Understanding a point mutation signature D54K in the caspase activation recruitment domain of NOD1 capitulating concerted immunity via atomistic simulation

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001[Mismatch]
   Google Scholar
• Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7(4), 248–249. https://doi.org/10.1038/nmeth0410-248
   PubMed Web of Science ®Google Scholar
• Allen, M. P., & Tildesley, D. J. (2017). Computer simulation of liquids. Oxford University Press.
   Google Scholar
• Altenhoff, A. M., Studer, R. A., Robinson-Rechavi, M., & Dessimoz, C. (2012). Resolving the ortholog conjecture: Orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Computational Biology, 8(5), e1002514. https://doi.org/10.1371/journal.pcbi.1002514
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. https://doi.org/10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N., & Yeh, L.-S L. (2004). UniProt: The universal protein knowledgebase. Nucleic Acids Research, 32(Database issue), D115–D119. https://doi.org/10.1093/nar/gkh131
   PubMed Web of Science ®Google Scholar
• Arnold, G. E., & Ornstein, R. L. (1997). Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: Cytochrome P450BM-3. Biophysical Journal, 73(3), 1147–1159. https://doi.org/10.1016/S0006-3495(97)78147-5
   PubMed Web of Science ®Google Scholar
• Bailey, T. L., & Elkan, C. (1995). Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21(1-2), 51–80. https://doi.org/10.1007/BF00993379
   Web of Science ®Google Scholar
• Bandyopadhyay, S., Sharan, R., & Ideker, T. (2006). Systematic identification of functional orthologs based on protein network comparison. Genome Research, 16(3), 428–435. https://doi.org/10.1101/gr.4526006
   PubMed Web of Science ®Google Scholar
• Barlow, D. J., & Thornton, J. M. (1983). Ion-pairs in proteins. Journal of Molecular Biology, 168(4), 867–885. https://doi.org/10.1016/s0022-2836(83)80079-5
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271. https://doi.org/10.1021/j100308a038
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., & Schwede, T. (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols, 4(1), 1–13. https://doi.org/10.1038/nprot.2008.197
   PubMed Web of Science ®Google Scholar
• Bork, P., & Koonin, E. V. (1996). Protein sequence motifs. Current Opinion in Structural Biology, 6(3), 366–376. https://doi.org/10.1016/S0959-440X(96)80057-1
   PubMed Web of Science ®Google Scholar
• Boyle, J. P., Parkhouse, R., & Monie, T. P. (2014). Insights into the molecular basis of the NOD2 signalling pathway. Open Biology, 4(12), 140178. https://doi.org/10.1098/rsob.140178
   PubMed Web of Science ®Google Scholar
• Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P. L., & Casadio, R. (2009). Functional annotations improve the predictive score of human disease-related mutations in proteins. Human Mutation, 30(8), 1237–1244. https://doi.org/10.1002/humu.21047
   PubMed Web of Science ®Google Scholar
• Canning, P., Ruan, Q., Schwerd, T., Hrdinka, M., Maki, J. L., Saleh, D., Suebsuwong, C., Ray, S., Brennan, P. E., Cuny, G. D., Uhlig, H. H., Gyrd-Hansen, M., Degterev, A., & Bullock, A. N. (2015). Inflammatory signaling by NOD-RIPK2 is inhibited by clinically relevant type II kinase inhibitors. Chemistry & Biology, 22(9), 1174–1184. https://doi.org/10.1016/j.chembiol.2015.07.017
   PubMedGoogle Scholar
• Carneiro, L. A. M., Travassos, L. H., & Philpott, D. J. (2004). Innate immune recognition of microbes through Nod1 and Nod2: Implications for disease. Microbes and Infection, 6(6), 609–616. https://doi.org/10.1016/j.micinf.2004.01.012
   PubMed Web of Science ®Google Scholar
• Caruso, R., Warner, N., Inohara, N., & Núñez, G. (2014). NOD1 and NOD2: Signaling, host defense, and inflammatory disease. Immunity, 41(6), 898–908. https://doi.org/10.1016/j.immuni.2014.12.010
