359
Views
14
CrossRef citations to date
0
Altmetric
Research Article

Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling

, , &
Pages 2436-2448 | Received 04 Apr 2017, Accepted 12 Jul 2017, Published online: 14 Aug 2017

References

  • Archer, E., Maigret, B., Escrieut, C., Pradayrol, L., & Fourmy, D. (2003). Rhodopsin crystal: New template yielding realistic models of G-protein-coupled receptors? Trends in Pharmacological Sciences, 24, 36–40. doi:10.1016/S0165-6147(02)00009-3
  • Bissantz, C., Logean, A., & Rognan, D. (2004). High-throughput modeling of human G-protein coupled receptors: Amino acid sequence alignment, three-dimensional model building, and receptor library screening. Journal of Chemical Information and Computer Sciences, 44, 1162–1176. doi:10.1021/ci034181a
  • Blüml, K., Mutschler, E., & Wess, J. (1994). Functional role in ligand binding and receptor activation of an asparagine residue present in the sixth transmembrane domain of all muscarinic acetylcholine receptors. Journal of Biological Chemistry, 269, 18870–18876.
  • Carlsson, J., Coleman, R. G., Setola, V., Irwin, J. J., Fan, H., Schlessinger, A., … Shoichet, B. K. (2011). Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nature Chemical Biology, 7, 769–778. doi:10.1038/nchembio.662
  • Cavasotto, C. N., & Palomba, D. (2015). Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chemical Communications, 51, 13576–13594. doi:10.1039/c5cc05050b
  • Cordomí, A., Edholm, O., & Perez, J. J. (2007). Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. Journal of Computational Chemistry, 28, 1017–1030. doi:10.1002/jcc.20579
  • Costanzi, S., Skorski, M., Deplano, A., Habermehl, B., Mendoza, M., Wang, K., … Gao, J. (2016). Homology modeling of a class A GPCR in the inactive conformation: A quantitative analysis of the correlation between model/templatesequence identity and model accuracy. Journal of Molecular Graphics and Modeling, 70, 140–152. doi:10.1016/j.jmgm.2016.10.004
  • Cutolo, P., Basdevant, N., Bernadat, G., Bachelerie, F., & Ha-Duong, T. (2017). Interaction of chemokine receptor CXCR4 in monomeric and dimeric state with its endogenous ligand CXCL12: Coarse-grained simulations identify differences. Journal of Biomolecular Structure and Dynamics, 35, 399–412. doi:10.1080/07391102.2016.1145142
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103, 8577–8593. doi:10.1063/1.470117
  • Evers, A., Gohlke, H., & Klebe, G. (2003). Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. Journal of Molecular Biology, 334, 327–345. doi:10.1016/j.jmb.2003.09.032
  • Fanelli, F., & De Benedetti, P. G. (2011). Update 1 of: Computational modeling approaches to structure function analysis of G protein-coupled receptors. Chemical Reviews, 111, PR438–PR535. doi: 10.1021/cr100437t
  • Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: A new approach for rapid accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47, 1739–1749. doi:10.1021/jm0306430
  • Gandhimathi, A., & Sowdhamini, R. (2016). Molecular modelling of human 5-hydroxytryptamine receptor (5-HT2A) and virtual screening studies towards the identification of agonist and antagonist molecules. Journal of Biomolecular Structure and Dynamics, 34, 952–970. doi:10.1080/07391102.2015.1062802
  • Goldfeld, D. A., Zhu, K., Beuming, T., & Friesner, R. A. (2013). Loop prediction for a GPCR homology model: Algorithms and results. Proteins, 81, 214–228. doi:10.1002/prot.24178
  • Grossfield, A. (2011). Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations. Biochimica Biophyica. Acta, 1808, 1868–1878. doi:10.1016/j.bbamem.2011.03.010
