Abstract
About 20% of the cancer incidences worldwide have been estimated to be associated with infections. However, the molecular mechanisms of exactly how they contribute to host tumorigenesis are still unknown. To evade host defense, pathogens hijack host proteins at different levels: sequence, structure, motif, and binding surface, i.e., interface. Interface similarity allows pathogen proteins to compete with host counterparts to bind to a target protein, rewire physiological signaling, and result in persistent infections, as well as cancer. Identification of host-pathogen interactions (HPIs)—along with their structural details at atomic resolution—may provide mechanistic insight into pathogen-driven cancers and innovate therapeutic intervention. HPI data including structural details is scarce and large-scale experimental detection is challenging. Therefore, there is an urgent and mounting need for efficient and robust computational approaches to predict HPIs and their complex (bound) structures. In this chapter, we review the first and currently only interface-based computational approach to identify novel HPIs. The concept of interface mimicry promises to identify more HPIs than complete sequence or structural similarity. We illustrate this concept with a case study on Kaposi’s sarcoma herpesvirus (KSHV) to elucidate how it subverts host immunity and helps contribute to malignant transformation of the host cells.
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References
Durmus S, Cakir T, Ozgur A, Guthke R (2015) A review on computational systems biology of pathogen-host interactions. Front Microbiol 6:235. https://doi.org/10.3389/fmicb.2015.00235
Stebbins CE, Galan JE (2001) Structural mimicry in bacterial virulence. Nature 412(6848):701–705. https://doi.org/10.1038/35089000
Sal-Man N, Biemans-Oldehinkel E, Finlay BB (2009) Structural microengineers: pathogenic Escherichia coli redesigns the actin cytoskeleton in host cells. Structure 17(1):15–19. https://doi.org/10.1016/j.str.2008.12.001
Kahn RA, Fu H, Roy CR (2002) Cellular hijacking: a common strategy for microbial infection. Trends Biochem Sci 27(6):308–314. https://doi.org/10.1016/S0968-0004(02)02108-4
Finlay BB, McFadden G (2006) Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell 124(4):767–782. https://doi.org/10.1016/j.cell.2006.01.034
Moody CA, Laimins LA (2010) Human papillomavirus oncoproteins: pathways to transformation. Nat Rev Cancer 10(8):550–560. https://doi.org/10.1038/nrc2886
Filippova M, Song H, Connolly JL, Dermody TS, Duerksen-Hughes PJ (2002) The human papillomavirus 16 E6 protein binds to tumor necrosis factor (TNF) R1 and protects cells from TNF-induced apoptosis. J Biol Chem 277(24):21730–21739. https://doi.org/10.1074/jbc.M200113200
Shirin H, Sordillo EM, Kolevska TK, Hibshoosh H, Kawabata Y, Oh SH, Kuebler JF, Delohery T, Weghorst CM, Weinstein IB, Moss SF (2000) Chronic helicobacter pylori infection induces an apoptosis-resistant phenotype associated with decreased expression of p27(kip1). Infect Immun 68(9):5321–5328
Guven-Maiorov E, Tsai CJ, Nussinov R (2016) Pathogen mimicry of host protein-protein interfaces modulates immunity. Semin Cell Dev Biol 58:136–145. https://doi.org/10.1016/j.semcdb.2016.06.004
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 260(4):604–620. https://doi.org/10.1006/jmbi.1996.0424
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 31(2):127–152. https://doi.org/10.3109/10409239609106582
Keskin O, Nussinov R (2005) Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel 18(1):11–24. https://doi.org/10.1093/protein/gzh095
Keskin O, Nussinov R (2007) Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure 15(3):341–354. https://doi.org/10.1016/j.str.2007.01.007
Cukuroglu E, Gursoy A, Nussinov R, Keskin O (2014) Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One 9(1):e86738. https://doi.org/10.1371/journal.pone.0086738
Muratcioglu S, Guven-Maiorov E, Keskin O, Gursoy A (2015) Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol 35:87–92. https://doi.org/10.1016/j.sbi.2015.10.001
Franzosa EA, Garamszegi S, Xia Y (2012) Toward a three-dimensional view of protein networks between species. Front Microbiol 3:428. https://doi.org/10.3389/fmicb.2012.00428
Franzosa EA, Xia Y (2011) Structural principles within the human-virus protein-protein interaction network. Proc Natl Acad Sci U S A 108(26):10538–10543. https://doi.org/10.1073/pnas.1101440108
Guven-Maiorov E, Tsai CJ, Nussinov R (2017) Structural host-microbiota interaction networks. PLoS Comput Biol 13(10):e1005579. https://doi.org/10.1371/journal.pcbi.1005579
Bhavsar AP, Guttman JA, Finlay BB (2007) Manipulation of host-cell pathways by bacterial pathogens. Nature 449(7164):827–834. https://doi.org/10.1038/nature06247
Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311(5758):239–242. https://doi.org/10.1126/science.1116804
von Schwedler UK, Stuchell M, Muller B, Ward DM, Chung HY, Morita E, Wang HE, Davis T, He GP, Cimbora DM, Scott A, Krausslich HG, Kaplan J, Morham SG, Sundquist WI (2003) The protein network of HIV budding. Cell 114(6):701–713
Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 104(18):7606–7611. https://doi.org/10.1073/pnas.0702332104
de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, Andre P, Rabourdin-Combe C, Lotteau V (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4:230. https://doi.org/10.1038/msb.2008.66
Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139(7):1255–1267. https://doi.org/10.1016/j.cell.2009.12.018
Zhang L, Villa NY, Rahman MM, Smallwood S, Shattuck D, Neff C, Dufford M, Lanchbury JS, Labaer J, McFadden G (2009) Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings. J Proteome Res 8(9):4311–4318. https://doi.org/10.1021/pr900491n
Khadka S, Vangeloff AD, Zhang C, Siddavatam P, Heaton NS, Wang L, Sengupta R, Sahasrabudhe S, Randall G, Gribskov M, Kuhn RJ, Perera R, LaCount DJ (2011) A physical interaction network of dengue virus and human proteins. Mol Cell Proteomics 10(12):M111.012187. https://doi.org/10.1074/mcp.M111.012187
Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ (2011) Global landscape of HIV-human protein complexes. Nature 481(7381):365–370. https://doi.org/10.1038/nature10719
Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Burckstummer T, Muller AC, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL, Colinge J, Superti-Furga G (2012) Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487(7408):486–490. https://doi.org/10.1038/nature11289
Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabasi AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Munger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M (2012) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 487(7408):491–495. https://doi.org/10.1038/nature11288
Guven Maiorov E, Keskin O, Gursoy A, Nussinov R (2013) The structural network of inflammation and cancer: merits and challenges. Semin Cancer Biol 23(4):243–251. https://doi.org/10.1016/j.semcancer.2013.05.003
Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R (2015) The architecture of the TIR domain signalosome in the toll-like Receptor-4 signaling pathway. Sci Rep 5:13128. https://doi.org/10.1038/srep13128
Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R (2015) A structural view of negative regulation of the toll-like receptor-mediated inflammatory pathway. Biophys J 109(6):1214–1226. https://doi.org/10.1016/j.bpj.2015.06.048
Acuner-Ozbabacan ES, Engin BH, Guven-Maiorov E, Kuzu G, Muratcioglu S, Baspinar A, Chen Z, Van Waes C, Gursoy A, Keskin O, Nussinov R (2014) The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics 15(Suppl 4):S2. https://doi.org/10.1186/1471-2164-15-S4-S2
Nourani E, Khunjush F, Durmus S (2015) Computational approaches for prediction of pathogen-host protein-protein interactions. Front Microbiol 6:94. https://doi.org/10.3389/fmicb.2015.00094
Brito AF, Pinney JW (2017) Protein-protein interactions in virus-host systems. Front Microbiol 8:1557. https://doi.org/10.3389/fmicb.2017.01557