   PubMed Web of Science ®Google Scholar
• Chakrabarti, P., & Bhattacharyya, R. (2007). Geometry of nonbonded interactions involving planar groups in proteins. Progress in Biophysics and Molecular Biology, 95(1-3), 83–137. https://doi.org/10.1016/j.pbiomolbio.2007.03.016
   PubMed Web of Science ®Google Scholar
• Cheatham, T. E. I., Miller, J. L., Fox, T., Darden, T. A., & Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle Mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. Journal of the American Chemical Society, 117(14), 4193–4194. https://doi.org/10.1021/ja00119a045
   Web of Science ®Google Scholar
• Cino, E. A., Choy, W.-Y., & Karttunen, M. (2012). Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations. Journal of Chemical Theory and Computation, 8(8), 2725–2740. https://doi.org/10.1021/ct300323g
   PubMed Web of Science ®Google Scholar
• Collier, T. A., Piggot, T. J., & Allison, J. R. (2020). Molecular dynamics simulation of proteins. In J. A. Gerrard & L. J. Domigan (Eds.), Methods in molecular biology (Clifton, N.J.) (vol. 2073, pp. 311–327). Springer US. https://doi.org/10.1007/978-1-4939-9869-2_17
   Google Scholar
• Coussens, N. P., Mowers, J. C., McDonald, C., Nuñez, G., & Ramaswamy, S. (2007). Crystal structure of the Nod1 caspase activation and recruitment domain. Biochemical and Biophysical Research Communications, 353(1), 1–5. https://doi.org/10.1016/j.bbrc.2006.11.122
   PubMed Web of Science ®Google Scholar
• de Castro, E., Sigrist, C. J. A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., Bairoch, A., & Hulo, N. (2006). ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research, 34(Web Server issue), W362–365. https://doi.org/10.1093/nar/gkl124
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. https://doi.org/10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Dodson, G. G., Lane, D. P., & Verma, C. S. (2008). Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Reports, 9(2), 144–150. https://doi.org/10.1038/sj.embor.7401160
   PubMed Web of Science ®Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003). HADDOCK: A protein − protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society, 125(7), 1731–1737. https://doi.org/10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Dyson, H. J., Wright, P. E., & Scheraga, H. A. (2006). The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences of the United States of America, 103(35), 13057–13061. https://doi.org/10.1073/pnas.0605504103
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. https://doi.org/10.1016/s0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Emmert, D. B., Stoehr, P. J., Stoesser, G., & Cameron, G. N. (1994). The European Bioinformatics Institute (EBI) databases. Nucleic Acids Research, 22(17), 3445–3449. https://doi.org/10.1093/nar/22.17.3445
   PubMed Web of Science ®Google Scholar
• Eswar, N., & Ramakrishnan, C. (2000). Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Engineering, 13(4), 227–238. https://doi.org/10.1093/protein/13.4.227
   PubMedGoogle Scholar
• Fang, J., Haasl, R. J., Dong, Y., & Lushington, G. H. (2005). Discover protein sequence signatures from protein-protein interaction data. BMC Bioinformatics, 6(1), 277. https://doi.org/10.1186/1471-2105-6-277
   PubMedGoogle Scholar
• Fernández-García, V., González-Ramos, S., Martín-Sanz, P., García-Del Portillo, F., Laparra, J. M., & Boscá, L. (2021). NOD1 in the interplay between microbiota and gastrointestinal immune adaptations. Pharmacological Research, 171, 105775. https://doi.org/10.1016/j.phrs.2021.105775
   PubMed Web of Science ®Google Scholar
• Frenkel, D., & Smit, B. (2001). Understanding molecular simulation: From algorithms to applications. Elsevier.
