Abstract
We review current advances in experimental as well as computational modeling and simulation approaches to structural systems biology, whose overall aim is to build quantitative models of signaling networks while retaining the crucial elements of molecular specificity. We briefly discuss the current and emerging experimental and computational methods, particularly focusing on hybrid and multiscale methods, and highlight several applications in cell signaling with quantitative and predictive capabilities. The scope of such models range from delineating protein–protein interactions to describing clinical implications.
Similar content being viewed by others
References
Agrawal, N. J., J. Nukpezah, and R. Radhakrishnan. Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis. PLoS Comput. Biol. 6(9):e1000926, 2010.
Alber, F., et al. Determining the architectures of macromolecular assemblies. Nature 450(7170):683–701, 2007.
Aloy, P., and R. B. Russell. Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell Biol. 7(3):188–197, 2006.
Ayton, G. S., and G. A. Voth. Multiscale simulation of protein mediated membrane remodeling. Semin. Cell Dev. Biol. 21(4):357–362, 2010.
Ayton, G. S., and G. A. Voth. Multiscale computer simulation of the immature HIV-1 virion. Biophys. J. 99(9):2757–2765, 2010.
Bessman, N. J., and M. A. Lemmon. Finding the missing links in EGFR. Nat. Struct. Mol. Biol. 19(1):1–3, 2012.
Bhalla, U. S., and R. Iyengar. Emergent properties of biological networks. Science 283:381–387, 1999.
Birtwistle, M. R., et al. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol. Syst. Biol. 3:144, 2007.
Boudeau, J., et al. Emerging roles of pseudokinases. Trends Cell Biol. 16(9):443–452, 2006.
Bursulaya, B. D., et al. Comparative study of several algorithms for flexible ligand docking. J. Comput. Aided Mol. Des. 17(11):755–763, 2003.
Camacho, J. C., et al. Scoring dockied conformations generated by rigid body protein–protein docking. Proteins 40:525–537, 2000.
Chen, B., and R. Tycko. Simulated self-assembly of the HIV-1 capsid: protein shape and native contacts are sufficient for two-dimensional lattice formation. Biophys. J. 100(12):3035–3044, 2011.
Chen, C., R. Saxena, and G. W. Wei. A multiscale model for virus capsid dynamics. Int. J. Biomed. Imaging 2010:308627, 2010.
Chen, H. M., et al. Evaluating molecular-docking methods for pose prediction and enrichment factors. J. Chem. Inf. Model. 46(1):401–415, 2006.
Citri, A., and Y. Yarden. EGF-ERBB signalling: towards the systems level. Nat. Rev. Mol. Cell Biol. 7(7):505–516, 2006.
Engelman, J. A., et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 316(5827):1039–1043, 2007.
Fernandez-Martinez, J., et al. Structure–function mapping of a heptameric module in the nuclear pore complex. J. Cell Biol. 196:419–434, 2012.
Fiser, A., and A. Sali. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374:461–491, 2003.
Gebremichael, Y., J. W. Chu, and G. A. Voth. Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis. Biophys. J. 95(5):2487–2499, 2008.
Hicks, S. D., and C. L. Henley. Coarse-grained protein–protein stiffnesses and dynamics from all-atom simulations. Phys. Rev. E 81(31):030903, 2010.
Hsieh, M. Y., et al. Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC Syst. Biol. 4:57, 2010.
Huse, M., and J. Kuriyan. The conformational plasticity of protein kinases. Cell 109:275–282, 2002.
Johnston, I. G., A. A. Louis, and J. P. Doye. Modelling the self-assembly of virus capsids. J. Phys. Condens. Matter 22(10):104101, 2010.
Karplus, M., and J. Kuriyan. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. USA 102(19):6679–6685, 2005.
Kholodenko, B. N. Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol. 7(3):165–176, 2006.
Kirchhausen, T. Three ways to make a vesicle. Nat. Rev. Mol. Cell Biol. 1(3):187–198, 2000.
Kloth, M. T., et al. STAT5b, a mediator of synergism between c-Src and the epidermal growth factor receptor. J. Biol. Chem. 278:1671–1679, 2003.
Liu, Y., et al. A multiscale computational approach to dissect early events in the Erb family receptor mediated activation, differential signaling, and relevance to oncogenic transformations. Ann. Biomed. Eng. 35(6):1012–1025, 2007.
Lynch, T. J., et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N. Engl. J. Med. 350(21):2129–2139, 2004.
Mohammadi, M., J. Schlessinger, and S. R. Hubbard. Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism. Cell 86(4):577–587, 1996.
Mohammadi, M., et al. Structures of tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors. Science 276:955–960, 1997.
Mohammadi, M., et al. Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain. EMBO J. 17:5896–5904, 1998.
Mosesson, Y., G. B. Mills, and Y. Yarden. Derailed endocytosis: an emerging feature of cancer. Nat. Rev. Cancer 8(11):835–850, 2008.
Mulloy, R., et al. Epidermal growth factor receptor mutants from human lung cancers exhibit enhanced catalytic activity and increased sensitivity to gefitinib. Cancer Res. 67(5):2325–2330, 2007.
Oved, S., and Y. Yarden. Molecular ticket to enter cells. Nature 416:133–136, 2002.
