Enhanced genome annotation using structural profiles in the program 3D-PSSM

Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London, WC2A 3PX, England.
Journal of Molecular Biology (Impact Factor: 3.96). 07/2000; 299(2):499-520. DOI: 10.1006/jmbi.2000.3741
Source: PubMed

ABSTRACT A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server:

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    • "The search was performed using BLAST (Altschul et al., 1990). In order to authenticate the search results sequence–structural alignments were performed using FUGUE (Shi et al., 2001) and 3D-PSSM (Kelley et al., 2000). The results indicated that the A-chain of the X-ray crystal structure of lactose permease from Escherichia coli (pdb code: 2V8N) could be used as a template for homology modeling. "
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    ABSTRACT: One of the oldest known gene clusters that are involved in biological oxidation processes is the sox operon. This operon is present in different microbial species. In the present study an attempt has been made to analyze the probable structural role of SoxT protein from Pseudaminobacter salicylatoxidans. This protein has been predicted to be a permease-like protein. A comparative model of the protein has been made and analyzed. The possible membrane spanning region of the protein has been detected by structural bioinformatics approach. The inducer of the sulfur oxidation process has been predicted. And thereby the plausible mechanism of the transport of the sulfur anion inside the bacterial cell has been elucidated. Since this is the first study regarding the structural aspect of the protein this study may shed light on the theory of the yet unknown molecular mechanism of the sulfur oxidation process by sox operon.
    Gene 03/2013; 521(1). DOI:10.1016/j.gene.2013.02.038 · 2.08 Impact Factor
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    • "New implementations for structure prediction on a genomic scale and for discriminating superfamilies from one another were added recently (Lobley, 2009). 3D-PSSM (Kelley et al., 2000) is using PSIPRED to predict the secondary structure of target proteins, and PSI-BLAST for sequence-profile alignments. The target profiles are aligned against 3D position-specific scoring matrices (PSSMs), which are generated for the templates within the fold library. "
    Protein Engineering, 02/2012; , ISBN: 978-953-51-0037-9
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    • "PTI-I inhibitors are proteins of approximately 8 kDa generally lacking disulfide bonds that contain a family signature sequence [FYW]- P-[EQH]-[LIV] 2 -G-x 2 -[STAGV]-x 2 that is located in the Nterminus of the peptide (Habib and Fazili, 2007; Hulo et al., 2008). However, UPI lacks this family signature (Figure 6a), and protein fold-recognition software (Kelley et al., 2000) predicted that it has only 15% structural homology to a putative serine PI. Promoter comparison between UPI and other predicted Arabidopsis PR-6 genes showed no shared defense-related cis-acting regulatory elements (Lescot et al., 2002). "
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    ABSTRACT: Protease inhibitors (PIs) function in the precise regulation of proteases, and are thus involved in diverse biological processes in many organisms. Here, we studied the functions of the Arabidopsis UNUSUAL SERINE PROTEASE INHIBITOR (UPI) gene, which encodes an 8.8 kDa protein of atypical sequence relative to other PIs. Plants harboring a loss-of-function UPI allele displayed enhanced susceptibility to the necrotrophic fungi Botrytis cinerea and Alternaria brassicicola as well as the generalist herbivore Trichoplusia ni. Further, ectopic expression conferred increased resistance to B. cinerea and T. ni. In contrast, the mutant has wild-type responses to virulent, avirulent and non-pathogenic strains of Pseudomonas syringae, thus limiting the defense function of UPI to necrotrophic fungal infection and insect herbivory. Expression of UPI is significantly induced by jasmonate, salicylic acid and abscisic acid, but is repressed by ethylene, indicating complex phytohormone regulation of UPI expression. The upi mutant also shows significantly delayed flowering, associated with decreased SOC1 expression and elevated levels of MAF1, two regulators of floral transition. Recombinant UPI strongly inhibits the serine protease chymotrypsin but also weakly blocks the cysteine protease papain. Interestingly, jasmonate induces intra- and extracellular UPI accumulation, suggesting a possible role in intercellular or extracellular functions. Overall, our results show that UPI is a dual-specificity PI that functions in plant growth and defense, probably through the regulation of endogenous proteases and/or those of biotic invaders.
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