   Google Scholar
• Fridh, V., & Rittinger, K. (2012). The tandem CARDs of NOD2: Intramolecular interactions and recognition of RIP2. PloS One, 7(3), e34375. https://doi.org/10.1371/journal.pone.0034375
   PubMed Web of Science ®Google Scholar
• Gabaldón, T., & Koonin, E. V. (2013). Functional and evolutionary implications of gene orthology. Nature Reviews. Genetics, 14(5), 360–366. https://doi.org/10.1038/nrg3456
   PubMed Web of Science ®Google Scholar
• Gallivan, J. P., & Dougherty, D. A. (1999). Cation-π interactions in structural biology. Proceedings of the National Academy of Sciences of the United States of America, 96(17), 9459–9464. https://doi.org/10.1073/pnas.96.17.9459
   PubMed Web of Science ®Google Scholar
• Gangadharappa, B. S., Sharath, R., Revanasiddappa, P. D., Chandramohan, V., Balasubramaniam, M., & Vardhineni, T. P. (2020). Structural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors. Journal of Biomolecular Structure & Dynamics, 38(13), 3757–3771. https://doi.org/10.1080/07391102.2019.1667265
   PubMed Web of Science ®Google Scholar
• Geerke, D. P., & van Gunsteren, W. F. (2006). Force field evaluation for biomolecular simulation: Free enthalpies of solvation of polar and apolar compounds in various solvents. Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 7(3), 671–678. https://doi.org/10.1002/cphc.200500510
   PubMed Web of Science ®Google Scholar
• Girardin, S. E., Boneca, I. G., Carneiro, L. A. M., Antignac, A., Jéhanno, M., Viala, J., Tedin, K., Taha, M.-K., Labigne, A., Zähringer, U., Coyle, A. J., DiStefano, P. S., Bertin, J., Sansonetti, P. J., & Philpott, D. J. (2003). NOD1 detects a unique muropeptide from gram-negative bacterial peptidoglycan. Science (New York, N.Y.), 300(5625), 1584–1587. https://doi.org/10.1126/science.1084677
   PubMed Web of Science ®Google Scholar
• Gohlke, H., & Case, D. A. (2004). Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. Journal of Computational Chemistry, 25(2), 238–250. https://doi.org/10.1002/jcc.10379
   PubMed Web of Science ®Google Scholar
• Goncharuk, S. A., Artemieva, L. E., Tabakmakher, V. M., Arseniev, A. S., & Mineev, K. S. (2018). CARD domain of rat RIP2 kinase: Refolding, solution structure, pH-dependent behavior and protein-protein interactions. PLoS One, 13(10), e0206244. https://doi.org/10.1371/journal.pone.0206244
   PubMed Web of Science ®Google Scholar
• Gong, Q., Long, Z., Zhong, F. L., Teo, D. E. T., Jin, Y., Yin, Z., Boo, Z. Z., Zhang, Y., Zhang, J., Yang, R., Bhushan, S., Reversade, B., Li, Z., & Wu, B. (2018). Structural basis of RIP2 activation and signaling. Nature Communications, 9(1)Article, 1. https://doi.org/10.1038/s41467-018-07447-9
   PubMedGoogle Scholar
• Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
   PubMed Web of Science ®Google Scholar
• Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., & McKusick, V. A. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research, 33(Database issue), D514–517. https://doi.org/10.1093/nar/gki033
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Heul, A. M. V., Fowler, C. A., Ramaswamy, S., & Piper, R. C. (2013). Ubiquitin regulates caspase recruitment domain-mediated signaling by nucleotide-binding oligomerization domain-containing proteins NOD1 and NOD2. The Journal of Biological Chemistry, 288(10), 6890–6902. https://doi.org/10.1074/jbc.M112.413781
   PubMed Web of Science ®Google Scholar
• Heul, A. M. V., Gakhar, L., Piper, R. C., & Subramanian, R. (2014). Crystal structure of a complex of NOD1 CARD and ubiquitin. PLoS One, 9(8), e104017. https://doi.org/10.1371/journal.pone.0104017
