A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm

Pasquier, Claude; Promponas, Vasilis J.; Palaios, Giorgos; Hamodrakas, J. S.; Hamodrakas, Stavros J.

doi:10.1093/protein/12.5.381

Cited by 156 publications

(96 citation statements)

References 11 publications

(16 reference statements)

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“…Clones were sequenced in both directions by dideoxy sequencing at the UCSF Biomolecular Resource Center. Analysis of sequence data was performed using the Basic Local Alignment Search Tool (BLAST) program of the National Center for Biotechnology Information (25), the DNASTAR program, and the PRED-TMR algorithm for transmembrane segment determination (26).…”

Section: Methodsmentioning

confidence: 99%

“…As also seen with falcipain-1, the falcipain-2 prodomain is unusually large, with minimal amino-terminal sequence conservation, but modest conservation of the most carboxyl-terminal sequence (for the 79 carboxyl-terminal amino acids of the falcipain-2 prodomain, identity was 34% between falcipain-1 and falcipain-2 and 33% between falcipain-2 and papain). Falcipain-2 lacks a typical signal sequence, but does contain a 20-amino acid hydrophobic stretch that is predicted by the PRED-TMR algorithm to represent a transmembrane domain (26).…”

Section: Falcipain-2 a P Falciparum Trophozoite Hemoglobinasementioning

confidence: 99%

See 1 more Smart Citation

Characterization of Native and Recombinant Falcipain-2, a Principal Trophozoite Cysteine Protease and Essential Hemoglobinase ofPlasmodium falciparum

Shenai¹,

Sijwali²,

Singh

et al. 2000

Journal of Biological Chemistry

337

362

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Trophozoites of the malaria parasite Plasmodium falciparum hydrolyze erythrocyte hemoglobin in an acidic food vacuole to provide amino acids for parasite protein synthesis. Cysteine protease inhibitors block hemoglobin degradation, indicating that a cysteine protease plays a key role in this process. A principal trophozoite cysteine protease was purified by affinity chromatography. Sequence analysis indicated that the protease is encoded by a previously unidentified gene, falcipain-2. Falcipain-2 was predominantly expressed in trophozoites, was concentrated in food vacuoles, and was responsible for at least 93% of trophozoite soluble cysteine protease activity. A construct encoding mature falcipain-2 and a small portion of the prodomain was expressed in Escherichia coli and refolded to active enzyme. Specificity for the hydrolysis of peptide substrates by native and recombinant falcipain-2 was very similar, and optimal at acid pH in a reducing environment. Under physiological conditions (pH 5.5, 1 mM glutathione), falcipain-2 hydrolyzed both native hemoglobin and denatured globin. Our results suggest that falcipain-2 can initiate cleavage of native hemoglobin in the P. falciparum food vacuole, that, following initial cleavages, the protease plays a key role in rapidly hydrolyzing globin fragments, and that a drug discovery effort targeted at this protease is appropriate.

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Section: Methodsmentioning

confidence: 99%

Section: Falcipain-2 a P Falciparum Trophozoite Hemoglobinasementioning

confidence: 99%

Characterization of Native and Recombinant Falcipain-2, a Principal Trophozoite Cysteine Protease and Essential Hemoglobinase ofPlasmodium falciparum

Shenai¹,

Sijwali²,

Singh

et al. 2000

Journal of Biological Chemistry

337

362

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“…We first performed an alignment between all sequences (ClustalW) (18) and then used the program TMpred (19) to predict in each sequence the location of the transmembrane regions.…”

Section: Methodsmentioning

confidence: 99%

Mutational Analysis of the Hexose Transporter of Plasmodium falciparum and Development of a Three-dimensional Model

Manning¹,

Woodrow²,

Zúñiga³

et al. 2002

Journal of Biological Chemistry

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Plasmodium falciparum infection kills more than 1 million children annually. Novel drug targets are urgently being sought as multidrug resistance limits the range of treatment options for this protozoan pathogen. PfHT1, the major hexose transporter of P. falciparum is a promising new target. We report detailed structurefunction studies on PfHT1 using site-directed mutagenesis approaches on residues located in helix V (Q169N) and helix VII ( 302 SGL 3 AGT). Studies with hexose analogues in these mutants have established that hexose recognition and permeation are intimately linked to these helices. A "fructose filter" effect results from the Q169N mutation (abolishing fructose uptake but preserving affinity and transport of glucose, as reported in Woodrow, C. J., Burchmore, R. J. S., and Krishna, S. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 9931-9936). Associated changes in competition for glucose uptake by C-2, C-3, and C-6 glucose analogues compared with native PfHT1 indicate subtle alterations in substrate interaction in this mutant. The K m values for glucose uptake in helix VII mutants are also similar to native PfHT1. Hydrogen bonding to positions C-5 and C-6 in glucose analogues becomes relatively more important in these mutants compared with native PfHT1. To increase understanding of hexose permeation pathways in PfHT1, we have developed the first three-dimensional model for PfHT1. As predicted for GLUT1, the principal mammalian glucose transporter, PfHT1 contains a main and an auxiliary channel. After modeling, the Q169N mutation leads predominantly to local structural changes, including displacement of neighboring helix IV. The 302 SGL position in helix VII lies in the same plane as Gln-169 in helix V but is also adjacent to the main hexose permeation pathway, consistent with results from experiments mutating this triplet motif. Furthermore, there are obvious structural and functional differences between GLUT1 and PfHT1 that can now be explored in detail using the approaches presented here.

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“…PREDiction of TM Regions (PRED-TMR) (117) is based on a standard hydrophobicity analysis to detect potential termini (starts and ends) of AHTM and TMB domains. Thereby, it predicts TM proteins discarding any highly hydrophobic stretches of residues without clear termini (117) (Table VIII). Fig.…”

Section: Protein Secondary Structure Predictionmentioning

confidence: 99%

State-of-the-art bioinformatics protein structure prediction tools (Review)

Michalopoulos

2011

Int J Mol Med

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Abstract. Knowledge of the native structure of a protein could provide an understanding of the molecular basis of its function. However, in the postgenomics era, there is a growing gap between proteins with experimentally determined structures and proteins without known structures. To deal with the overwhelming data, a collection of automated methods as bioinformatics tools which determine the structure of a protein from its amino acid sequence have emerged. The aim of this paper is to provide the experimental biologists with a set of cutting-edge, carefully evaluated, user-friendly computational tools for protein structure prediction that would be helpful for the interpretation of their results and the rational design of new experiments.

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A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm

Cited by 156 publications

References 11 publications

Characterization of Native and Recombinant Falcipain-2, a Principal Trophozoite Cysteine Protease and Essential Hemoglobinase ofPlasmodium falciparum

Characterization of Native and Recombinant Falcipain-2, a Principal Trophozoite Cysteine Protease and Essential Hemoglobinase ofPlasmodium falciparum

Mutational Analysis of the Hexose Transporter of Plasmodium falciparum and Development of a Three-dimensional Model

State-of-the-art bioinformatics protein structure prediction tools (Review)

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