Protein structure fold recognition

Wallace, B. A., and Janes, R. W. (2001). Synchrotron radiation circular dichroism spectroscopy of proteins Secondary structure, fold recognition and structural genomics. Curr. Opin. Chem. Biol. 5, 567-571. 

Essen, L., Siegert, R., Lehmann, W.D., Oesterhelt, D. 1998. Lipid patches in membrane protein oligomers crystal structure of the bacteriorhodopsin-Iipid complex. Proc. Natl. Acad. Sci. USA 95 11673-11678. Ferguson, A.D., Welte, W., Hofmann, E., Lindner, B., Holst, O., Coulton, J.W., et al. 2000. A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins. Structure Fold. Des. 8 585-592. 

Hughey, PROTEINS Structure, Function, and Genetics, 53,491 (2003). Combining Local-Structure, Fold-Recognition, and New Fold Methods for Protein Structure Prediction. 

Rice, D.W., et al. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. /. Mol. Biol. 267 1026-1038, 1997. 

Proteins derive their powerful and diverse capacity for molecular recognition and catalysis from their ability to fold into defined secondary and tertiary structures and display specific functional groups at precise locations in space. Functional protein domains are typically 50-200 residues in length and utilize a specific sequence of side chains to encode folded structures that have a compact hydrophobic core and a hydrophilic surface. Mimicry of protein structure and function by non-natural ohgomers such as peptoids wiU not only require the synthesis of >50mers with a variety of side chains, but wiU also require these non-natural sequences to adopt, in water, tertiary structures that are rich in secondary structure. 

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. 

PROTEIN FOLD RECOGNITION USING SEQUENCE PROFILES AND ITS APPLICATION IN STRUCTURAL GENOMICS... 

A vital component of globular protein structure, yet one that is very hard to characterize, is the (3-turn. These have importance in folding the protein and are often recognition sites for interactions, but have many detailed structural variations that lead to a variety of spectral signatures. Several researchers have attempted to categorize turns by detection of bands at... 

DNA-binding proteins contact their recognition sequences via defined structural elements, termed DNA-binding motifs (overview Pabo Sauer, 1992 Burley, 1994). DNA-binding motifs are often found in structural elements of the protein which can fold independently from the rest of the protein and therefore represent separate DNA-binding domains. They can, however, also occur within sequence elements which can not independently fold, but whose folding depends on the tertiary structure of the rest of the protein. 

Computation proteome annotation is the process of proteome database mining, which includes structure/fold prediction and functionality assignment. Methodologies of secondary structure prediction and problems of protein folding are discussed. Approaches to identify functional sites are presented. Protein structure databases are surveyed. Secondary structure predictions and pattern/fold recognition of proteins using the Internet resources are described. 

PROTEIN FOLDING PROBLEMS AND FUNCTIONAL SITES 12.2.1. Fold Recognition and Structure Alignment... 

Only protein structures solved to resolution better than 3.0 A from the Protein Data Bank are considered. The 3D templates are generated with CORA (Conserved Residue Attributes) for recognition of structural relatives in each fold group (Orengo, 1999). The CATH Architectural descriptions that denote the arrangements of secondary structures are given in Table 12.2. 

The 3D-PSSM (Kelley et ah, 2000) server at http //www.bmm.icnet.uk/ 3dpssm/ offers online protein fold recognition. On the submission form, enter your e-mail address and a one-line description of the query protein, then paste the query sequence into the sequence box and click the Submit button. The query sequence is used to search the Fold library for homologues. You will be informed of the URL where the result is located for 4 days. The output includes a summary table (hits with statistics models that can be viewed with RasMol classifications and links) and fold recognition by 3D-PSSM with a printout as exemplified in Figure 12.13. The alignment displays consensus sequence, secondary structures (C for coil, E for extended, and H for helix), and core score (0 for exterior to 9 for interior core). 

Figure 12.13. Protein fold recognition by 3D PSSB. The summary fold recognition results of cod alcohol dehydrogenase analyzed by 3D PSSB (secondary structure predic-...

PSIPRED Automatic sequence alignment, protein fold recognition, and secondary structure prediction web server 173 bioinf.cs.ucl.ac.uk/psipred/... 

A. Kolinski, J.M. Bujnicki, Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 61(S7), 84-97 (2005)... 

The correctness of hits corresponding to families with known structural information is further verified by employing the protein fold recognition method PHYRE (Protein Homology/analogY Recognition Engine) version 0.2, which assesses the compatibility of a sequence to a three-dimensional structure (29). 

PTPS (6-Pyruvoyl Tetmhydropterin Synthase). 6-Pyruvoyl tetrahy-dropterin synthase catalyzes formation of tetrahydrobiopterin biosynthesis. Tetrahydrobiopterin is a cofactor for several important enzymes, such as aromatic amino acid hydroxylases and nitric oxide synthase (57). H. pylori protein HPAG1 0913 shares homology with members of the protein domain family PTPS. H. pylori protein shares poor sequence identity of 14% with the PTPS profile at an E-value of 10 10 and covers about 95% of the length of the profile. Fold recognition results also confirm the relationship between H. pylori protein and the PTPS protein domain family. A fold recognition algorithm ensures fitness of the H. pylori protein sequence on the three-dimensional structure of PTPS from... 

---