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. 27–28. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Inohara, N., Koseki, T., del Peso, L., Hu, Y., Yee, C., Chen, S., Carrio, R., Merino, J., Liu, D., Ni, J., & Núñez, G. (1999). Nod1, an Apaf-1-like activator of caspase-9 and nuclear factor-kappaB. The Journal of Biological Chemistry, 274(21), 14560–14567. https://doi.org/10.1074/jbc.274.21.14560
   PubMed Web of Science ®Google Scholar
• Inohara, N., Koseki, T., Lin, J., del Peso, L., Lucas, P. C., Chen, F. F., Ogura, Y., & Núñez, G. (2000). An induced proximity model for NF-kappa B activation in the Nod1/RICK and RIP signaling pathways. The Journal of Biological Chemistry, 275(36), 27823–27831. https://doi.org/10.1074/jbc.M003415200
   PubMed Web of Science ®Google Scholar
• Inoue, H., Nishio, H., Takada, H., Sakai, Y., Nanishi, E., Ochiai, M., Onimaru, M., Chen, S. J., Matsui, T., & Hara, T. (2016). Activation of Nod1 signaling induces fetal growth restriction and death through fetal and maternal vasculopathy. journal of Immunology (Baltimore, Md.: 1950), 196(6), 2779–2787. https://doi.org/10.4049/jimmunol.1500295
   PubMed Web of Science ®Google Scholar
• Janeway, C. A., & Medzhitov, R. (2002). Innate immune recognition. Annual Review of Immunology, 20(1), 197–216. https://doi.org/10.1146/annurev.immunol.20.083001.084359
   PubMed Web of Science ®Google Scholar
• Jenuth, J. P. (2000). The NCBI. Publicly available tools and resources on the Web. Methods in Molecular Biology (Clifton, N.J.), 132, 301–312. https://doi.org/10.1385/1-59259-192-2:301
   PubMedGoogle Scholar
• Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6679–6685. https://doi.org/10.1073/pnas.0408930102
   PubMed Web of Science ®Google Scholar
• Ke, Q., Gong, X., Liao, S., Duan, C., & Li, L. (2022). Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations. Journal of Molecular Liquids, 365, 120116. https://doi.org/10.1016/j.molliq.2022.120116
   Web of Science ®Google Scholar
• Koonin, E. V. (2005). Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics, 39(1), 309–338. https://doi.org/10.1146/annurev.genet.39.073003.114725
   PubMedGoogle Scholar
• Koukos, P. I., & Glykos, N. M. (2014). On the application of good-turing statistics to quantify convergence of biomolecular simulations. Journal of Chemical Information and Modeling, 54(1), 209–217. https://doi.org/10.1021/ci4005817
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014). ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(Database issue), D980–985. https://doi.org/10.1093/nar/gkt1113
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, D., Redfern, O., & Orengo, C. (2007). Predicting protein function from sequence and structure. Nature Reviews. Molecular Cell Biology, 8(12), 995–1005. https://doi.org/10.1038/nrm2281
   PubMed Web of Science ®Google Scholar
• Lee, M. S., & Kim, Y.-J. (2007). Signaling pathways downstream of pattern-recognition receptors and their cross talk. Annual Review of Biochemistry, 76(1), 447–480. https://doi.org/10.1146/annurev.biochem.76.060605.122847
   PubMedGoogle Scholar
• Maharana, J., Pradhan, S. K., & De, S. (2017). NOD1CARD might be using multiple interfaces for RIP2-mediated CARD-CARD interaction: Insights from molecular dynamics simulation. PLoS One, 12(1), e0170232. https://doi.org/10.1371/journal.pone.0170232
   PubMed Web of Science ®Google Scholar
• Majumdar, I., Nagpal, I., & Paul, J. (2017). Homology modeling and in silico prediction of Ulcerative colitis associated polymorphisms of NOD1. Molecular and Cellular Probes, 35, 8–19. https://doi.org/10.1016/j.mcp.2017.05.009
   PubMed Web of Science ®Google Scholar
• Manon, F., Favier, A., Núñez, G., Simorre, J.-P., & Cusack, S. (2007a). Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK. Journal of Molecular Biology, 365(1), 160–174. https://doi.org/10.1016/j.jmb.2006.09.067
   PubMed Web of Science ®Google Scholar
