Abstract
Recent advances have led to the emergence of molecular biomechanics as an essential element of modern biology. These efforts focus on theoretical and experimental studies of the mechanics of proteins and nucleic acids, and the understanding of the molecular mechanisms of stress transmission, mechanosensing and mechanotransduction in living cells. In particular, single-molecule biomechanics studies of proteins and DNA, and mechanochemical coupling in biomolecular motors have demonstrated the critical importance of molecular mechanics as a new frontier in bioengineering and life sciences. To stimulate a more systematic study of the basic issues in molecular biomechanics, and attract a broader range of researchers to enter this emerging field, here we discuss its significance and relevance, describe the important issues to be addressed and the most critical questions to be answered, summarize both experimental and theoretical/computational challenges, and identify some short-term and long-term goals for the field. The needs to train young researchers in molecular biomechanics with a broader knowledge base, and to bridge and integrate molecular, subcellular and cellular level studies of biomechanics are articulated.
Similar content being viewed by others
References
Aksimentiev, A., I. A. Balabin, R. H. Fillingame, and K. Schulten. Insights into the molecular mechanism of rotation in the F-o sector of ATP synthase. Biophys. J. 86:1332–1344, 2004.
Alexander, N. R., et al. Extracellular matrix rigidity promotes invadopodia activity. Curr. Biol. 18:1295–1299, 2008.
Allen, F., et al. Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Syst. J. 40:310–327, 2001.
Autumn, K., and N. Gravish. Gecko adhesion: evolutionary nanotechnology. Philos. Trans. R. Soc. Lond. A 366:1575–1590, 2008.
Bao, G. Mechanics of biomolecules. J. Mech. Phys. Solids 50:2237–2274, 2002.
Bao, G., W. J. Rhee, and A. Tsourkas. Fluorescent probes for live-cell RNA detection. Annu. Rev. Biomed. Eng. 11:25–47, 2009.
Bao, G., A. Tsourkas, and P. J. Santangelo. Engineering nanostructured probes for sensitive intracellular gene detection. Mech. Chem. Biosyst. 1:23–36, 2004.
Basson, M. D. An intracellular signal pathway that regulates cancer cell adhesion in response to extracellular forces. Cancer Res. 68:2–4, 2008.
Bathe, M. A finite element framework for computation of protein normal modes and mechanical response. Proteins 70:1595–1609, 2008.
Bell, G. I. Models for the specific adhesion of cells to cells. Science 200:618–627, 1978.
Bisgrove, B. W., and H. J. Yost. The roles of cilia in developmental disorders and disease. Development 133:4131–4143, 2006.
Block, S. M., L. S. B. Goldstein, and B. J. Schnapp. Bead movement by single kinesin molecules studied with optical tweezers. Nature 348:348–352, 1990.
Brau, R. R., P. B. Tarsa, J. M. Ferrer, P. Lee, and M. J. Lang. Interlaced optical force-fluorescence measurements for single molecule biophysics. Biophys. J. 91:1069–1077, 2006.
Brower-Toland, B. D., et al. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl Acad. Sci. USA 99:1960–1965, 2002.
Chen, J., and J. A. Lopez. Interactions of platelets with subendothelium and endothelium. Microcirculation 12:235–246, 2005.
Choquet, D., D. P. Felsenfeld, and M. P. Sheetz. Extracellular matrix rigidity causes strengthening of integrin-cytoskeleton linkages. Cell 88:39–48, 1997.
Davies, P. F., and S. C. Tripathi. Mechanical stress mechanisms and the cell. An endothelial paradigm. Circ. Res. 72:239–245, 1993.
Dean, D. H., L. Han, C. Ortiz, and A. J. Grodzinsky. Nanoscale conformation and compressibility of cartilage aggrecan using micro-contact printing and atomic force microscopy. Macromolecules 38:4047–4049, 2005.
Dembo, M., D. C. Torney, K. Saxman, and D. Hammer. The reaction-limited kinetics of membrane-to-surface adhesion and detachment. Proc. R. Soc. Lond. B Biol. Sci. 234:55–83, 1988.
Deng, L., N. J. Fairbank, D. J. Cole, J. J. Fredberg, and G. N. Maksym. Airway smooth muscle tone modulates mechanically induced cytoskeletal stiffening and remodeling. J. Appl. Physiol. 99:634–641, 2005.
Effler, J. C., P. A. Iglesias, and D. N. Robinson. A mechanosensory system controls cell shape changes during mitosis. Cell Cycle 6:30–35, 2007.
