Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method

Cserző, Miklós; Wallin, Erik; Simon, István; Heijne, Gunnar von; Elofsson, Arne

doi:10.1093/protein/10.6.673

Cited by 963 publications

(635 citation statements)

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“…To identify conserved domains in FdTonB we analysed the sequence using the National Center for Biotechnology Information (NCBI) Conserved Domains Database (Marchler-Bauer et al, 2009). Putative transmembrane regions were identified using the DAS Transmembrane Prediction server (Cserzö et al, 1997). Sequence similarity analysis to detect FdTonB homologues was conducted using the NCBI BLAST program (Altschul et al, 1990).…”

Section: Methodsmentioning

confidence: 99%

“…Using the DAS Transmembrane Prediction server (Cserzö et al, 1997), we identified the domain encompassing amino acids 21-41 as a putative transmembrane domain. A conserved SXXXH motif (amino acids 29-33), which delimits the minimum required energy-transduction element of TonB proteins, is found within the predicted transmembrane a-helix ( Fig.…”

Section: Bioinformatic Analysis Of Fdtonbmentioning

confidence: 99%

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FdTonB is involved in the photoregulation of cellular morphology during complementary chromatic adaptation in Fremyella diplosiphon

Pattanaik

Montgomery

2010

Microbiology

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We have characterized a Fremyella diplosiphon TonB protein (FdTonB) and investigated its function during complementary chromatic adaptation. Sequence similarity analysis of FdTonB (571 aa) led to identification of several conserved domains characteristic of TonB proteins, including an N-terminal transmembrane domain, a central proline-rich spacer and a C-terminal TonB-related domain (TBRD). We identified a novel glycine-rich domain containing (Gly-X) n repeats. To assess FdTonB function, we constructed a DtonB mutant through homologous recombination based upon truncation of the central proline-rich spacer, glycine-rich domain and TBRD. Our DtonB mutant exhibited an aberrant cellular morphology under green light, with expanded cell width compared to the parental wild-type (WT) strain. The cellular morphology of the DtonB mutant recovered upon WT tonB expression. Interestingly, tonB expression was found to be independent of RcaE. As DtonB and WT strains respond in the same way when grown under iron-replete versus iron-limited conditions, our results suggest that FdTonB is not involved in the classic TonB function of mediating cellular adaptation to iron limitation, but exhibits a novel function related to the photoregulation of cellular morphology in F. diplosiphon.

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Section: Methodsmentioning

confidence: 99%

Section: Bioinformatic Analysis Of Fdtonbmentioning

confidence: 99%

FdTonB is involved in the photoregulation of cellular morphology during complementary chromatic adaptation in Fremyella diplosiphon

Pattanaik

Montgomery

2010

Microbiology

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“…Although Lpp signal peptide cleavage sites are not predicted, the graphical display from this service was particularly useful as it provided an indication of the lengths of predicted signal peptide n-and h-regions relative to the position of the possible lipobox cysteine. Where sequence features required further clarification, other methods for predicting transmembrane domains were also applied including TopPred2 (Claros & von Heijne, 1994 ; http :\\bioweb.pasteur.fr\seqanal\interfaces\ toppred.html) and DAS (Cserzo et al, 1997 ;http :\\www. sbc.su.se\"miklos\DAS\).…”

