scholarly journals Active site sequence representation of human kinases outperforms full sequence for affinity prediction and inhibitor generation: 3D effects in a 1D model

Author(s):  
Jannis Born ◽  
Tien Huynh ◽  
Astrid Stroobants ◽  
Wendy Cornell ◽  
Matteo Manica
1998 ◽  
Vol 42 (2) ◽  
pp. 436-439 ◽  
Author(s):  
T. R. Walsh ◽  
W. A. Neville ◽  
M. H. Haran ◽  
D. Tolson ◽  
D. J. Payne ◽  
...  

ABSTRACT The Aeromonas veronii bv. sobria metallo-β-lactamase gene, imiS, was cloned. The imiS open reading frame extends for 762 bp and encodes a protein of 254 amino acids with a secreted modified protein of 227 amino acids and a predicted pI of 8.1. To confirm the predicted sequence, purified ImiS was digested and the resulting peptides were identified, yielding an identical sequence for ImiS, with 98% identity to CphA. Both possessed the putative active-site sequence Asn-Tyr-His-Thr-Asp at positions 88 to 92, which is unique to the Aeromonas metallo-β-lactamases.


2003 ◽  
Vol 71 (7) ◽  
pp. 4119-4126 ◽  
Author(s):  
Kannan Kunchithapautham ◽  
B. Padmavathi ◽  
R. B. Narayanan ◽  
P. Kaliraj ◽  
Alan L. Scott

ABSTRACT Thioredoxins are a family of small redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase. This results in a supply of reducing equivalents that cells use in a wide variety of biological reactions, which include maintaining reduced forms of the enzymes important for protection against damage from high-energy oxygen radicals, the regulation of transcription factor activity, and the inhibition of apoptosis. Here we report on a new member of the thioredoxin family of proteins from the filarial nematode Brugia malayi, Bm-TRX-1, which defines a new subclass of 16-kDa thioredoxins that occur widely in nematodes, including Caenorhabditis elegans. In addition to being larger than the thioredoxins found in mammalian and bacterial species, the putative active site sequence of Bm-TRX-1, WCPPC, does not conform to the highly conserved WCGPC reported for thioredoxins from mammals to bacteria. Interestingly, an allelic form of Bm-TRX-1 was identified with an active site sequence WCPQC, which appears to be unique to the thioredoxins from filarial species. Bm-TRX-1 was between 98% and 35% identical to thioredoxins from other nematodes and ≈20% identical to the thioredoxins from mammals and Escherichia coli. Bm-TRX-1 was constitutively transcribed throughout the B. malayi life cycle, and Bm-TRX protein was detectable in somatic extracts and excretory-secretory products from adults and microfilariae. Recombinant Bm-TRX-1 had thiodisulfide reductase activity, as measured by the reduction of insulin, and protected DNA from the nicking activity of oxygen radicals. Overexpression of Bm-TRX-1 in a human monocyte cell line negatively regulated tumor necrosis factor alpha-induced p38 mitogen-activated protein kinase activity, suggesting a possible role of the 16-kDa Bm-TRX-1 in immunomodulation.


1971 ◽  
Vol 123 (1) ◽  
pp. 75-82 ◽  
Author(s):  
J. Kay ◽  
A. P. Ryle

Porcine pepsin C is inactivated rapidly and irreversibly by diazoacetyl-dl-norleucine methyl ester in the presence of cupric ions at pH values above 4.5. The inactivation is specific in that complete inactivation accompanies the incorporation of 1mol of inhibitor residue/mol of enzyme and evidence has been obtained to suggest that the reaction occurs with an active site residue. The site of reaction is the β-carboxyl group of an aspartic acid residue in the sequence Ile-Val-Asp-Thr. This sequence is identical with the active-site sequence in pepsin and the significance of this in terms of the different activities of the two enzymes is discussed.


1982 ◽  
Vol 363 (1) ◽  
pp. 487-492 ◽  
Author(s):  
Hajis-Jürgen SCHNEIDER ◽  
Ursula ILLIG ◽  
Elfriede MÜLLER ◽  
Bernt LINZEN ◽  
Friedrich LOTTSPEICH ◽  
...  

1972 ◽  
Vol 149 (1) ◽  
pp. 169-174 ◽  
Author(s):  
Bernard Friedenson ◽  
Irvin E. Liener

2018 ◽  
Author(s):  
Jiajie Xiao ◽  
William H. Turkett

AbstractBackgroundThe Peroxiredoxins (Prx) are a family of proteins that play a major role in antioxidant defense and peroxide-regulated signaling. Six distinct Prx subgroups have been defined based on analysis of structure and sequence regions in proximity to the Prx active site. Analysis of other sequence regions of these annotated proteins may improve the ability to distinguish subgroups and uncover additional representative sequence regions beyond the active site.ResultsThe space of Prx subgroup classifiers is surveyed to highlight similarities and differences in the available approaches. Exploiting the recent growth in annotated Prx proteins, a whole sequence-based classifier is presented that employs support vector machines and a k-mer (k=3) sequence representation.Distinguishing k-mers are extracted and located relative to published active site regions.ConclusionsThis work demonstrates that the 3-mer based classifier can attain high accuracy in subgroup annotation, at rates similar to the current state-of-the-art. Analysis of the classifier’s automatically derived models show that the classification decision is based on a combination of conserved features, including a significant number of residue regions that have not been previously suggested as informative by other classifiers but for which there is evidence of functional relevance.


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