MIMOX: a web tool for phage display based epitope mapping
© Huang et al; licensee BioMed Central Ltd. 2006
Received: 21 June 2006
Accepted: 12 October 2006
Published: 12 October 2006
Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them.
We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results.
A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox.
Since the pioneering work of Smith and co-workers [1–3], phage display technology has been widely used in both basic research such as the exploration of protein-protein interaction sites and networks [2–5], and applied research such as the development of new drugs, diagnostics, and vaccines [6–8]. Phage display has also become a promising epitope mapping method, which has been applied in many fields such as allergology and oncology. The phage display based epitope mapping is usually accomplished through comparing the sequence of mimotopes (antibody-selected phage displayed peptides) to the antigen. In some cases, the mimotope sequence is identical or very similar to a sequence in the antigen, there by indicating the location of the native epitope. These cases are rare however, and usually the mimotope sequence has little, if any, similarity with the antigen sequence. Compared with traditional epitope mapping methods such as solving the crystal structure of the antigen-antibody complex or scanning overlapping peptides of the antigen, phage display based epitope mapping is generally much cheaper and less arduous.
Though epitope mapping based on phage display can be done manually, it is quite tedious and time-consuming to compare a set of mimotopes to the antigen without computational support. The low sequence similarity between the mimotope and the antigen often makes the mapping even harder. To solve these problems, several groups have researched algorithms and programs that assist and automate phage display based epitope mapping [12–17]. According to their dependency on antigen structure, the existing programs for phage display based epitope mapping can be classified into three categories. Program in the first category such as FINDMAP, only work with sequence data from the mimotopes and antigen. The second category needs both the sequence data and the antigen structure. SiteLight, 3DEX, and Mapitope[16, 17] belong to this category. A very recently published work: MIMOP makes the third category, which integrates the two different approaches and can work with or without the antigen structure. Though implemented differently, all the existing programs have succeeded in given cases. However, most of the existing tools have not been implemented as a freely available online service until now, making it less convenient for the community to access, utilize, and evaluate them.
In the present study, we describe a web-based tool for phage display based epitope mapping named MIMOX. It was coded with Perl as a CGI program and can be used to align a set of mimotopes and derive a consensus sequence. The consensus sequence, or a single mimotope sequence, can then be mapped on to the antigen structure, and potential epitopes determined by spatial clustering of the mapped residues. The results mapped on to the antigen's 3D structure can then be viewed interactively. To validate this web-based tool, we compared the results from MIMOX with the results from other computational tools and experimentally identified native epitopes in several case studies.
Overall architecture of MIMOX
Deriving consensus sequence from a set of mimotopes
As described above, MIMOX wraps ClustalW to align a set of mimotope sequences and then allows the alignment to be viewed, edited, and analyzed through an embedded version of JalView. Based on the review by Smith et al , we also implemented a simple statistical method in the script mimocs.pl to derive a consensus sequence from the alignment. Firstly, the script counts the appearance of each kind of amino acid at each position in the alignment and calculates the percentage frequency of each one. The frequency of a given amino acid X at the position i of the alignment (f xi ) is defined as
Mapping sequence to the corresponding antigen structure
Since the mimotopes and the native epitope on the antigen bind to the same antibody, it is assumed that the mimotopes and the native epitope have similar physicochemical properties and similar spatial organization. This assumption is the basis of the MIMOX algorithm. The mapping process of MIMOX is based on the input sequence (such as the consensus sequence) and the uploaded antigen structure. A fragment of the sequence can also be used as input.
Firstly, for each position in the input sequence, MIMOX searches the uploaded PDB structure for matching residues and places them into an array of candidate residues for that position. Two matching modes are available at present. One is strict mode, which means the type of mimotope residue must match the antigen residue exactly. The other is called conservative mode, which means similar residues are also included in the candidate residue array. There are 5 groups of similar residues (L, I, V; T, S; E, D; Q, N; K, R; F, W) in MIMOX, which has been described in previous section.
