SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

Viklund, Håkan; Bernsel, Andreas; Skwark, Marcin J.; Elofsson, Arne

doi:10.1093/bioinformatics/btn550

Cited by 213 publications

(182 citation statements)

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“…In essence, a great concentration of turn-promoting residues is found in the region connecting HR1 and HR2. Thus, in the membrane-bound form, we can expect the turn of viroporin 2B to be centered on 56 RNYED 60 . Interestingly, previous mutagenesis studies using the CBV 2B protein showed that the negatively charged residues found in this short hydrophilic turn between HR1 and HR2 are indeed important for the membrane-active character of 2B protein (16).…”

Section: Discussionmentioning

confidence: 99%

Membrane Integration of Poliovirus 2B Viroporin

Martínez-Gil

Bañó‐Polo

Redondo

et al. 2011

J Virol

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Virus infections can result in a variety of cellular injuries, and these often involve the permeabilization of host membranes by viral proteins of the viroporin family. Prototypical viroporin 2B is responsible for the alterations in host cell membrane permeability that take place in enterovirus-infected cells. 2B protein can be localized at the endoplasmic reticulum (ER) and the Golgi complex, inducing membrane remodeling and the blockade of glycoprotein trafficking. These findings suggest that 2B has the potential to integrate into the ER membrane, but specific information regarding its biogenesis and mechanism of membrane insertion is lacking. Here, we report experimental results of in vitro translation-glycosylation compatible with the transloconmediated insertion of the 2B product into the ER membrane as a double-spanning integral membrane protein with an N-/C-terminal cytoplasmic orientation. A similar topology was found when 2B was synthesized in cultured cells. In addition, the in vitro translation of several truncated versions of the 2B protein suggests that the two hydrophobic regions cooperate to insert into the ER-derived microsomal membranes.Virus infections can lead to a variety of cellular injuries, and usually these involve the restructuring of host membrane systems. Viroporins are a group of small virally encoded proteins that interact with cellular membranes to modify permeability and promote the release of viral particles. A typical feature exhibited by viroporins is the presence of at least one membrane-spanning helix anchoring the protein into membranes. After membrane insertion, their oligomerization creates hydrophilic channels or pores (22).Poliovirus is the enterovirus prototype member of the Picornaviridae family. This small, nonenveloped, icosahedral virus possesses a single-stranded 7.5-kb positive-sense RNA genome that encodes a single polyprotein. Polyprotein processing by virus-encoded proteases yields the structural P1 region proteins that encapsidate viral RNA and the nonstructural P2 and P3 region proteins involved in the replication of the viral RNA and membrane permeabilization (2). Nonstructural 2B protein is one of the products generated on processing the P2 region (62). Viroporin 2B has been identified as one of the viral proteins responsible for the alterations in host cell membrane permeability that take place in enterovirus-infected cells. Different 2B proteins expressed in cells have been localized at the endoplasmic reticulum (ER), Golgi complex, and, to a lesser extent, to the plasma and mitochondrial membranes (18,31,49,58). Biochemical and structural data indicate that viroporins form homo-oligomers that create pores in the ER and Golgi complex membranes (1,16,17,30,59). However, experimental data dealing with the mechanism of the membrane integration of the 2B product are lacking to date.The poliovirus 2B viroporin protein is hydrophobic overall and rather small (97 amino acids). Hydrophobicity within the viroporin 2B sequence seems to cluster in two main regions (F...

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Section: Discussionmentioning

confidence: 99%

Membrane Integration of Poliovirus 2B Viroporin

Martínez-Gil

Bañó‐Polo

Redondo

et al. 2011

J Virol

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“…Secondary structure predictions were made by SAM and PSI-PRED (19,22). Transmembrane helix topology predictions were made using TMHMM, Memsat, and Spoctopus (22,31,39). Tertiary predictions were performed using RosettaMembrane (2).…”

Section: Construction Of Csfv Mutantsmentioning

confidence: 99%

Classical Swine Fever Virus p7 Protein Is a Viroporin Involved in Virulence in Swine

