava, A. V. (2001). Review Proteins with repeated sequence—structural prediction and modeling./. Struct. Biol. 134, 132-144. 

McDonnell, A. V., Menke, M., Palmer, N., King, J., Cowen, L., and Berger, B. (2006). Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. Proteins 63, 976-985. 

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