Xylanase homology modeling using the inverse protein folding approach

Chen, Xiannong; Whitmire, David; Bowen, J. Phillip

doi:10.1002/pro.5560050415

Cited by 8 publications

(2 citation statements)

References 18 publications

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“…In comparative modeling, manual adjustments of sequence alignments are used in model building 71. When sequence‐structure alignments generated from fold recognition methods are not suitable for modeling, alignments are made by visual examination of the secondary structural patterns of the target sequence and the template structure 72. To be consistent with most of the threading results of other B30.2‐like domains, we built a model of pyrin based on two Ig‐like folds to infer potential functional sites (Fig.…”

Section: Resultsmentioning

confidence: 99%

Significance of the International Year of Chemistry 2011

Jin

2010

Chemistry A European J

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Section: Resultsmentioning

confidence: 99%

Significance of the International Year of Chemistry 2011

Jin

2010

Chemistry A European J

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“…It showed that structurally conserved regions were reasonably well modeled while non-homologous regions were not. Conformational analysis on numerous modeled structures and their subsequently X-ray determined structures was undertaken [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48]. In 1994, John Moult and his colleagues initiated the critical assessment of techniques for protein structure prediction (CASP) experiments [49] which allowed a worldwide survey of comparative modeling algorithms for a bona fide blind prediction of protein structures [50][51][52][53].…”

Section: Introductionmentioning

confidence: 99%

Identification of Functionally Important Residues in Proteins Using Comparative Models

Chen¹,

Pellequer

2004

CMC

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Rational design in protein engineering leads to significant progresses in medicinal chemistry research. It alleviates the difficulty of exploring unreasonable biological functions. Combining with analysis of biophysical-chemical properties, a three-dimensional (3D) structure provides fruitful information for rational design by revealing functionally important residues. Comparative (homology) modeling, one of the 3D structural prediction techniques, takes advantage of that homologous proteins share similarity in their 3D structures despite the lack of sequence similarity. Of the most value, 3D models provide functional clues even though the function may have been modified during evolution. We illustrate here two applications to medicinal chemistry research where comparative models made a significant improvement on the understanding of relevant biological functions of two proteins. These multiple collaborative projects involve the identification of solvent-exposed residues in a membrane anchoring domain of human coagulation factor V, and revealing critical residues in the interfaces of an antibody and a polynuclear aromatic hydrocarbon ligand. Since the protocol of comparative modeling technique we employed is essential to proposing useful hypotheses for experimental testing, we also present our methodology underlying our modeling programs. Our results show that inaccuracies in comparative models do not hamper functional evaluation as long as an in depth analysis of 3D structures is performed.

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Protein fold analysis of the B30.2-like domain

Seto¹,

Liu²,

Zajchowski³

et al. 1999

Proteins

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The B30.2-like domain occurs in some members of a diverse and growing family of proteins containing zinc-binding B-box motifs, whose functions include regulation of cell growth and differentiation. The B30.2-like domain is also found in proteins without the zinc-binding motifs, such as butyrophilin (a transmembrane glycoprotein) and stonustoxin (a secreted cytolytic toxin). Currently, the function for the B30.2-like domain is not clear and the structure of a protein containing this domain has not been solved. The secondary structure prediction methods indicate that the B30.2-like domain consists of fifteen or fewer beta-strands. Fold recognition methods identified different structural topologies for the B30.2-like domains. Secondary structure prediction, deletion and lack of local sequence identity at the C-terminal region for certain members of the family, and packing of known core structures suggest that a structure containing two beta domains is the most probable of these folds. The most C-terminal sequence motif predicted to be a beta-strand in all B30.2-like domains is a potential subdomain boundary based on the sequence-structure alignments. Models of the B30.2-like domains were built based on immunoglobulin-like folds identified by the fold recognition methods to evaluate the possibility of the B30.2 domain adopting known folds and infer putative functional sites. The SPRY domain has been identified as a subdomain within the B30.2-like domain. If the B30.2-like domain is a subclass of the SPRY domain family, then this analysis would suggest that the SPRY domains are members of the immunoglobulin superfamily.

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Xylanase homology modeling using the inverse protein folding approach

Cited by 8 publications

References 18 publications

Significance of the International Year of Chemistry 2011

Significance of the International Year of Chemistry 2011

Identification of Functionally Important Residues in Proteins Using Comparative Models

Protein fold analysis of the B30.2-like domain

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