Gladue

Holinka

Largo

et al. 2012

J Virol

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The nonstructural protein p7 of classical swine fever virus (CSFV) is a small hydrophobic polypeptide with an apparent molecular mass of 6 to 7 kDa. The protein contains two hydrophobic stretches of amino acids interrupted by a short charged segment that are predicted to form transmembrane helices and a cytosolic loop, respectively. Using reverse genetics, partial in-frame deletions of p7 were deleterious for virus growth, demonstrating that CSFV p7 function is critical for virus production in cell cultures. A panel of recombinant mutant CSFVs was created using alanine scanning mutagenesis of the p7 gene harboring sequential three- to six-amino-acid residue substitutions spanning the entire protein. These recombinant viruses allowed the identification of the regions within p7 that are critical for virus production in vitro. In vivo , some of these viruses were partially or completely attenuated in swine relative to the highly virulent parental CSFV Brescia strain, indicating a significant role of p7 in CSFV virulence. Structure-function analyses in model membranes emulating the endoplasmic reticulum lipid composition confirmed that CSFV p7 is a pore-forming protein, and that pore-forming activity resides in the C-terminal transmembrane helix. Therefore, p7 is a viroporin which is clearly involved in the process of CSFV virulence in swine.

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“…Machine learning-based predictors, trained and validated using topology data derived from structural data combined with evolutionary information, now achieve prediction accuracies in the range 80-90% (2,3). Another approach, based on an experimental scale of position-specific amino acid contributions to membrane insertion free energy, achieves similar accuracy suggesting that predicting TMP topology from first principles is an achievable goal (4).…”

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confidence: 96%

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

Nugent

Jones

2012

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

176

152

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A new de novo protein structure prediction method for transmembrane proteins (FILM3) is described that is able to accurately predict the structures of large membrane proteins domains using an ensemble of two secondary structure prediction methods to guide fragment selection in combination with a scoring function based solely on correlated mutations detected in multiple sequence alignments. This approach has been validated by generating models for 28 membrane proteins with a diverse range of complex topologies and an average length of over 300 residues with results showing that TM-scores > 0.5 can be achieved in almost every case following refinement using MODELLER. In one of the most impressive results, a model of mitochondrial cytochrome c oxidase polypeptide I was obtained with a TM-score > 0.75 and an rmsd of only 5.7 Å over all 514 residues. These results suggest that FILM3 could be applicable to a wide range of transmembrane proteins of as-yetunknown 3D structure given sufficient homologous sequences.structural bioinformatics | protein modeling | compressed sensing | amino acid contacts A lpha-helical transmembrane proteins (TMPs) constitute roughly 30% of a typical genome and play critical roles in a diverse range of biological processes whereas many are also important drug targets. Despite the recent increase in the number of solved TMP crystal structures, coverage of TMP fold space remains sparse, particularly at high resolutions, with close to 300 unique structures deposited as of 2011 (1). Computational methods to predict TMP structure are therefore vital in helping to further our knowledge of the structure and function of these proteins.To date, TMP structure prediction has been dominated by topology prediction. Machine learning-based predictors, trained and validated using topology data derived from structural data combined with evolutionary information, now achieve prediction accuracies in the range 80-90% (2, 3). Another approach, based on an experimental scale of position-specific amino acid contributions to membrane insertion free energy, achieves similar accuracy suggesting that predicting TMP topology from first principles is an achievable goal (4).As with globular proteins, predicting the structure of TMPs by homology modeling is very effective particularly when TMP-specific methods are used (5); however, the paucity of solved structures means that homology modeling can only be applied to a minority of TMP families. With this in mind, a small number of de novo modeling approaches, which attempt to build 3D models for TMPs without the use of homology to known structures, have also been developed.FILM (6), a modification of the globular protein structure prediction method FRAGFOLD (7, 8), attempts to assemble folds from supersecondary structural fragments taken from a library of highly resolved protein structures using simulated annealing. FILM differs from FRAGFOLD in the addition of a membrane environment potential, derived from the statistical analysis of 640 transmembrane helices, by measuri...

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SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

Abstract: SPOCTOPUS is available as a web server and both the source code and benchmark data are available for download at http://octopus.cbr.su.se/

Cited by 213 publications

References 10 publications

Membrane Integration of Poliovirus 2B Viroporin

Membrane Integration of Poliovirus 2B Viroporin

Classical Swine Fever Virus p7 Protein Is a Viroporin Involved in Virulence in Swine

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

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