Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

Schäffer, Alejandro A.; Aravind, L.; Madden, Thomas; Shavirin, Serge; Spouge, John L.; Wolf, Yuri I.; Koonin, Eugene V.; Altschul, Stephen F.

doi:10.1093/nar/29.14.2994

Cited by 1,275 publications

(995 citation statements)

References 57 publications

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“…The input data for MODELLER were: (a) the template structure, corresponding to the experimentally-determined structure of human serum albumin, monomer A, obtained from the Protein Data Bank code 1AO6, and (b) a sequence alignment of BSA and human serum albumin, obtained by using the program BLAST [46,47].…”

Section: Computer Modelingmentioning

confidence: 99%

Role of copper,zinc-superoxide dismutase in catalyzing nitrotyrosine formation in murine liver

Zhu

Zhang

Roneker

et al. 2008

Free Radical Biology and Medicine

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The solely known function of Cu,Zn-superoxide dismutase (SOD1) is to catalyze the dismutation of superoxide anion into hydrogen peroxide. Our objective was to determine if SOD1 catalyzed murine liver protein nitration induced by acetaminophen (APAP) and lipopolysaccharide (LPS). Liver and plasma samples were collected from young adult SOD1 knockout mice (SOD1-/-) and wild-type (WT) mice at 5 or 6 h after an ip injection of saline, APAP, or LPS. Hepatic nitrotyrosine formation was induced by APAP and LPS only in the WT mice. The diminished hepatic protein nitration in the SOD1-/-mice was not directly related to plasma nitrite and nitrate concentrations. Similar genotype differences were seen in liver homogenates treated with a bolus of peroxynitrite. Adding only the holo, but not the apo-SOD1 enzyme into the liver homogenates enhanced the reaction in an activity-dependent fashion and nearly eliminated the genotype difference at the high doses. Mass Spectrometry showed 4 more nitrotyrosine residues in bovine serum albumin and 10 more nitrated protein candidates in the SOD1-/-liver homogenates by peroxynitrite with added SOD1. In conclusion, the diminished hepatic protein nitration mediated by APAP or LPS in the SOD1-/-mice was due to the lack of SOD1 activity per se. Keywords SOD1; Protein nitration; Acetaminophen; Peroxynitrite; Lipopolysaccharide; Mouse Although copper,zinc-superoxide dismutase (SOD1) has been widely considered a major intracellular antioxidant enzyme in mammals, its solely known function is to catalyze the conversion of superoxide anion into less active hydrogen peroxide. Indeed, SOD1 is protective against oxidative stress associated with acute paraquat toxicity, myocardial ischemia/reperfusion injury, and N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced dopaminergic neurodegeneration [1][2][3]. Mice deficient in SOD1 develop Address correspondence to: Xin Gen Lei, Department of Animal Science, Cornell University, Ithaca, NY 14853, Tel. 607-254-4703; Fax. 607-255-9829; E-Mail: XL20@cornell.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. [7,8]. These paradoxical findings strongly suggest that SOD1 may exert functions more than just superoxide dismutation. In fact, SOD1 was shown to promote peroxynitrite-mediated nitrotyrosine formation in vitro [9,10]. NIH Public AccessPeroxynitrite is formed by a rapid diffusion-limited, radical-radical coupling reaction between nitric oxide (NO) and superoxide anion [11,12] [24,25,33,34] provide us with an unprecedented opportunity to study the in vivo role of SOD1 in nitrotyrosine formation. Furtherm...

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Section: Computer Modelingmentioning

confidence: 99%

Role of copper,zinc-superoxide dismutase in catalyzing nitrotyrosine formation in murine liver

Zhu

Zhang

Roneker

et al. 2008

Free Radical Biology and Medicine

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“…PSI-BLAST [4,37] is an extremely sensitive comparison tool that has revealed homologies between sequences that previously were recognized only from structure comparison [38]. PSI-BLAST seeks to provide accurate statistical estimates for the similarities it finds [37], although it occasionally gives good scores to unrelated sequences ( Figure 2).…”

Section: Progress In Sequence Similarity Searchingmentioning

confidence: 99%

“…PSI-BLAST seeks to provide accurate statistical estimates for the similarities it finds [37], although it occasionally gives good scores to unrelated sequences ( Figure 2). This sometimes produces misleading results, as the iterative nature of PSI-BLAST makes the inclusion of a nonhomologous sequence in the PSSM difficult to detect.…”

Section: Progress In Sequence Similarity Searchingmentioning

confidence: 99%

The limits of protein sequence comparison?

Pearson

Sierk

2005

Current Opinion in Structural Biology

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Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized.

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“…Then, the amino acid sequences of 1F6D, 1IOV, 1L6I, 1YGP, 1Z8D, 2ATI, 2C4M, 2QLL, 2QN1, 2ZB2, 3CEH, 3DD1, 3SOJ, 4EJ2 and FJ754277.1, were employed in a search for similar amino acid sequences of insects in the nonredundant (nr) database of the NCBI Portal (http://blast.ncbi.nlm. nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome, accessed on September 5, 2013), using the software BLASTP 2.2.28+ 32,33 with DELTA-BLAST 34 set to the default parameters. Only the resulting amino acid sequences with query coverage and identity higher than 90% and 36%, respectively, were selected for the next step, which comprised alignment of all sequences of amino acids from glycogen phosphorylases, as described above.…”

Section: Glycogen Phosphorylasementioning

confidence: 99%

URSOLIC ACID AND CIS-TILIROSIDE PRODUCED BY Merremia tomentosa AFFECT OVIPOSITION OF Leucoptera coffeella ON COFFEE PLANTS

Júnior¹,

Lopes²,

Alves³

et al. 2018

Quim. Nova

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publicado na web em 18/01/2018To contribute to the development of new products to control the coffee leaf miner (Leucoptera coffeella), which is a major pest for coffee plants, this work aimed to select plant species able to produce substances active against this insect and to identify the active substances in the selected plant and their protein targets in the insect. Among the extracts of nineteen plant species, only that from leaves of Merremia tomentosa (Choisy) Hall. f. (Convolvulaceae) reduced the oviposition of L. coffeella on leaves of coffee plants. This extract was submitted to successive fractionation steps to achieve the isolation and identification of two active substances, ursolic acid (UA) and cis-tiliroside (CT). An in silico study showed that UA inhibits glycogen phosphorylases (GP) by binding to their allosteric site, while CT probably inhibits xanthine dehydrogenases (XT). As both GP and XT appear to be essential enzymes for insects, these results suggest that, during evolution, L. coffeella learned to identify plants producing inhibitors of these enzymes to avoid oviposition on such plants. Thus, both UA and CT have potential to be used as lead compounds in the development of new products for the control of the coffee leaf miner.

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Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

Cited by 1,275 publications

References 57 publications

Role of copper,zinc-superoxide dismutase in catalyzing nitrotyrosine formation in murine liver

Role of copper,zinc-superoxide dismutase in catalyzing nitrotyrosine formation in murine liver

The limits of protein sequence comparison?

URSOLIC ACID AND CIS-TILIROSIDE PRODUCED BY Merremia tomentosa AFFECT OVIPOSITION OF Leucoptera coffeella ON COFFEE PLANTS

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