  • Haga, K., Kruse, A. C., Asada, H., Yurugi-Kobayashi, T., Shiroishi, M., Zhang, C., … Kobayashi, T. (2012). Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Nature, 482, 547–551. doi:10.1038/nature10753
  • Han, S. J., Hamdan, F. F., Kim, S. K., Jacobson, K. A., Bloodworth, L. M., Li, B., & Wess, J. (2005). Identification of an agonist-induced conformational change occurring adjacent to the ligand-binding pocket of the M3 muscarinic acetylcholine receptor. Journal Biological Chemistry, 280, 34849–34858. doi:10.1074/jbc.M506711200
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926–935. doi:10.1063/1.445869
  • Kaminski, G., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. Journal of Physical Chemistry B, 105, 6474–6487. doi:10.1021/jp003919d
  • Katritch, V., Cherezov, V., & Stevens, R. C. (2013). Structure-function of the G protein–coupled receptor superfamily. Annual Review of Pharmacology and Toxicology, 53, 531–556. doi:10.1146/annurev-pharmtox-032112-135923
  • Kobilka, B. (2013). The structural basis of G-protein-coupled receptor signaling (Nobel Lecture). Angewante Chemie International Edition, 52, 6380–6388. doi:10.1002/anie.201302116
  • Kow, R. L., & Nathanson, N. M. (2012). Muscarinic receptors become crystal clear. Nature, 482, 480–481. doi:10.1038/482480a
  • Kruse, A. C., Hu, J., Pan, A. C., Arlow, D. H., Rosenbaum, D. M., Rosemond, E., … Kobilka, B. K. (2012). Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature, 482, 552–556. doi:10.1038/nature10867
  • Kufareva, I., Katritch, V., Participants of GPCR Dock 2013, Stevens, R. C., & Abagyan, R. (2014). Advances in GPCR modeling evaluated by the GPCR dock 2013 assessment: Meeting new challenges. Structure, 22, 1120–1139. doi:10.1016/j.str.2014.06.012
  • Labute, P. (2008). Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins, 75, 187–205.
  • Latek, D., Pasznik, P., Carlomagno, T., & Filipek, S. (2013). Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS ONE, 8, e56742. doi:10.1371/journal.pone.0056742
  • Lin, S., Gether, U., & Kobilka, B. K. (1996). Ligand stabilization of the β2 adrenergic receptor: Effect of DTT on receptor conformation monitored by circular dichroism and fluorescence spectroscopy. Biochemistry, 35, 14445–14451. doi:10.1021/bi961619+
  • Lupala, C. S., Rasaeifar, B., Gomez-Gutierrez, P., & Perez, J. J. (2015). Effect of template selection on the construction of atomistic models of GPCRs by homology modeling. Journal of Biomolecular Structure and Dynamics, 33, 127–128. doi:10.1080/07391102.2015.1032830
  • Martinez-Archundia, M., Cordomi, A., Garriga, P., & Perez, J. J. (2012). Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site. Journal of Biomedicine and Biotechnology, 1–12. Article ID 789741. doi: 10.1155/2012/789741
  • Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13, 952–962. doi:10.1002/jcc.540130805
  • Mobarec, J. C., Sanchez, R., & Filizola, M. (2009). Modern homology modeling of G-protein coupled receptors: Which structural template to use? Journal of Medicinal Chemistry, 52, 5207–5216. doi:10.1021/jm9005252
  • Nayeem, A., Sitkoff, D., & Krystek, S., Jr. (2006). A comparative study of available software for high-accuracy homology modeling: From sequence alignments to structural models. Protein Science, 15, 808–824. doi:10.1110/ps.051892906
  • Nowroozi, A., & Shahlaei, M. (2017). A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: A case study on human bombesin receptor subtype-3. Journal of Biomolecular Structure and Dynamics, 35, 250–272. doi:10.1080/07391102.2016.1140593