Durmus Tekir S, Cakir T, Ardic E, Sayilirbas AS, Konuk G, Konuk M, Sariyer H, Ugurlu A, Karadeniz I, Ozgur A, Sevilgen FE, Ulgen KO (2013) PHISTO: pathogen-host interaction search tool. Bioinformatics 29(10):1357–1358. https://doi.org/10.1093/bioinformatics/btt137
Kumar R, Nanduri B (2010) HPIDB--a unified resource for host-pathogen interactions. BMC Bioinformatics 11(Suppl 6):S16. https://doi.org/10.1186/1471-2105-11-S6-S16
Vialas V, Nogales-Cadenas R, Nombela C, Pascual-Montano A, Gil C (2009) Proteopathogen, a protein database for studying Candida albicans--host interaction. Proteomics 9(20):4664–4668. https://doi.org/10.1002/pmic.200900023
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42(Database issue):D581–D591. https://doi.org/10.1093/nar/gkt1099
Urban M, Pant R, Raghunath A, Irvine AG, Pedro H, Hammond-Kosack KE (2015) The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Res 43(Database issue):D645–D655. https://doi.org/10.1093/nar/gku1165
Xiang Z, Tian Y, He Y (2007) PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol 8(7):R150. https://doi.org/10.1186/gb-2007-8-7-r150
Bleves S, Dunger I, Walter MC, Frangoulidis D, Kastenmuller G, Voulhoux R, Ruepp A (2014) HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res 42(Database issue):D671–D676. https://doi.org/10.1093/nar/gkt925
Guirimand T, Delmotte S, Navratil V (2015) VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res 43(Database issue):D583–D587. https://doi.org/10.1093/nar/gku1121
Li Y, Wang C, Miao Z, Bi X, Wu D, Jin N, Wang L, Wu H, Qian K, Li C, Zhang T, Zhang C, Yi Y, Lai H, Hu Y, Cheng L, Leung KS, Li X, Zhang F, Li K, Li X, Wang D (2015) ViRBase: a resource for virus-host ncRNA-associated interactions. Nucleic Acids Res 43(Database issue):D578–D582. https://doi.org/10.1093/nar/gku903
Calderone A, Licata L, Cesareni G (2015) VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res 43(Database issue):D588–D592. https://doi.org/10.1093/nar/gku830
Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A (2011) HCVpro: hepatitis C virus protein interaction database. Infect Genet Evol 11(8):1971–1977. https://doi.org/10.1016/j.meegid.2011.09.001
Arnold R, Boonen K, Sun MG, Kim PM (2012) Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods 57(4):508–518. https://doi.org/10.1016/j.ymeth.2012.06.011
Doolittle JM, Gomez SM (2011) Mapping protein interactions between dengue virus and its human and insect hosts. PLoS Negl Trop Dis 5(2):e954. https://doi.org/10.1371/journal.pntd.0000954
Tyagi N, Krishnadev O, Srinivasan N (2009) Prediction of protein-protein interactions between Helicobacter pylori and a human host. Mol BioSyst 5(12):1630–1635. https://doi.org/10.1039/b906543c
Xu Q, Xiang EW, Yang Q (2011) Transferring network topological knowledge for predicting protein-protein interactions. Proteomics 11(19):3818–3825. https://doi.org/10.1002/pmic.201100146
Remmele CW, Luther CH, Balkenhol J, Dandekar T, Muller T, Dittrich MT (2015) Integrated inference and evaluation of host-fungi interaction networks. Front Microbiol 6:764. https://doi.org/10.3389/fmicb.2015.00764
Evans P, Dampier W, Ungar L, Tozeren A (2009) Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med Genet 2:27. https://doi.org/10.1186/1755-8794-2-27
Zhang M, Su S, Bhatnagar RK, Hassett DJ, Lu LJ (2012) Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One 7(7):e41202. https://doi.org/10.1371/journal.pone.0041202
Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z (2015) Prediction of host – pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics 16:100. https://doi.org/10.1186/s12859-015-0535-y
Doolittle JM, Gomez SM (2010) Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 7:82. https://doi.org/10.1186/1743-422X-7-82
de Chassey B, Meyniel-Schicklin L, Aublin-Gex A, Navratil V, Chantier T, Andre P, Lotteau V (2013) Structure homology and interaction redundancy for discovering virus-host protein interactions. EMBO Rep 14(10):938–944. https://doi.org/10.1038/embor.2013.130
Petrenko P, Doxey AC (2015) mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. Bioinformatics 31(4):590–592. https://doi.org/10.1093/bioinformatics/btu681
Krishnadev O, Srinivasan N (2011) Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria. Int J Biol Macromol 48(4):613–619. https://doi.org/10.1016/j.ijbiomac.2011.01.030
Dyer MD, Murali TM, Sobral BW (2007) Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 23(13):i159–i166. https://doi.org/10.1093/bioinformatics/btm208
Doxey AC, McConkey BJ (2013) Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence 4(6):453–466. https://doi.org/10.4161/viru.25180
Mahajan G, Mande SC (2017) Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. BMC Bioinformatics 18(1):201. https://doi.org/10.1186/s12859-017-1550-y
Mariano R, Wuchty S (2017) Structure-based prediction of host-pathogen protein interactions. Curr Opin Struct Biol 44:119–124. https://doi.org/10.1016/j.sbi.2017.02.007
Becerra A, Bucheli VA, Moreno PA (2017) Prediction of virus-host protein-protein interactions mediated by short linear motifs. BMC Bioinformatics 18(1):163. https://doi.org/10.1186/s12859-017-1570-7
Jones KR, Whitmire JM, Merrell DS (2010) A tale of two toxins: helicobacter pylori CagA and VacA modulate host pathways that impact disease. Front Microbiol 1:115. https://doi.org/10.3389/fmicb.2010.00115
Manente L, Perna A, Buommino E, Altucci L, Lucariello A, Citro G, Baldi A, Iaquinto G, Tufano MA, De Luca A (2008) The Helicobacter pylori’s protein VacA has direct effects on the regulation of cell cycle and apoptosis in gastric epithelial cells. J Cell Physiol 214(3):582–587. https://doi.org/10.1002/jcp.21242
Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A (2007) Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16(12):2585–2596. https://doi.org/10.1110/ps.073228407
Drayman N, Glick Y, Ben-nun-shaul O, Zer H, Zlotnick A, Gerber D, Schueler-Furman O, Oppenheim A (2013) Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement. Cell Host Microbe 14(1):63–73. https://doi.org/10.1016/j.chom.2013.05.005
Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB (2004) Structure-based assembly of protein complexes in yeast. Science 303(5666):2026–2029. https://doi.org/10.1126/science.1092645
Rajasekharan S, Rana J, Gulati S, Sharma SK, Gupta V, Gupta S (2013) Predicting the host protein interactors of Chandipura virus using a structural similarity-based approach. Pathog Dis 69(1):29–35. https://doi.org/10.1111/2049-632X.12064
Zhang A, He L, Wang Y (2017) Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. BMC Bioinformatics 18(1):145. https://doi.org/10.1186/s12859-017-1500-8
Lee SA, Chan CH, Tsai CH, Lai JM, Wang FS, Kao CY, Huang CY (2008) Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics 9(Suppl 12):S11. https://doi.org/10.1186/1471-2105-9-S12-S11
Krishnadev O, Srinivasan N (2008) A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite. In Silico Biol 8(3–4):235–250
Schulze S, Henkel SG, Driesch D, Guthke R, Linde J (2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol 6:65. https://doi.org/10.3389/fmicb.2015.00065
Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R (2017) Prediction of host-pathogen interactions for helicobacter pylori by interface mimicry and implications to gastric cancer. J Mol Biol 429(24):3925–3941. https://doi.org/10.1016/j.jmb.2017.10.023
Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490(7421):556–560. https://doi.org/10.1038/nature11503
Zhang QC, Petrey D, Norel R, Honig BH (2010) Protein interface conservation across structure space. Proc Natl Acad Sci U S A 107(24):10896–10901. https://doi.org/10.1073/pnas.1005894107
Gao M, Skolnick J (2010) Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci U S A 107(52):22517–22522. https://doi.org/10.1073/pnas.1012820107
Kundrotas PJ, Zhu Z, Janin J, Vakser IA (2012) Templates are available to model nearly all complexes of structurally characterized proteins. Proc Natl Acad Sci U S A 109(24):9438–9441. https://doi.org/10.1073/pnas.1200678109
Franzosa EA, Xia Y (2012) Structural models for host-pathogen protein-protein interactions: assessing coverage and bias. Pac Symp Biocomput:287–298
Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56(1):143–156. https://doi.org/10.1002/prot.10628
Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 6(9):1341–1354. https://doi.org/10.1038/nprot.2011.367
Keskin O, Nussinov R, Gursoy A (2008) PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol 484:505–521. https://doi.org/10.1007/978-1-59745-398-1_30
Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A (2014) PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Res 42(Web Server issue):W285–W289. https://doi.org/10.1093/nar/gku397
Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A (2005) PRISM: protein interactions by structural matching. Nucleic Acids Res 33(Web Server):W331–W336. https://doi.org/10.1093/nar/gki585
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331(1):281–299
Wang C, Schueler-Furman O, Baker D (2005) Improved side-chain modeling for protein-protein docking. Protein Sci 14(5):1328–1339. https://doi.org/10.1110/ps.041222905
Wang C, Bradley P, Baker D (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373(2):503–519. https://doi.org/10.1016/j.jmb.2007.07.050
Duarte JM, Srebniak A, Scharer MA, Capitani G (2012) Protein interface classification by evolutionary analysis. BMC Bioinformatics 13:334. https://doi.org/10.1186/1471-2105-13-334
Uhlen M, Bjorling E, Agaton C, Szigyarto CA, Amini B, Andersen E, Andersson AC, Angelidou P, Asplund A, Asplund C, Berglund L, Bergstrom K, Brumer H, Cerjan D, Ekstrom M, Elobeid A, Eriksson C, Fagerberg L, Falk R, Fall J, Forsberg M, Bjorklund MG, Gumbel K, Halimi A, Hallin I, Hamsten C, Hansson M, Hedhammar M, Hercules G, Kampf C, Larsson K, Lindskog M, Lodewyckx W, Lund J, Lundeberg J, Magnusson K, Malm E, Nilsson P, Odling J, Oksvold P, Olsson I, Oster E, Ottosson J, Paavilainen L, Persson A, Rimini R, Rockberg J, Runeson M, Sivertsson A, Skollermo A, Steen J, Stenvall M, Sterky F, Stromberg S, Sundberg M, Tegel H, Tourle S, Wahlund E, Walden A, Wan J, Wernerus H, Westberg J, Wester K, Wrethagen U, Xu LL, Hober S, Ponten F (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4(12):1920–1932. https://doi.org/10.1074/mcp.M500279-MCP200
Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson A, Kampf C, Sjostedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Ponten F (2015) Proteomics. Tissue-based map of the human proteome. Science 347(6220):1260419. https://doi.org/10.1126/science.1260419
Yang H, Ke Y, Wang J, Tan Y, Myeni SK, Li D, Shi Q, Yan Y, Chen H, Guo Z, Yuan Y, Yang X, Yang R, Du Z (2011) Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network. Infect Immun 79(11):4413–4424. https://doi.org/10.1128/IAI.05622-11
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303
Huang d W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1–13. https://doi.org/10.1093/nar/gkn923
Huang d W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. https://doi.org/10.1038/nprot.2008.211
Dissinger NJ, Damania B (2016) Recent advances in understanding Kaposi's sarcoma-associated herpesvirus. F1000Res 5:F1000. https://doi.org/10.12688/f1000research.7612.1
Luther SA, Cyster JG (2001) Chemokines as regulators of T cell differentiation. Nat Immunol 2(2):102–107. https://doi.org/10.1038/84205
Acknowledgments
This project has been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. This study utilized the high-performance computational capabilities of the Biowulf PC/Linux cluster at the National Institutes of Health (NIH), Bethesda, MD (http://biowulf.nih.gov).
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Guven-Maiorov, E., Tsai, CJ., Ma, B., Nussinov, R. (2019). Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. In: Sikosek, T. (eds) Computational Methods in Protein Evolution. Methods in Molecular Biology, vol 1851. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8736-8_18
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DOI: https://doi.org/10.1007/978-1-4939-8736-8_18
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