• Mathe, E., Olivier, M., Kato, S., Ishioka, C., Hainaut, P., & Tavtigian, S. V. (2006). Computational approaches for predicting the biological effect of p53 missense mutations: A comparison of three sequence analysis based methods. Nucleic Acids Research, 34(5), 1317–1325. https://doi.org/10.1093/nar/gkj518
   PubMed Web of Science ®Google Scholar
• Mayle, S., Boyle, J. P., Sekine, E., Zurek, B., Kufer, T. A., & Monie, T. P. (2014). Engagement of nucleotide-binding oligomerization domain-containing protein 1 (NOD1) by receptor-interacting protein 2 (RIP2) is insufficient for signal transduction. The Journal of Biological Chemistry, 289(33), 22900–22914. https://doi.org/10.1074/jbc.M114.557900
   PubMed Web of Science ®Google Scholar
• McDonald, C., Inohara, N., & Nuñez, G. (2005). Peptidoglycan signaling in innate immunity and inflammatory disease. The Journal of Biological Chemistry, 280(21), 20177–20180. https://doi.org/10.1074/jbc.R500001200
   PubMed Web of Science ®Google Scholar
• Moreira, L. O., & Zamboni, D. S. (2012). NOD1 and NOD2 signaling in infection and inflammation. Frontiers in Immunology, 3, 328. https://doi.org/10.3389/fimmu.2012.00328
   PubMed Web of Science ®Google Scholar
• Ng, P. C., & Henikoff, S. (2003). SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Research, 31(13), 3812–3814. https://doi.org/10.1093/nar/gkg509
   PubMed Web of Science ®Google Scholar
• Nilges, M. (1995). Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. Journal of Molecular Biology, 245(5), 645–660. https://doi.org/10.1006/jmbi.1994.0053
   PubMed Web of Science ®Google Scholar
• Nixon, K. C., & Carpenter, J. M. (1993). On outgroups. Cladistics: The International Journal of the Willi Hennig Society, 9(4), 413–426. https://doi.org/10.1111/j.1096-0031.1993.tb00234.x
   PubMedGoogle Scholar
• O’Donovan, C., Martin, M. J., Gattiker, A., Gasteiger, E., Bairoch, A., & Apweiler, R. (2002). High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Briefings in Bioinformatics, 3(3), 275–284. https://doi.org/10.1093/bib/3.3.275
   PubMedGoogle Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
   PubMed Web of Science ®Google Scholar
• Palacios-Rodríguez, Y., García-Laínez, G., Sancho, M., Gortat, A., Orzáez, M., & Pérez-Payá, E. (2011). Polypeptide modulators of caspase recruitment domain (CARD)-CARD-mediated protein-protein interactions. The Journal of Biological Chemistry, 286(52), 44457–44466. https://doi.org/10.1074/jbc.M111.255364
   PubMed Web of Science ®Google Scholar
• Park, J.-H., Kim, Y.-G., McDonald, C., Kanneganti, T.-D., Hasegawa, M., Body-Malapel, M., Inohara, N., & Núñez, G. (2007). RICK/RIP2 mediates innate immune responses induced through Nod1 and Nod2 but not TLRs. Journal of Immunology (Baltimore, Md.: 1950), 178(4), 2380–2386. https://doi.org/10.4049/jimmunol.178.4.2380
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., Mooney, S. D., & Radivojac, P. (2020). Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications, 11(1), 5918. https://doi.org/10.1038/s41467-020-19669-x
   PubMed Web of Science ®Google Scholar
• Peterson, M. E., Chen, F., Saven, J. G., Roos, D. S., Babbitt, P. C., & Sali, A. (2009). Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Science: A Publication of the Protein Society, 18(6), 1306–1315. https://doi.org/10.1002/pro.143
   PubMed Web of Science ®Google Scholar
• Petrey, D., Chen, T. S., Deng, L., Garzon, J. I., Hwang, H., Lasso, G., Lee, H., Silkov, A., & Honig, B. (2015). Template-based prediction of protein function. Current Opinion in Structural Biology, 32, 33–38. https://doi.org/10.1016/j.sbi.2015.01.007
   PubMed Web of Science ®Google Scholar