  • Ostermeier, C., & Michel, H. (1997). Crystallization of membrane proteins. Current Opinion on Structural Biolology, 7, 697–701. doi:10.1016/S0959-440X(97)80080-2
  • Overington, J. P., Al-Lazikani, B., & Hopkins, A. L. (2006). How many drug targets are there? Nature Reviews on Drug Discovery, 5, 993–996. doi:10.1038/nrd2199
  • Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., & Miyano, M. (2000). Crystal structure of rhodopsin: A G protein-coupled receptor. Science, 289, 739–745. doi:10.1126/science.289.5480.739
  • Rajagopal, S., Rajagopal, K., & Lefkowitz, R. J. (2010). Teaching old receptors new tricks: Biasing seven-transmembrane receptors. Nature Reviews on Drug Discovery, 9, 373–386. doi:10.1038/nrd3024
  • Rataj, K., Witek, J., Mordalski, S., Kosciolek, T., & Bojarski, A. J. (2014). Impact of template choice on homology model efficiency in virtual screening. Journal of Chemical Information and Computer Modeling, 54, 1661–1668. doi:10.1021/ci500001f
  • Rodríguez, D., Ranganathan, A., & Carlsson, J. (2014). Strategies for improved modeling of GPCR-drug complexes: Blind predictions of serotonin receptors bound to ergotamine. Journal of Chemical Information and Computer Modeling, 54, 2004–2021. doi:10.1021/ci5002235
  • Sadiq, S. K., Guixà-González, R., Dainese, E., Pastor, M., De Fabritiis, G., & Selent, J. (2013). Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. Current Medicinal Chemistry, 20, 22–38.
  • Salon, J. A., Lodowski, D. T., & Palczewski, K. (2011). The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacology Reviews, 63, 901–937. doi:10.1124/pr.110.003350
  • Schiöth, H. B., & Fredriksson, R. (2005). The GRAFS classification system of G-protein coupled receptors in comparative perspective. General and Comparative Endocrinology, 142, 94–101. doi:10.1016/j.ygcen.2004.12.018
  • Shimamura, T., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., … Iwata, S. (2011). Structure of the human histamine H1 receptor complex with doxepin. Nature, 475, 65–70. doi:10.1038/nature10236
  • Shonberg, J., Kling, R. C., Gmeiner, P., & Löber, S. (2015). GPCR crystal structures: Medicinal chemistry in the pocket. Bioorganic and Medicinal Chemistry, 23, 3880–3906. doi:10.1016/j.bmc.2014.12.034
  • Simms, J., Hall, N. E., Lam, P. H. C., Miller, L. J., Christopoulos, A., Abagyan, R., & Sexton, P. M. (2009). Homology modeling of GPCRs. Methods in Molecular Biology, 552, 97–113. doi:10.1007/978-1-60327-317-6_7
  • Spyrakis, F., & Cavasotto, C. N. (2015). Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Archives of Biochemistry and Biophysics, 583, 105–119. doi:10.1016/j.abb.2015.08.002
  • Thomas, T., McLean, K. C., McRobb, F. M., Manallack, D. T., Chalmers, D. K., & Yuriev, E. (2014). Homology modeling of human muscarinic acetylcholine receptors. Journal of Chemical Information and Computer Modeling, 54, 243–253. doi:10.1021/ci400502u
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718. doi:10.1002/jcc.20291
  • Venkatakrishnan, A. J., Deupi, X., Lebon, G., Tate, C. G., Schertler, G. F., & Babu, M. M. (2013). Molecular signatures of G-protein-coupled receptors. Nature, 494, 186–194. doi:10.1038/nature11896
  • Worth, C. L., Kleinau, G., & Krause, G. (2009). Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PLoS ONE, 4, e7011. doi:10.1371/journal.pone.0007011
  • Zhu, M., & Li, M. (2012). Revisiting the homology modeling of G-protein coupled receptors: β1-Adrenoceptor as an example. Molecular BioSystems, 8, 1686–1693. doi:10.1039/c2mb05491d

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.