SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments

Geourjon, Christophe; Deléage, Gilbert

doi:10.1093/bioinformatics/11.6.681

Cited by 1,262 publications

(921 citation statements)

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“…The amino acid sequence analysis of ScMnn4p revealed a striking lysine/glutamic acid repeat region and also predicted the presence of a-helical conformation. Secondary-structure analysis of Ker1p (Geourjeon & Deleage, 1995), coiledcoil structures (Lupas et al, 1991) and transmembrane domains (Hofmann & Stoffel, 1992) prediction according to Expasy analysis (see Table 3) predicted a transmembrane localization.…”

Section: Resultsmentioning

confidence: 99%

The Candida albicans pH-regulated KER1 gene encodes a lysine/glutamic-acid-rich plasma-membrane protein that is involved in cell aggregation

et al. 2004

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Immunoscreening of a Candida albicans cDNA library with a polyclonal germ-tube-specific antibody (pAb anti-gt) resulted in the isolation of a gene encoding a lysine/glutamic-acid-rich protein, which was consequently designated KER1. The nucleotide and deduced amino acid sequences of this gene displayed no significant homology with any other known sequence. KER1 encodes a 134 kDa lysine (14·5 %)/glutamic acid (16·7 %) protein (Ker1p) that contains two potential transmembrane segments. KER1 was expressed in a pH-conditional manner, with maximal expression at alkaline pH and lower expression at pH 4·0, and was regulated by RIM101. A Δker1/Δker1 null mutant grew normally but was hyperflocculant under germ-tube-inducing conditions, yet this behaviour was also observed in stationary-phase cells grown under other incubation conditions. Western blotting analysis of different subcellular fractions, using as a probe a monospecific polyclonal antibody raised against a highly antigenic domain of Ker1p (pAb anti-Ker1p), revealed the presence of a 134 kDa band in the purified plasma-membrane fraction from the wild-type strain that was absent in the homologous preparation from Δker1/Δker1 mutant. The pattern of cell-wall protein and mannoprotein species released by digestion with β-glucanases, reactive towards pAbs anti-gt and anti-Ker1p, as well as against concanavalin A, was also different in the Δker1/Δker1 mutant. Mutant strains also displayed an increased cell-surface hydrophobicity and sensitivity to Congo red and Calcofluor white. Overall, these findings indicate that the mutant strain was affected in cell-wall composition and/or structure. The fact that the ker1 mutant had attenuated virulence in systemic mouse infections suggests that this surface protein is also important in host–fungus interactions.

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Section: Resultsmentioning

confidence: 99%

The Candida albicans pH-regulated KER1 gene encodes a lysine/glutamic-acid-rich plasma-membrane protein that is involved in cell aggregation

et al. 2004

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“…Sequencing showed a splice site mutation in the last nucleotide position in intron 2, about 121-1G > A, to be responsible for the total exon 3 skipping. Predictions of the secondary protein structure by an IBCPWeb server analysis 15,16 showed the 926T > C mutation to result in limitation of a beta-sheet domain and the 121-1G > A mutation to alter a large domain of both coils and helixes to a small domain of only coils.…”

Section: Danish Mutations and Haplotypes In Pycnodysostosismentioning

confidence: 99%

Cathepsin K gene mutations and 1q21 haplotypes in patients with pycnodysostosis in an outbred population

et al. 2000

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The molecular genetics of the autosomal recessive disorder pycnodysostosis was studied in five independent families from an outbred Caucasian population. We found two new mutations and one recently described mutation in the cathepsin K gene by sequencing DNA from eight patients with pycnodysostosis: a one base transition in exon 8, c926T > C, causing a single amino acid substitution leucine ® proline, L309P; A 3' splice site mutation in intron 2, c121-1G > A, causing deletion of all exon 3, 41V-81Mdel; and the exon 3 missense mutation c236G > A leading to residue G79E. In three of the families patients were homozygous for 926T > C. In the remaining two families patients were heterozygous for 926T > C and 121-1G > A in one case, and for 926T > C and 236G > A in the other case. Assays using genomic DNA were developed for all three mutations. We tested 150 healthy control persons and observed the mutation frequencies: 0 to 300 for 121-1G > A and 236G > A and 1 to 150 for 926T > C. One patient from each family was haplotyped with eight microsatellite markers surrounding the cathepsin K gene on chromosome 1q21. A very rare, P = 1.8 ؋ 10 -6 to P = 0.0004, and highly preserved area around the presumed disease locus was common to all the patients. This haplotype was found on seven chromosomes identical by state, IBS, out of the possible eight carrying the 926T > C mutation. Founder effect, locus homogeneity, and allele heterogeneity regarding pycnodysostosis within this population are discussed. Finally, the first pregnancy and delivery described in a patient with pycnodysostosis is reported.

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“…Secondary structure of the selected protein was predicted employing NPS server [25] using various methods viz. DPM [26], DSC [27], GOR4 [28], HNNC [29], PHD [30], Predator [31], SOPMA [32], SIMPA96 [33] and secondary consensus [34] keeping default parameters for 4 state predictions keeping output width=70.…”

Section: Secondary Structure Prediction From Target Sequencementioning

confidence: 99%

Structural analysis of the Babesia microti thioredoxin reductase: a potential drug target for babesiosis treatment

Arora¹,

Banerjee²,

Narasu³

2018

biomedicalresearch

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Babesia microti, the causative agent of human babesiosis which was endemic in United States and parts of Europe with sporadic cases in other regions is expanding its geographical range. Being a common transfusion threat, Babesia has become a cause of concern in researchers and epidemiologists. Human babesiosis is now recognized as an emerging disease and gains more attention now than ever before. Thioredoxin reductase, a promising drug target in apicomplexan parasite has been validated in several species. This study focused on in-silico analysis of physicochemical properties, functional and structural aspects of thioredoxin reductase of B. microti. Comparative modeling approach was adopted for developing the three dimensional structural model of Thioredoxin reductase of Babesia microti. The model developed was found to be of reasonably good stereo-chemical quality by structure validation servers. This study will provide valuable insights about the function and structure of the enzyme thioredoxin reductase of B. microti and aid in developing effective chemotherapeutic agents for control and treatment of Babesia.

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SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments

Cited by 1,262 publications

References 0 publications

The Candida albicans pH-regulated KER1 gene encodes a lysine/glutamic-acid-rich plasma-membrane protein that is involved in cell aggregation

The Candida albicans pH-regulated KER1 gene encodes a lysine/glutamic-acid-rich plasma-membrane protein that is involved in cell aggregation

Cathepsin K gene mutations and 1q21 haplotypes in patients with pycnodysostosis in an outbred population

Structural analysis of the Babesia microti thioredoxin reductase: a potential drug target for babesiosis treatment

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