• Pham, A.-T., Ghilardi, A. F., & Sun, L. (2023). Recent advances in the development of RIPK2 modulators for the treatment of inflammatory diseases. Frontiers in Pharmacology, 14, 1127722. https://doi.org/10.3389/fphar.2023.1127722
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., Ascher, D. B., & Blundell, T. L. (2014). DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42(Web Server issue)issue, W314–W319. https://doi.org/10.1093/nar/gku411
   PubMedGoogle Scholar
• Schonbrun, J., Wedemeyer, W. J., & Baker, D. (2002). Protein structure prediction in 2002. Current Opinion in Structural Biology, 12(3), 348–354. https://doi.org/10.1016/s0959-440x(02)00336-6
   PubMed Web of Science ®Google Scholar
• Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., & van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. The Journal of Physical Chemistry A, 103(19), 3596–3607. https://doi.org/10.1021/jp984217f
   Web of Science ®Google Scholar
• Sheridan, R. P., & Venkataraghavan, R. (1992). A systematic search for protein signature sequences. Proteins, 14(1), 16–28. https://doi.org/10.1002/prot.340140105
   PubMed Web of Science ®Google Scholar
• Sigrist, C. J. A., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., & Hulo, N. (2010). PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Research, 38(Database issue)issue, D161–166. https://doi.org/10.1093/nar/gkp885
   PubMed Web of Science ®Google Scholar
• Sigrist, C. J. A., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., & Bucher, P. (2002). PROSITE: A documented database using patterns and profiles as motif descriptors. Briefings in Bioinformatics, 3(3), 265–274. https://doi.org/10.1093/bib/3.3.265
   PubMedGoogle Scholar
• Sigrist, C. J. A., De Castro, E., Langendijk-Genevaux, P. S., Le Saux, V., Bairoch, A., & Hulo, N. (2005). ProRule: A new database containing functional and structural information on PROSITE profiles. Bioinformatics (Oxford, England), 21(21), 4060–4066. https://doi.org/10.1093/bioinformatics/bti614
   PubMed Web of Science ®Google Scholar
• Smith, L. J., Daura, X., & van Gunsteren, W. F. (2002). Assessing equilibration and convergence in biomolecular simulations. Proteins, 48(3), 487–496. https://doi.org/10.1002/prot.10144
   PubMed Web of Science ®Google Scholar
• Sonnhammer, E. L. L., & Koonin, E. V. (2002). Orthology, paralogy and proposed classification for paralog subtypes. Trends in Genetics: TIG, 18(12), 619–620. https://doi.org/10.1016/s0168-9525(02)02793-2
   PubMed Web of Science ®Google Scholar
• Srimathi, T., Robbins, S. L., Dubas, R. L., Hasegawa, M., Inohara, N., & Park, Y. C. (2008). Monomer/dimer transition of the caspase-recruitment domain of human Nod1. Biochemistry, 47(5), 1319–1325. https://doi.org/10.1021/bi7016602
   PubMed Web of Science ®Google Scholar
• Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology, 57(5), 758–771. https://doi.org/10.1080/10635150802429642
   PubMed Web of Science ®Google Scholar
• Stenson, P. D., Mort, M., Ball, E. V., Shaw, K., Phillips, A., & Cooper, D. N. (2014). The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics, 133(1), 1–9. https://doi.org/10.1007/s00439-013-1358-4
   PubMed Web of Science ®Google Scholar
• Takeuchi, O., & Akira, S. (2010). Pattern recognition receptors and inflammation. Cell, 140(6), 805–820. https://doi.org/10.1016/j.cell.2010.01.022
   PubMed Web of Science ®Google Scholar
• Tanabe, T., Chamaillard, M., Ogura, Y., Zhu, L., Qiu, S., Masumoto, J., Ghosh, P., Moran, A., Predergast, M. M., Tromp, G., Williams, C. J., Inohara, N., & Núñez, G. (2004). Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition. The EMBO Journal, 23(7), 1587–1597. https://doi.org/10.1038/sj.emboj.7600175
   PubMed Web of Science ®Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680. https://doi.org/10.1093/nar/22.22.4673