The array of candidate residues for each position is then added to an array of arrays. MIMOX finds all the residue neighbour pairs between consecutive candidate residue arrays in the array of arrays. Whether two residues are neighbours is determined by the distance between the two residues and the distance threshold value. If the distance between two residues is below the threshold, the two residues are taken as a neighbour pair. MIMOX provides three methods to calculate neighbour residue pairs. One method is to take the distance between the Cα atoms of the two amino acids as the distance between the two residues. Using Cα atoms may better reflect the backbone positions. The second method is to use the distance between the Cβ atoms, which may better reflect the side chain position (Cα atom is still used when it is a glycine because it does not have a Cβ atom). The third method described below, is based on the distances between all the heavy atoms of the two amino acids. All of the distances mentioned above are Euclidean distances, calculated as:
where D21 means the distance between atom 2 and atom 1 and x2, y2, z2, x1, y1, z1 are coordinates of atom 2 and atom 1. When the methods based on Cα or Cβ atom position are used, the default distance threshold is 7.0 angstroms, as it approximates the upper limit for noncovalent interactions in macromolecular structures. When the third method is used, the distance threshold is calculated as
DT = DF × (vdwAtom1 + vdwAtom2)
where DT is the distance threshold, DF is the Distance Factor (given by user), and vdwAtom is the Van der Waals radius of the atom. The default DF value is 1.11. If two residues have a pair of heavy atoms which are nearer than the distance threshold calculated from their Van der Waals radius, the two residues are taken as a neighbour pair.
MIMOX then recursively links the neighbour pairs until all possible ways of forming the input sequence are made. Each result is then ranked according to the sum of the absolute residue accessibility of each residue calculated from the NACCESS result file. In the end, the results are displayed in a table with hyperlinks to call the script parsa.pl which can parse and display the accessibility data in detail, and the script jmol.pl to view the result interactively mapped onto the antigen structure.
Results and discussion
Web interface of MIMOX
To test MIMOX, we have applied it to several cases taken from other similar research and literature. We compared the results from MIMOX with the results from other computational tools and the native epitope itself if the epitope is known in the CED database. It should be pointed out that cases using monoclonal antibodies are most appropriate for testing. However, in order to compare with previously published tools, some less appropriate cases (using polyclonal antibodies) taken from the corresponding literature are also used. More case studies [see Additional file 1] can also be found on the test dataset page of MIMOX.
The first case is taken from FINDMAP. In 1999, Jesaitis and co-workers used an anti-actin polyclonal antibody to select a phage displayed random peptide library; VPHPTWMR was one of the consensus sequences they derived from the selected mimotopes. They manually mapped VPHPTWMR to the known structure of actin [PDB: 1ATN] and suggested that it might correspond to residues: V129, P130, H101, P102, T358, W356, M355, R372. In 2003, Mumey et al used FINDMAP to align VPHPTWMR to the actin sequence without utilizing information on the antigen structure. The result from FINDMAP shows VPHPTWMR can be mapped to residues as V129, P130, H101, P102, T103, W356, M355, R372. FINDMAP mapped the input sequence to a slightly different set of residues (using T103 instead of T358). When running MIMOX with all parameters as defaults, we got no result. However, after the distance threshold is changed to 12 Å (the maximum distance allowed in MIMOX), we find that the two mappings above are returned as candidate cluster 5 and candidate cluster 17. As the side chain of some amino acids (such as arginine) can span a distance as great as 12 Å, MIMOX takes this value as the maximum allowable distance. This distance restriction is also used by Mapitope[16, 17]. In this case, the need for the higher distance threshold is due to R372 which lies some distance from the other mapped residues. MIMOX also suggested other possibilities such as cluster 1(V96, P102, H101, P130, T358, W356, M355, R372) which has a bigger solvent accessible surface, and cluster 26 (V96, P98, H101, P102, T103, W356, M355, R372), which clearly has 3 sequential segments, i.e. VPHPT, WM, and R.
The second case is taken from work by Enshell-Seijffers. They used monoclonal antibody 17b, which is against HIV gp120 envelope glycoprotein, to select a phage displayed random peptide library and got a set of 11 mimotopes. Analyzing the mimotopes with Mapitope, they suggest that the 17b epitope might consist of the following residues and segments: L111, LKPCVK (116–121), P124, VITQ (200–203), CPKV (205–208), RIK (419–421), I423, I424, K432, P437, P438. The structure of HIV gp120 envelope glycoprotein in complex with 17b has been solved [PDB: 1GC1] and 17b epitope has been recorded in the CED database as CE0058, which is composed of CK(119,121) + VTQAC(200,202–205) + RKQI(419,421–423) + KMYP (432,434,435,437). Among the 24 Mapitope predicted residues, 11 are contact residues of the 17b epitope. Using default parameters, MIMOX derived a consensus sequence, [LV] RP [LT] [KR] LRE [LP] [RT] X [-R], from 17b mimotopes. MIMOX finds no result matching the whole consensus sequence. Using LRLR, a fragment of the consensus sequence as the input sequence and running MIMOX in conservative match mode with other parameters as defaults, the top result is I423, K421, I420, and R419; the 4th result is V200, K121, L122, K432 and the 5th result is I423, K432, L122, and K121. Taking the top 5 results together, 13 residues are suggested by MIMOX and 6 of them are contact residues of the 17b epitope. In this case, Mapitope gives more complete and elaborate result.
The last case is taken from MIMOP. BO2C11 is a human monoclonal antibody against human coagulation factor VIII. Villard et al selected two phage displayed random peptide libraries with BO2C11 and got a set of 27 mimotopes. Very recently, Moreau et al have applied their newly developed tool MIMOP to analyze these mimotopes. Combining the two methods MimAlign and MimCons in MIMOP, the BO2C11 epitope is predicted be composed of a segment YFTNMF (2195–2200) and residues T2202, K2207, R2215, R2220, Q2222. The structure of human coagulation factor VIII in complex with BO2C11 has been solved [PDB: 1IQD] and the BO2C11 epitope has been recorded in the CED database as CE0176, which consists of FTNMF (2196–2200), R2215, RPQV (2220–2223), SLLT (2250–2253), HQ (2315–2316). Using default parameters, MIMOX derived a consensus sequence of [NQKR] [HST] RWSNRSS [ST] from those mimotopes. Again, the whole length consensus sequence returns no mapping results. However, when we use QH, RWSN, RSSS, three sequential fragments that cover the whole consensus sequence, as input sequences and running MIMOX in conservative match mode with all other parameters as defaults, the top 3 results of each of the partial sequences overlap with the MIMOP result and the native BO2C11 epitope well. For example, the third result of the input QH suggested by MIMOX is Q2316, H2315; the third result of the input RWSN suggested by MIMOX is R2220, F2196, T2197, N2198; the first result of the input RSSS suggested by MIMOX is R2215, S2216, T2202, T2197 and third result is K2249, S2250, S2254, T2253.
Taking together, our initial case studies show that MIMOX can fully or partially repeat results from manual mapping, other existing tools, and also provide novel suggestions. MIMOX is designed to be a tool which is more interactive than automatic. We acknowledge that tuning the probe sequences and parameters are often required to get good results. This interactive process gives hints to users step by step and greatly decreases the load of the server and prevents the loss of some reasonable results. MIMOX lists all the matched results with no prediction threshold. This allows users to find the reasonable results by themselves based on their background knowledge on a given antibody, a given antigen and a given phage display experiment. Nevertheless, according to the test dataset page of MIMOX, the true epitope (or its segments) often falls in the top 5 (if the there are only a few result entries) or top 10% (if the there are many result entries) of the results. Where the real epitope is unknown, we would suggest running MIMOX with a range of parameters and consensus sequence derived fragments to find overlapping or otherwise promising (high surface accessibility) candidate.
Related software comparison
As we have mentioned previously, several groups have researched algorithms and programs that may assist and automate phage display based epitope mapping. Based on the dependency on antigen structure, the existing programs can be classified into three categories. FINDMAP belongs to the first category, which is independent of any structural information. FINDMAP has been implemented as a C++ program. It aligns a probe (e.g. a consensus sequence derived from a set of mimotopes) to the sequence of native antigen, allowing any permutation of the probe sequence. It uses a two-part scoring system to evaluate the quality of alignments and a branch-and-bound algorithm to find an alignment with maximum score.
The programs in the second category include SiteLight, 3DEX, Mapitope, and MIMOX. SiteLight was implemented in C++ and it has been tested on Red Hat Linux. First, the program divides native protein surface into overlapping patches based on geodesic distances between residues; then aligns each mimotope in the library with each patch and scores and sorts them; finally, high scoring matches are selected iteratively until 25% of the native protein is covered. Another program 3DEX was implemented in Visual Basic and could only run on Windows. It divides a sequence into a set of overlapping subsequences with a user-defined length (3-maximum length of mimotope). Then, it searches for matching residues at each position of the above subsequences against the sequence or PDB structure of native protein and links the neighbours iteratively until the first subsequence is complete. This is repeated for the following subsequences to complete the mimotope and return the result. Mapitope was also implemented in C++ and its algorithm was first described by Enshell-Seijffers in 2003. Briefly, Mapitope deconvolutes a set of mimotope sequences into a set of overlapping amino acids pairs (AAP). Then a set of major statistically significant pairs (SSP) are identified based on the AAP. Later, the SSP are mapped and clustered in the antigen structure. Finally, the most elaborate and diverse clusters on the antigen surface are identified and regarded as the predicted epitope candidates[16, 17].
MIMOP, a work published very recently, comprises the third category. MIMOP includes two approaches. One is called MimAlign, which can predict potential epitopic regions (PER) from mimotope and antigen sequences, and from the antigen structure if available. The other called MimCons, can predict PER from mimotope sequences but requires the antigen structure. It seems that MIMOP can work with or without the antigen structure from the published case studies. However, the sequence of the only case that is independent of antigen structure is just a continuous subsequence of the antigen sequence. Thus, more studies are still needed to prove that MimAlign can work without antigen structure information.
Comparing available programs related to MIMOX
available on request
Like all software, bugs will have crept into MIMOX during the programming. We expect users will send their feedback to help us maintain and improve MIMOX in the future. A new version of MIMOX with more user definable options and supporting multiple-chain antigens will be implemented in the future, allowing epitopes formed by residues from different polypeptide chains to also be predicted. A systematic evaluation and comparison study with all available tools including MIMOX that assist phage display based epitope mapping is also under our consideration.
MIMOX, a web application for phage display based epitope mapping has been coded with Perl. It is helpful for molecular biologists to identify the native epitope of an antibody based on the antigen structure and a set of mimotope sequences they get through phage display technology. As a publicly accessible web tool in this area, MIMOX is very convenient for the community to access, utilize, and evaluate, complementing other existing programs.
Availability and requirements
Project Name: MIMOX
Project Homepage: http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox
Operating System: Platform independent
Programming Language: Perl
Other Requirements: Java1.2 or higher
License: GNU GPL
Any Restrictions to use by non-academics: none
Common Gateway Interface
GNU's Not UNIX
General Public License
Human Immunodeficiency Virus
Protein Data Bank
We thank our lab colleagues Dr Masumi Itoh for help with the server and Dr Nobuya Tanaka for help with coding. We also thank Dr Simon Hubbard for permitting us to use NACCESS program. This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology and the Japan Science and Technology Agency. The computational resource was provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University. The support from NSFC project (30600138) is also acknowledged.
- Smith GP: Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 1985, 228(4705):1315–1317. 10.1126/science.4001944View ArticlePubMedGoogle Scholar
- Scott JK, Smith GP: Searching for peptide ligands with an epitope library. Science 1990, 249(4967):386–390. 10.1126/science.1696028View ArticlePubMedGoogle Scholar
- Smith GP, Petrenko VA: Phage Display. Chem Rev 1997, 97(2):391–410. 10.1021/cr960065dView ArticlePubMedGoogle Scholar
- Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, et al.: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 2002, 295(5553):321–324. 10.1126/science.1064987View ArticlePubMedGoogle Scholar
- Thom G, Cockroft AC, Buchanan AG, Candotti CJ, Cohen ES, Lowne D, Monk P, Shorrock-Hart CP, Jermutus L, Minter RR: Probing a protein-protein interaction by in vitro evolution. Proc Natl Acad Sci USA 2006, 103(20):7619–7624. 10.1073/pnas.0602341103PubMed CentralView ArticlePubMedGoogle Scholar
- Wang LF, Yu M: Epitope identification and discovery using phage display libraries: applications in vaccine development and diagnostics. Curr Drug Targets 2004, 5(1):1–15. 10.2174/1389450043490668View ArticlePubMedGoogle Scholar
- Riemer AB, Kurz H, Klinger M, Scheiner O, Zielinski CC, Jensen-Jarolim E: Vaccination with cetuximab mimotopes and biological properties of induced anti-epidermal growth factor receptor antibodies. J Natl Cancer Inst 2005, 97(22):1663–1670.View ArticlePubMedGoogle Scholar
- Li M, Yan Z, Han W, Zhang Y: Mimotope vaccination for epitope-specific induction of anti-CD20 antibodies. Cell Immunol 2006, 239(2):136–143.View ArticlePubMedGoogle Scholar
- Ganglberger E, Grunberger K, Sponer B, Radauer C, Breiteneder H, Boltz-Nitulescu G, Scheiner O, Jensen-Jarolim E: Allergen mimotopes for 3-dimensional epitope search and induction of antibodies inhibiting human IgE. Faseb J 2000, 14(14):2177–2184. 10.1096/fj.99-1000comView ArticlePubMedGoogle Scholar
- Riemer AB, Kraml G, Scheiner O, Zielinski CC, Jensen-Jarolim E: Matching of trastuzumab (Herceptin) epitope mimics onto the surface of Her-2/neu – a new method of epitope definition. Mol Immunol 2005, 42(9):1121–1124. 10.1016/j.molimm.2004.11.003View ArticlePubMedGoogle Scholar
- Jesaitis AJ, Gizachew D, Dratz EA, Siemsen DW, Stone KC, Burritt JB: Actin surface structure revealed by antibody imprints: evaluation of phage-display analysis of anti-actin antibodies. Protein Sci 1999, 8(4):760–770.PubMed CentralView ArticlePubMedGoogle Scholar
- Halperin I, Wolfson H, Nussinov R: SiteLight: binding-site prediction using phage display libraries. Protein Sci 2003, 12(7):1344–1359. 10.1110/ps.0237103PubMed CentralView ArticlePubMedGoogle Scholar
- Mumey BM, Bailey BW, Kirkpatrick B, Jesaitis AJ, Angel T, Dratz EA: A new method for mapping discontinuous antibody epitopes to reveal structural features of proteins. J Comput Biol 2003, 10(3–4):555–567. 10.1089/10665270360688183View ArticlePubMedGoogle Scholar
- Schreiber A, Humbert M, Benz A, Dietrich U: 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem 2005, 26(9):879–887. 10.1002/jcc.20229View ArticlePubMedGoogle Scholar
- Moreau V, Granier C, Villard S, Laune D, Molina F: Discontinuous epitope prediction based on mimotope analysis. Bioinformatics 2006, 22(9):1088–1095. 10.1093/bioinformatics/btl012View ArticlePubMedGoogle Scholar
- Enshell-Seijffers D, Denisov D, Groisman B, Smelyanski L, Meyuhas R, Gross G, Denisova G, Gershoni JM: The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. J Mol Biol 2003, 334(1):87–101. 10.1016/j.jmb.2003.09.002View ArticlePubMedGoogle Scholar
- Tarnovitski N, Matthews LJ, Sui J, Gershoni JM, Marasco WA: Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides. J Mol Biol 2006, 359(1):190–201. 10.1016/j.jmb.2006.03.008View ArticlePubMedGoogle Scholar
- Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, et al.: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611–1618. 10.1101/gr.361602PubMed CentralView ArticlePubMedGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673–4680.PubMed CentralView ArticlePubMedGoogle Scholar
- Clamp M, Cuff J, Searle SM, Barton GJ: The Jalview Java alignment editor. Bioinformatics 2004, 20(3):426–427. 10.1093/bioinformatics/btg430View ArticlePubMedGoogle Scholar
- Hubbard SJ, Thornton JM: NACCESS. Department of Biochemistry and Molecular Biology, University College London; 1993.Google Scholar
- Draper DE: Themes in RNA-protein recognition. J Mol Biol 1999, 293(2):255–270. 10.1006/jmbi.1999.2991View ArticlePubMedGoogle Scholar
- Huang J, Honda W: CED: a conformational epitope database. BMC Immunol 2006, 7(1):7. 10.1186/1471-2172-7-7PubMed CentralView ArticlePubMedGoogle Scholar
- Test data for MIMOX[http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox/test]
- Villard S, Lacroix-Desmazes S, Kieber-Emmons T, Piquer D, Grailly S, Benhida A, Kaveri SV, Saint-Remy JM, Granier C: Peptide decoys selected by phage display block in vitro and in vivo activity of a human anti-FVIII inhibitor. Blood 2003, 102(3):949–952. 10.1182/blood-2002-06-1886View ArticlePubMedGoogle Scholar
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