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A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation Scott Montgomerie1, Joseph A

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A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation Scott Montgomerie1, Joseph A W202–W209 Nucleic Acids Research, 2008, Vol. 36, Web Server issue Published online 15 May 2008 doi:10.1093/nar/gkn255 PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation Scott Montgomerie1, Joseph A. Cruz1, Savita Shrivastava1, David Arndt1, Mark Berjanskii1 and David S. Wishart1,2,* 1Department of Computing Science and Department of Biological Sciences, University of Alberta and 2National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8 Downloaded from https://academic.oup.com/nar/article-abstract/36/suppl_2/W202/2506231 by guest on 20 March 2019 Received February 1, 2008; Revised April 12, 2008; Accepted April 20, 2008 ABSTRACT an entire bacterial genome in as little as a week (1). It is clear that our capacity to sequence organisms far PROTEUS2 is a web server designed to support outpaces our capacity to manually annotate their genomes comprehensive protein structure prediction and (2). As a result, there is a growing interest in develop- structure-based annotation. PROTEUS2 accepts ing software to facilitate automated or semi-automated either single sequences (for directed studies) or genome annotation (3). At the same time, there is an multiple sequences (for whole proteome annotation) increasing desire to develop automated methods that can and predicts the secondary and, if possible, tertiary generate comprehensive annotations—annotations that structure of the query protein(s). Unlike most other provide detailed information about each protein’s func- tools or servers, PROTEUS2 bundles signal peptide tion, location, interacting partners, substrates, pathways identification, transmembrane helix prediction, and structure. Our laboratory has a long-standing interest transmembrane b-strand prediction, secondary in developing comprehensive, automated genome/pro- structure prediction (for soluble proteins) and homol- teome annotation tools (3–5). We also believe that high- quality structure prediction and modeling can play an ogy modeling (i.e. 3D structure generation) into a important role in facilitating genome annotation. We are single prediction pipeline. Using a combination of not alone in this view. Indeed, structure prediction and progressive multi-sequence alignment, structure- structure modeling (i.e. homology modeling) are quickly based mapping, hidden Markov models, multi- becoming a routine part of many protein analyses and component neural nets and up-to-date databases proteome annotation efforts (6). Annotation systems such of known secondary structure assignments, as BASYS (4), BACMAP (5), PEDANT (7) and others PROTEUS is able to achieve among the highest all depend on large-scale secondary structure predictions reported levels of predictive accuracy for signal to assist in identifying possible functions, to determine peptides (Q2 = 94%), membrane spanning helices subcellular locations or to identify structural genomics (Q2 = 87%) and secondary structure (Q3 score of targets. 81.3%). PROTEUS2’s homology modeling services Beyond its application to routine annotation, structure also provide high quality 3D models that compare prediction can also be used to assess organism-specific trends in secondary structure content, to identify protein favorably with those generated by SWISS-MODEL ˚ folds, to identify domains, and to estimate the proportion and 3D JigSaw (within 0.2 A RMSD). The average of ‘unfolded’ or unstructured proteins in a given genome PROTEUS2 prediction takes »3 min per query (8–10). It is also common to use structure predictions or sequence. The PROTEUS2 server along with source structure modeling to decide where and how to subclone code for many of its modules is accessible a http:// protein fragments for expression, where to join or insert wishart.biology.ualberta.ca/proteus2. gene fragments, or where to add affinity tags for protein purification. It is also possible to use secondary structure prediction to calibrate circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) measure- INTRODUCTION ments when monitoring the folding or unfolding proteins Ten years ago, the sequencing of whole genomes was a with no known 3D structure (11). formidable, multi-year challenge. Now, thanks to advances Over the past decade, a number of excellent structure in DNA sequencing technology, it is possible to sequence prediction and structure modeling servers have emerged. *To whom correspondence should be addressed. Tel: +780 492 0383; Fax: +780 492 5305; Email: [email protected] ß 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Research, 2008, Vol. 36, Web Server issue W203 These include Porter (12) and PsiPred (13) for secondary PROGRAM DESCRIPTION structure prediction of soluble proteins, SWISS-MODEL PROTEUS2 is composed of two parts, a front-end web- (14) and 3D JigSaw (15) for homology modeling, interface (written in Perl and HTML) and a back-end TMHMM (16) for transmembrane helix prediction, Pred- consisting of five different structure prediction programs TMBB for transmembrane b-barrel prediction (17) and (written in Java, Perl and C/C++) along with four local SignalP (18) for signal peptide prediction. However, most databases (about 310 Mbytes in size). The front-end of these tools are highly specialized, single application accepts both FASTA and raw sequence data. The servers that perform only one type of prediction, for just sequences may be either pasted or typed into the one sequence at a time. Consequently, if a newly sequenced text box or uploaded through a file browse button. protein does not fit neatly into one of the standard The server accepts both single sequence and multiple Downloaded from https://academic.oup.com/nar/article-abstract/36/suppl_2/W202/2506231 by guest on 20 March 2019 prediction categories it is difficult to get a very complete sequence files. As part of the server interface, users must or well-annotated result. For instance, if a protein (such as select the kingdom to which the source organism belongs OmpA) happens to have a signal peptide, an N-terminal À membrane spanning domain, and a C-terminal soluble (Gram+, Gram and Eukaryote) to improve the quality cytoplasmic domain that is homologous to a known 3D of the signal peptide predictions. For multi-sequence structure, a user may have to visit at least four different web submissions users must provide an email address to which servers to get a complete structural analysis of the protein. the results can be sent. Trying to merge these disparate results into a single, The output for a typical PROTEUS2 prediction coherent prediction would require a significant amount of consists of several pages of hyperlinked or scrollable text manual inspection, reformatting and alignment. If one files (Figure 1) including sequence/structure alignments, wished to analyze hundreds of proteins of a similar nature, predictions for signal peptide location and cleavage sites, such a task would prove to be very challenging, especially membrane spanning regions (both helices and b-strands) given the fact that very few structure prediction tools and putative or known domains. Signal peptide segments support local installations. Indeed, even fewer are dis- are marked with an ‘S’, membrane spanning helices are tributed as open source applications. As a result, the identified with a ‘T’, membrane b-strands are identified integration, local installation or customization of these with a ‘B’, regular helices are marked with an ‘H’, regular tools is almost impossible. b-strands with an ‘E’, coil regions with a ‘C’ and signal Another limitation to essentially all secondary structure peptide cleavage sites with a lowercase ‘c’. PROTEUS2 prediction systems is the fact that they do not fully exploit also generates confidence scores for each type of the information that is already available in the protein secondary structure (additional details about the con- structure databases (i.e. the PDB). We have recently fidence scores are available on PROTEUS2 documenta- shown that by finding sequence homologues in the PDB tion pages). If a 3D structure is generated, the PDB and by using a process called 3D-to-2D mapping, it is coordinates, information about the matching PDB struc- possible to increase the accuracy of secondary structure ture, the predicted alignment, the sequence identity, the prediction (of soluble proteins) by as much as 10% (19). number of modeled residues and a hyperlink to view the A similar approach has recently been applied to Porter as resulting structure through the WebMol viewer (21) are a means of significantly improving its secondary structure provided. Users may override PROTEUS2 default choice predictions (20). Applying this simple structure mapping of structure templates by preselecting a PDB file under protocol to predicting the structure of transmembrane the PROTEUS2 options menu. It is also possible to toggle helix or transmembrane b-barrel, proteins could poten- the energy minimization option on or off to improve either tially improve their corresponding prediction accuracies the quality or speed of structure generation. by a similar amount. In order to perform its structure predictions most In an effort to address some of the current shortcomings
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