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. 2003 Jul 1;31(13):3333–3336. doi: 10.1093/nar/gkg534

Motif3D: relating protein sequence motifs to 3D structure

Anna Gaulton 1,*, Teresa K Attwood 1
PMCID: PMC168941  PMID: 12824320

Abstract

Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

INTRODUCTION

A common approach in sequence analysis is the construction of multiple sequence alignments for protein families, in order to identify conserved amino acid ‘motifs’ that may have structural or functional significance. Such motifs form the basis of many protein family databases where they are used as signatures to identify further members of the families they describe. PRINTS, and its automatically generated supplement prePRINTS, house an extensive collection of diagnostic ‘fingerprints’ for protein superfamilies, families and subtypes, each comprising multiple conserved motifs (1). Since fingerprint motifs are identified solely on the basis of sequence similarity, with no prior knowledge of function, it is of interest to identify where the conserved amino acids lie in the three-dimensional (3D) structure and to what extent they represent known functional regions. While PRINTS entries detail the positions of the motifs in each protein sequence and contain links to the relevant Protein Data Bank [PDB, (2)] structures, there has previously been no widely available method for visualising the fingerprint motifs on the 3D structure. Motif 3D is a web-based protein structure viewer, designed specifically to allow regions of interest to be highlighted on protein structures and, in particular, to allow PRINTS/prePRINTS fingerprints to be visualised.

A number of programs have previously been described that allow sequence conservation and structural information to be related. These include: JOY (3), a program that allows multiple sequence alignments to be annotated with structural information; COMBOSA3D (4), which enables protein structures to be shaded according to the degree of amino acid conservation in a corresponding alignment; and LigBase (5), a collection of conserved ligand binding sites in protein sequences and structures. However, none of these resources allow specific amino acid motifs, either identified manually or from protein family databases, to be visualised on 3D structures. Two of the protein family databases do provide methods for visualising the conserved sequence motifs they contain. 3D-Blocks enables the motifs of the Blocks database to be viewed on PDB structures (6) and 3MOTIF (7) displays motifs and regular expressions from eMOTIF (8), Blocks and PROSITE (9). In addition, the PDBsum database (10) and the program PdbMotif (11) also allow highlighting of PROSITE regular expressions on PDB structures. However, all of these methods have the disadvantage that full functionality can only be achieved either by installation of the Chime plugin (http://www.mdlchime.com/chime), which is not available for all platforms, or by download of scripts for use with a local copy of the RASMOL program (12). While 3D-Blocks does allow the structure to be viewed with no helper application, this feature is not fully interactive and display options are limited. Motif 3D is written as a Java applet and is therefore platform independent, requiring no download or installation procedure. All that is required is a Java-enabled web browser, capable of displaying frames (e.g. Netscape or Internet Explorer). The user then has access to the full features of Motif 3D and can change display options and colour schemes, highlight regions of interest or view fingerprints. The functionality of Motif 3D has been further extended for the rhodopsin-like G protein-coupled receptors (GPCRs): the addition of a multiple sequence alignment now allows the motifs of any of the >200 fingerprints making up this superfamily to be displayed on the only crystal structure solved to date, that of bovine rhodopsin [PDB ID: 1F88 (13)].

USING Motif3D

Input/output

In order to view fingerprints using Motif 3D, the required input is a Protein Data Bank ID code (PDB code) and the ID code of a relevant fingerprint from either PRINTS or prePRINTS. However, there are a number of ways in which the viewer can be launched, depending on the requirements of the user and their familiarity with the software and with PRINTS. Figure 1 shows the input form for Motif 3D, available at http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

  • The simplest way to launch Motif3D is by clicking the link above the input form. This will start the viewer with no fingerprint and a default structure (bovine rhodopsin—1F88), and is recommended for new users who may want to experiment with the various features of the software and are not necessarily interested in a particular structure or fingerprint.

  • For advanced users, who want to view the motifs of a fingerprint on a particular structure and know the relevant ID codes, a simple submission form is provided (on the left hand side of the input page) where users can enter the PDB code of the structure, the ID code for the fingerprint and the database it is from (PRINTS or prePRINTS).

  • It is likely, however, that many users will be interested in viewing a specific structure or fingerprint, but perhaps do not know the necessary ID codes or which structures are relevant to particular fingerprints. A second form (on the right hand side of the input page) therefore provides a range of search options using the BLAST (14) and FingerPRINTScan (15) programs. If a PDB code is entered, the user is provided with a list of fingerprints that can be displayed on that structure ( just over half of the structures in the PDB currently have matches to fingerprints in PRINTS or prePRINTS). Conversely, if a fingerprint ID code is entered, a list is returned of structures that are related to that fingerprint (∼54% of fingerprints in PRINTS and 28% of those in prePRINTS can be viewed on one or more structures from the PDB). In addition to these options, a protein sequence can be entered. In this case, a search of the PDB returns a list of similar structures, each of which can then be used to launch Motif 3D (by clicking the ‘View Struc-ture’ link) or to find relevant fingerprints that can be viewed on the structure (by clicking the ‘Find Fingerprints’ link).

  • Finally, Motif 3D can also be invoked directly either from PRINTS or prePRINTS entries for which structures are available [by clicking the ‘View Structure’ link that appears at the top of the entry (Fig. 2)], or following a FingerPRINTScan search (by selecting the ‘3D-view’ link in the results table).

Figure 1.

Figure 1

Open in a new tab

Screen capture of the Motif3D input page available at http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html. The ‘Click here to try Motif3D’ link can be used to launch the viewer directly, with default parameters. The left hand form is used to launch Motif3D with a specific fingerprint ID and PDB code, if these are known. The right hand form provides a range of search facilities that allow users to enter a PDB code, fingerprint or sequence and find relevant structures and fingerprints with which to launch the viewer.

Figure 2.

Figure 2

Open in a new tab

Screen capture showing results of launching Motif3D from a fingerprint entry. Clicking the ‘View Structure’ link at the top of the entry starts Motif3D with the motifs of the fingerprint (e.g. NEUROTENSINR) highlighted on an appropriate structure (e.g. 1F88). The accompanying web page provides instructions for use and other information about the program.

In all cases, once Motif3D has been launched, the full range of features are available and different structures and fingerprints can be viewed as required.

Features of Motif 3D

Once a structure has been loaded into Motif 3D, it can be rotated by dragging with the mouse. Other features can be selected from the menus along the top of the viewer as follows.

  • The File menu allows a new protein structure to be loaded by entering the four-character PDB code (e.g. 1F88). An option is also provided to allow the user to close the viewer.

  • The View menu provides a ‘Bold’ option and allows the background colour to be changed from black to white. These options may be particularly useful if the image is to be printed.

  • As many PDB structures consist of multiple subunits, the Display menu allows individual chains in the structure to be viewed or hidden. Where a PDB file contains multiple models of  the same chain (e.g. structures solved by NMR) an option can be selected to display only a single model.

  • In addition to the default colour scheme (black and white), structures can be coloured either by amino acid properties (acidic, basic, polar, aliphatic-hydrophobic, aromatic- hydrophobic, special structural properties or disulphide bond-forming) or by secondary structure type (helix, sheet, turn or random coil) by selecting the appropriate option on the Colours menu.

  • The Selection menu can be used to highlight a region manually (by entering the start and end points), to highlight the motifs of a PRINTS fingerprint (by selecting the fingerprint ID code), or to clear previous selections. A range of colours can be used, allowing multiple selections to be visualised simultaneously.

  • Finally, the Help menu provides further guidance on the use of the viewer.

Figure 2 shows the results of launching Motif 3D from a PRINTS entry (NEUROTENSINR). The viewer is launched with the structure of bovine rhodopsin (1F88) and the motifs of the neurotensin receptor fingerprint are mapped onto the structure. The web page from which the viewer is launched provides instructions and examples of its use and also contains an information frame, which is updated when a new fingerprint is viewed to advise the user of any problems that may have occurred in running the FingerPRINTScan program.

DISCUSSION

If the full potential of protein family databases is to be realised, methods must be available to relate the sequence features they contain to their positions in the protein's 3D structure. Motif 3D provides one such method and has been applied specifically to visualising fingerprints from the PRINTS and prePRINTS databases. By incorporation of multiple sequence alignments, the functionality of the viewer can be extended to allow motifs in sequences that do not have solved structures to be mapped onto the structure of a homologue. This feature has so far been implemented for the rhodopsin-like GPCR superfamily, permitting >200 fingerprints describing the superfamily, its families and receptor subtypes to be compared. This is important because it allows family- and receptor subtype-specific motifs to be related to particular structural and functional regions of the proteins they characterise—thus, while motifs of the superfamily fingerprint map directly onto the common 7-transmembrane scaffold, family-level motifs can be seen to map to areas likely to be involved in ligand binding and those at subtype level to regions important to G protein-coupling. In future, this capability could be extended to other protein families by incorporation of further multiple alignments. Other planned developments include linking the viewer to an alignment editor, allowing motifs identified in a sequence alignment to be highlighted on a structure. Motif3D may also be extended to permit motifs and domains represented in other family databases to be displayed.

Acknowledgments

ACKNOWLEDGEMENTS

We are grateful to the MRC for individual support (A.G.).

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