Engler, A. J., S. Sen, H. L. Sweeney, and D. E. Discher. Matrix elasticity directs stem cell lineage specification. Cell 126:677–689, 2006.
Evans, E. Probing the relation between force—lifetime—and chemistry in single molecular bonds. Annu. Rev. Biophys. Biomol. Struct. 30:105–128, 2001.
Evans, E., K. Ritchie, and R. Merkel. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces. Biophys. J. 68:2580–2587, 1995.
Fischer, T., A. Agarwal, and H. Hess. A smart dust biosensor powered by kinesin motors. Nat. Nanotechnol. 4:162–166, 2009.
Florin, E. L., V. T. Moy, and H. E. Gaub. Adhesion forces between individual ligand–receptor pairs. Science 264:415–417, 1994.
Furuike, S., T. Ito, and M. Yamazaki. Mechanical unfolding of single filamin A (ABP-280) molecules detected by atomic force microscopy. FEBS Lett. 498:72–75, 2001.
Gao, M., D. Craig, V. Vogel, and K. Schulten. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. J. Mol. Biol. 323:939–950, 2002.
Gautam, M., A. Gojova, and A. I. Barakat. Flow-activated ion channels in vascular endothelium. Cell Biochem. Biophys. 46:277–284, 2006.
Ghosh, K., et al. Tumor-derived endothelial cells exhibit aberrant Rho-mediated mechanosensing and abnormal angiogenesis in vitro. Proc. Natl Acad. Sci. USA 105:11305–11310, 2008.
Gullingsrud, J., and K. Schulten. Gating of MscL studied by steered molecular dynamics. Biophys. J. 85:2087–2099, 2003.
Harris, P. C., and V. E. Torres. Understanding pathogenic mechanisms in polycystic kidney disease provides clues for therapy. Curr. Opin. Nephrol. Hypertens. 15:456–463, 2006.
Hess, H., and V. Vogel. Molecular shuttles based on motor proteins: active transport in synthetic environments. J. Biotechnol. 82:67–85, 2001.
Hoffmann, C., G. Gaietta, M. Bünemann, S. R. Adams, S. Oberdorff-Maass, B. Behr, J. P. Vilardaga, R. Y. Tsien, M. H. Ellisman, and M. J. Lohse. A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat. Methods 2:171–176, 2005.
Howard, J. Mechanical signaling in networks of motor and cytoskeletal proteins. Annu. Rev. Biophys. 38:217–234, 2009.
Howie, H. L., M. Glogauer, and M. So. The N-gonorrhoeae type IV pilus stimulates mechanosensitive pathways and cytoprotection through a pilT-dependent mechanism. PLoS Biol. 3:627–637, 2005.
Huang, W., and M. J. Lang. Mechanical design of translocating motor proteins. Cell Biochem. Biophys. 54:11–22, 2009.
Huang, B., W. Q. Wang, M. Bates, and X. W. Zhuang. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–813, 2008.
Hudspeth, A. J., Y. Choe, A. D. Mehta, and P. Martin. Putting ion channels to work: mechanoelectrical transduction, adaptation, and amplification by hair cells. Proc. Natl Acad. Sci. USA 97:11765–11772, 2000.
Hwang, W., M. J. Lang, and M. Karplus. Force generation in kinesin hinges on cover-neck bundle formation. Structure 16:62–71, 2008.
Hytonen, V. P., and V. Vogel. How force might activate talin’s vinculin binding sites: SMD reveals a structural mechanism. PLoS Comput. Biol. 4:e24, 2008.
Ingber, D. E. Cellular mechanotransduction: putting all the pieces together again. FASEB J. 20:811–827, 2006.
Iozzo, R. V. (ed.). Proteoglycans: Structure, Biology, and Molecular Interactions. New York: Marcel Dekker, 2000.
Jares-Erijman, E. A., and T. M. Jovin. Imaging molecular interactions in living cells by FRET microscopy. Curr. Opin. Chem. Biol. 10:409–416, 2006.
Johnson, C. P., H. Y. Tang, C. Carag, D. W. Speicher, and D. E. Discher. Forced unfolding of proteins within cells. Science 317:663–666, 2007.
Kamm, R. D., and M. R. Kaazempur-Mofrad. On the molecular basis for mechanotransduction. Mech. Chem. Biosyst. 1:201–209, 2004.
Khalil, A. S., D. C. Appleyard, A. K. Labno, A. Georges, M. