TeXshade: shading and labeling of multiple sequence alignments
  using LaTeX2e

Beitz, Eric

doi:10.1093/bioinformatics/16.2.135

Cited by 314 publications

(230 citation statements)

References 14 publications

Supporting

Mentioning

227

Contrasting

Unclassified

Order By: Relevance

“…Structure-based protein alignments were calculated by using the CLUSTAL method with the PAM250 matrix. Alignments and topology plots were generated by using the TEXSHADE and TEXTOPO programs (14,15). For a structural model of PfAQP aquaglyceroporin, the alignment with GlpF was manually adjusted.…”

Section: Methodsmentioning

confidence: 99%

Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis

Beitz

Pavlovic-Djuranovic

Yasui

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

The selectivity of aquaporins for water and solutes is determined by pore diameter. Paradoxically, the wider pores of glycerol facilitators restrict water passage by an unknown mechanism. Earlier we characterized an aquaglyceroporin from Plasmodium falciparum with high permeability for both glycerol and water. We use point mutations to demonstrate that amino acids directly lining the pore are not responsible for the excellent water permeability of the Plasmodium aquaglyceroporin but affect permeability of pentitols. Within a conserved WET triad in the extracellular C-loop we identified a Plasmodium aquaglyceroporin-specific glutamate (E125) located in proximity to a conserved arginine (R196) at the pore mouth. Mutation of E125 to serine largely abolished water permeability. Concomitantly, the activation energy for water permeation was increased by 4 kcal͞mol. Mutation of the adjacent tryptophan to cysteine led to irreversible inhibition of water passage by Hg 2؉ . This unequivocally proves the proximity of the couple W124͞E125 close to the pore mouth. We conclude that in the Plasmodium aquaglyceroporin the electrostatic environment at the extracellular pore entry regulates water permeability.A functional divide separates the two major branches of the aquaporin family into water specific channels (orthodox aquaporins) and solute facilitators with restricted water permeability [aquaglyceroporins; reviewed by Borgnia et al. (1)]. Prototypes of either group, mammalian aquaporin (AQP1) (2-4) and Escherichia coli glycerol facilitator (GlpF) (5, 6) have been structurally resolved with high resolution and shown to be surprisingly similar (7). The carbon backbone of AQP1 and GlpF can be superimposed with minor deviations. Both pore layouts are characterized by a ladder of evenly spaced main chain carbonyl oxygens in Ϸ3.2-Å steps in an otherwise hydrophobic environment (positions 66-68 and 189-191 in Fig. 1B). The oxygens funnel water or solute molecules through the pore via hydrogen bonding. The ladder is interrupted in the center of the channel by amide nitrogens from two invariant asparagines [N70(68) and N193(203) in Fig. 1B; the prototypical GlpF sequence is used as a reference throughout and the respective GlpF amino acids and positions are added in parenthesis as descriptors whenever an amino acid aquaglyceroporin from Plasmodium falciparum (PfAQP) is mentioned]. The pore center is separated from the carbonyl ladder by an Ϸ5.5-Å wide hydrophobic ring on either side. Further, both pore types share a positively charged arginine in juxtaposition to two aromatic residues at the extracellular pore entry [R196(206), W50(48), and F190(200)] in Fig. 1B).The water specificity of orthodox aquaporins is rationalized by a constriction of Ϸ2.8 Å in the arginine͞aromatic region, which perfectly matches the size of a water molecule and excludes the more protuberant glycerol (4). Aquaglyceroporins have pores of Ϸ3.5 Å to accommodate the passage of glycerol and other uncharged solutes but paradoxically impede water permeation (6)...

show abstract

Section: Methodsmentioning

confidence: 99%

Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis

Beitz

Pavlovic-Djuranovic

Yasui

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

show abstract

“…For each model, the CHL molecule was taken from its respective template and energy minimized in the catalytic site. Multiple sequence alignment representation, as well as calculation of sequence identity and similarity, was done with TEXShade (Beitz, 2000). Structure images were generated with PyMOL 1.7.1.3 (Schrödinger, 2010).…”

Section: Methodsmentioning

confidence: 99%

Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida

et al. 2016

View full text Add to dashboard Cite

Aeromonas salmonicida subsp. salmonicida is a fish pathogen known to have a rich plasmidome. In the present study, we discovered an isolate of this bacterium bearing an additional unidentified small plasmid. After having sequenced the DNA of that isolate by nextgeneration sequencing, it appeared that the new small plasmid is a ColE1-type replicon plasmid, named here pAsa7. This plasmid bears a functional chloramphenicol-acetyltransferase-encoding gene (cat-pAsa7) previously unknown in A. salmonicida and responsible for resistance to chloramphenicol. A comparison of pAsa7 with pAsa2, the only known ColE1-type replicon plasmid usually found in A. salmonicida subsp. salmonicida, revealed that even if both plasmids share a high structural similarity, it is still unclear if pAsa7 is a derivative of pAsa2 since they showed several mutations at the nucleotide level. Transcriptomic analysis revealed that the catpAsa4 gene, another chloramphenicol-acetyltransferase-encoding gene, found on the large plasmid pAsa4, was significantly more transcribed than cat-pAsa7. This was correlated with a higher chloramphenicol resistance for isolates bearing pAsa4 compared with the one having pAsa7. Finally, a phylogenetic analysis showed that both CAT-pAsa4 and CAT-pAsa7 proteins were in different clusters. The clustering was supported by the identity of residues involved in the catalytic site. In addition, to give a better understanding of the large drug-resistance panel of A.salmonicida, this study reinforces the hypothesis that A. salmonicida subsp. salmonicida is a considerable reservoir for mobile genetic elements such as plasmids.

show abstract

“…Phylogenetic analyses were carried out using TREECON (version 3.1b) using the Kimura model and the neighbour-joining method (Van de Peer & De Wachter, 1994). Substitutions (synonymous and non-synonymous), types of site and p distances (pS and pN) were calculated by the Nei-Gojobori method, whereas overall mean distances and group distances were computed using the Kimura two-parameter model, using MEGA3 (version 3.1) (Kumar et al, 2004 On: Sun, 13 May 2018 07:20:17 alignments were produced using the alignment shading software TeXshade (Beitz, 2000).…”

Section: Methodsmentioning

confidence: 99%

A cross-reactive neisserial antigen encoded by the NMB0035 locus shows high sequence conservation but variable surface accessibility

Arenas

Abel

Sánchez

et al. 2008

Journal of Medical Microbiology

View full text Add to dashboard Cite

The meningococcal NMB0035 locus encodes a 47 kDa outer-membrane protein that is highly conserved antigenically, and is able to induce antibodies during infection and bactericidal responses in vitro. This study analysed the surface exposure of this protein using specific antibodies in flow cytometry assays and determined its nucleotide sequence in 33 Neisseria strains. Genomic analyses revealed no significant differences in the nucleotide or amino acid sequences, but flow cytometry showed that surface accessibility was highly variable among the strains. These results suggest that masking by and/or association with lipo-oligosaccharides or other membrane molecules can be crucial for antigen accessibility, which must be thoroughly analysed in new vaccine candidates.

show abstract

TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e

Abstract: eric.beitz@uni-tuebingen.de

Cited by 314 publications

References 14 publications

Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis

Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis

Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida

A cross-reactive neisserial antigen encoded by the NMB0035 locus shows high sequence conservation but variable surface accessibility

Contact Info

Product

Resources

About