   PubMed Web of Science ®Google Scholar
• Tina, K. G., Bhadra, R., & Srinivasan, N. (2007). PIC: Protein interactions calculator. Nucleic Acids Research, 35(Web Server issue), W473–W476. https://doi.org/10.1093/nar/gkm423
   PubMed Web of Science ®Google Scholar
• Trindade, B. C., & Chen, G. Y. (2020). NOD1 and NOD2 in inflammatory and infectious diseases. Immunological Reviews, 297(1), 139–161. https://doi.org/10.1111/imr.12902
   PubMed Web of Science ®Google Scholar
• van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Wallner, B., & Elofsson, A. (2003). Can correct protein models be identified? Protein Science: A Publication of the Protein Society, 12(5), 1073–1086. https://doi.org/10.1110/ps.0236803
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue)issue, W407–410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Willard, L., Ranjan, A., Zhang, H., Monzavi, H., Boyko, R. F., Sykes, B. D., & Wishart, D. S. (2003). VADAR: A web server for quantitative evaluation of protein structure quality. Nucleic Acids Research, 31(13), 3316–3319. https://doi.org/10.1093/nar/gkg565
   PubMed Web of Science ®Google Scholar
• Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B., Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S., & Richardson, D. C. (2018). MolProbity: More and better reference data for improved all-atom structure validation. Protein Science: A Publication of the Protein Society, 27(1), 293–315. https://doi.org/10.1002/pro.3330
   PubMed Web of Science ®Google Scholar
• Wu, C. H., Yeh, L.-S L., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z., Kourtesis, P., Ledley, R. S., Suzek, B. E., Vinayaka, C. R., Zhang, J., & Barker, W. C. (2003a). The protein information resource. Nucleic Acids Research, 31(1), 345–347. https://doi.org/10.1093/nar/gkg040
   PubMed Web of Science ®Google Scholar
• Wu, C. H., Nikolskaya, A., Huang, H., Yeh, L.-S L., Natale, D. A., Vinayaka, C. R., Hu, Z.-Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R. S., Suzek, B. E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J. L., Chung, S., Castro-Alvear, J., Dinkov, G., & Barker, W. C. (2003b). The protein information resource. Nucleic Acids Research, 32(Database issue), D112–D114. https://doi.org/10.1093/nar/gkh097
   Google Scholar
• Xiang, Z. (2006). Advances in homology protein structure modeling. Current Protein & Peptide Science, 7(3), 217–227. https://doi.org/10.2174/138920306777452312
   PubMed Web of Science ®Google Scholar
• Yip, Y. L., Famiglietti, M., Gos, A., Duek, P. D., David, F. P. A., Gateau, A., & Bairoch, A. (2008). Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Human Mutation, 29(3), 361–366. https://doi.org/10.1002/humu.20671
   PubMed Web of Science ®Google Scholar
• Yu, W., Clyne, M., Khoury, M. J., & Gwinn, M. (2010). Phenopedia and genopedia: Disease-centered and gene-centered views of the evolving knowledge of human genetic associations. Bioinformatics (Oxford, England), 26(1), 145–146. https://doi.org/10.1093/bioinformatics/btp618
   PubMed Web of Science ®Google Scholar
• Zemla, A. (2003). LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Research, 31(13), 3370–3374. https://doi.org/10.1093/nar/gkg571
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Berman, P., & Miller, W. (1998a). Alignments without low-scoring regions. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 5(2), 197–210. https://doi.org/10.1089/cmb.1998.5.197
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Schäffer, A. A., Miller, W., Madden, T. L., Lipman, D. J., Koonin, E. V., & Altschul, S. F. (1998b). Protein sequence similarity searches using patterns as seeds. Nucleic Acids Research, 26(17), 3986–3990. https://doi.org/10.1093/nar/26.17.3986
   PubMed Web of Science ®Google Scholar