Paez, J. G., et al. EGFR mutations in lung, cancer: correlation with clinical response to gefitinib therapy. Science 304(5676):1497–1500, 2004.
Periole, X., et al. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput. 5(9):2531–2543, 2009.
Purvis, J., V. Ilango, and R. Radhakrishnan. Role of network branching in eliciting differential short-term signaling responses in the hyper-sensitive epidermal growth factor receptor mutants implicated in lung cancer. Biotechnol. Prog. 24(3):540–553, 2008.
Purvis, J., et al. Efficacy of tyrosine kinase inhibitors in the mutants of the epidermal growth factor receptor: a multiscale molecular/systems model for phosphorylation and inhibition. In: Proceedings of the Foundations in Systems Biology II. Stuttgart: IRB Verlag, 2007, pp. 289–294.
Ramanan, V., et al. Systems biology and physical biology of clathrin-mediated endocytosis. Integr. Biol. 3(8):803–815, 2011.
Saunders, M. G., and G. A. Voth. Coarse-graining of multiprotein assemblies. Curr. Opin. Struct. Biol. 22:144–150, 2012.
Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 103:211–225, 2000.
Schulze, W. X., L. Deng, and M. Mann. Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol. Syst. Biol. 1:E1–E13, 2005.
Shi, F., et al. ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation. Proc. Natl. Acad. Sci. USA 107:7692–7697, 2010.
Shih, A. J., J. Purvis, and R. Radhakrishnan. Molecular systems biology of ErbB1 signaling: bridging the gap through multiscale modeling and high-performance computing. Mol. BioSyst. 4(12):1151–1159, 2008.
Shih, A. J., S. E. Telesco, and R. Radhakrishnan. Analysis of somatic mutations in cancer: molecular mechanisms of activation in the ErbB family of receptor tyrosine kinases. Cancers 3(1):1195–1231, 2011.
Shih, A., et al. The role for molecular modeling in multiscale cancer models. In: Multiscale Cancer Modeling of Cancer. Mathematical and Computational Biology Series, edited by T. S. Deisboeck, and G. Stamatakos. Boca Raton: Chapman & Hall/CRC, 2010, pp. 31–43.
Shih, A., et al. Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond interaction networks in ErbB family kinases. Biochem. J. 436:241–251, 2011.
Sorkin, A., et al. Epidermal growth factor receptor interaction with clathrin adaptors is mediated by the Tyr974-containing internalization motif. J. Biol. Chem. 271(23):13377–13384, 1996.
Stark, H., et al. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409(6819):539–542, 2001.
Suenaga, A., et al. Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal. Growth Factor Recept. 96(6):2278–2288, 2009.
Tama, F., and C. L. Brooks. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35:115–133, 2006.
Taylor, W. R., and Z. Katsimitsoulia. A coarse-grained molecular model for actin-myosin simulation. J. Mol. Graph. Model. 29(2):266–279, 2010.
Telesco, S. E., and R. Radhakrishnan. Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study. Biophys. J. 96(6):2321–2334, 2009.
Telesco, S. E., A. Shih, Y. Liu, and R. Radhakrishnan. Investigating molecular mechanisms of activation and mutation of the HER2 receptor tyrosine kinase through computational modeling and simulation. Cancer Research Journal 4(4):1–35, 2011.
Telesco, S. E., et al. A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network. Mol. BioSyst. 7(6):2066–2080, 2011.
Wang, E. (ed.). Cancer Systems Biology. Mathematical and Computational Biology Series. London: CRC Press/Taylor and Francis, 2010.
E, W., and B. Engquist. Multiscale modeling in computation. Notices AMS 50(9):1062–1070, 2003.
E, W., B. Engquist, and Z. Y. Huang. Heterogeneous multiscale method: a general methodology for multiscale modeling. Phys. Rev. B 67(9):092101, 2003.
Westerhoff, H. V., and B. O. Palsson. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22(10):1249–1252, 2004.
Yarden, Y., and M. X. Sliwkowski. Untangling the ErbB signaling network. Nat. Rev. Mol. Cell Biol. 2:127–137, 2001.
Zhang, X., et al. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell 125(6):1137–1149, 2006.
Acknowledgments
We acknowledge financial support from NSF grants CBET-0853389 and CBET-0853539. Computational resources were provided in part by the National Partnership for Advanced Computational Infrastructure (NPACI) under the allocation grant MRAC MCB060006. S.E.T. was supported by the National Institutes of Health under Ruth L. Kirschstein National Research Service Award 2T32HL007954 from the NIH-NHLBI, a National Science Foundation Graduate Research Fellowship, and a Graduate Assistantship in Areas of National Need (GAANN) from the Department of Education.
Conflicts of Interest
No conflicts of interest apply to this manuscript and related work.
Author information
Authors and Affiliations
Corresponding author
Additional information
Associate Editor Michael R. King oversaw the review of this article.
Rights and permissions
About this article
Cite this article
Telesco, S.E., Radhakrishnan, R. Structural Systems Biology and Multiscale Signaling Models. Ann Biomed Eng 40, 2295–2306 (2012). https://doi.org/10.1007/s10439-012-0576-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10439-012-0576-6