Section: Methodsmentioning

confidence: 99%

Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes

2002

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INTRODUCTIONThe bacterial cell envelope is of major significance as the focal point for interaction between the bacterium and its environment, notably the host in the case of bacterial pathogens. Bacterial cell envelope proteins thus carry out numerous important functions including roles in adhesion, nutrient acquisition and a variety of interactions with host defences. In Gram-positive bacteria the matrix of peptidoglycan and other wall polymers surrounding the cell is not an efficient barrier to the passage of small macromolecules, due both to its inherent structural permeability and to its turnover during normal cell growth. Indeed, peptidoglycan may be sufficiently permeable as to allow the passage of globular proteins of up to "50 kDa in size (Demchick & Koch, 1996 ;Dijkstra & Keck, 1996). Consequently, in the absence of a retentive outer membrane, Grampositive bacteria have evolved distinct mechanisms for retaining proteins within their cell envelopes, including covalent linkage to the peptidoglycan and non-covalent binding to teichoic acids and other cell envelope polymers (Navarre & Schneewind, 1999 ;Cossart & Jonquieres, 2000 ;Janulczyk & Rasmussen, 2001). Also significant among these mechanisms is membraneanchoring of bacterial lipoproteins (Lpps) by covalent N-terminal lipidation (Braun & Wu, 1994 ; Sutcliffe & Russell, 1995). Lpps in Gram-positive bacteria perform important roles as substrate-binding proteins (SBPs) in ABC transporter systems ; in antibiotic resistance ; in cell signalling ; in protein export and folding ; in sporulation and germination ; in conjugation and various other functions (Sutcliffe & Russell, 1995 valent to those carried out by periplasmic proteins of Gram-negative bacteria.The archetypal bacterial Lpp is the murein lipoprotein of Escherichia coli characterized by Braun and coworkers (reviewed in Braun & Wu, 1994). Structural studies revealed that a diacylglycerol moiety is thioether linked to an N-terminal cysteine of this Lpp and that this lipid group serves to orientate the protein by anchoring it to the inner leaflet of the outer membrane. Chemically identical lipid modifications have since been proposed, primarily on the basis of protein sequence analysis (see below), for a great many proteins in both Gram-positive and Gram-negative bacteria, although relatively few have received extensive biochemical characterization.Biosynthesis of bacterial lipoprotein of the ' Braun ' type proceeds via a well conserved pathway that is apparently unique to prokaryotes (Fig. 1). Following signal-peptidedirected export of the prolipoprotein (proLpp), the enzyme prolipoprotein diacylglycerol transferase (Lgt) uses phospholipid substrates and catalyses the addition of a diacylglycerol lipid unit onto the thiol of a crucial conserved cysteine which is located within a ' lipobox ' motif at the cleavage region of the proLpp signal peptide (Sankaran et al., 1995 ; Qi et al., 1995). Subsequently, the signal peptide is removed by a specific lipoprotein signal peptidase II (Lsp) enzyme which ...

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“…This process was repeated iteratively until most of the amino acids were below 95% cutoff value and residue which lies above 95% cutoff value were subjected to loop modeling in MODELLER. Finally, GPR87 model showing the best PROCHECK and ERRAT plot was then subjected to native protein folding energy evaluation using ProSA server (Wiederstein et al, 2007 DOI:http://dx.doi.org/10.7314/APJCP.2013.14.12.7473 Computational 3-D Analysis of Human GPR87 Protein of: Implications for Structure-Based Drug Design Transmembrane helices prediction and function assignment of GPR87 protein Different servers like DAS, TMHMM, HMMTOP, TMpred, TopPred, SOSUI, SPLIT, and Predictprotein (PHD) servers were accessed to predict and validate the transmembrane helical region (TM region) of GPR87 protein (Hofmann et al, 1993;Claros et al, 1994;Cserzo et al, 1994;Hirokawa et al, 1998;Tusnády et al, 1998;Krogh et al, 2001;Juretic et al, 2002;Jones et al, 2004;Rost et al, 2004). To know the novel functions of GPR87 protein by using a SVMProt server with the aim of support vector machine learning techniques (SVM) which classifies protein into functional families from its primary sequences i.e.…”

Section: Model Validationmentioning

confidence: 99%

Computational Analysis of the 3-D structure of Human GPR87 Protein: Implications for Structure-Based Drug Design

Rani

Nischal²,

Sahoo³

et al. 2013

Asian Pacific Journal of Cancer Prevention

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The G-protein coupled receptor 87 (GPR87) is a recently discovered orphan GPCR which means that the search of their endogenous ligands has been a novel challenge. GPR87 has been shown to be overexpressed in squamous cell carcinomas (SCCs) or adenocarcinomas in lungs and bladder. The 3D structure of GPR87 was here modeled using two templates (2VT4 and 2ZIY) by a threading method. Functional assignment of GPR87 by SVM revealed that along with transporter activity, various novel functions were predicted. The 3D structure was further validated by comparison with structural features of the templates through Verify-3D, ProSA and ERRAT for determining correct stereochemical parameters. The resulting model was evaluated by Ramachandran plot and good 3D structure compatibility was evidenced by DOPE score. Molecular dynamics simulation and solvation of protein were studied through explicit spherical boundaries with a harmonic restraint membrane water system. A DRY-motif (Asp-Arg-Tyr sequence) was found at the end of transmembrane helix3, where GPCR binds and thus activation of signals is transduced. In a search for better inhibitors of GPR87, in silico modification of some substrate ligands was carried out to form polar interactions with Arg115 and Lys296. Thus, this study provides early insights into the structure of a major drug target for SCCs.

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Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method

Cited by 963 publications

References 1 publication

FdTonB is involved in the photoregulation of cellular morphology during complementary chromatic adaptation in Fremyella diplosiphon

FdTonB is involved in the photoregulation of cellular morphology during complementary chromatic adaptation in Fremyella diplosiphon

Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes

Computational Analysis of the 3-D structure of Human GPR87 Protein: Implications for Structure-Based Drug Design

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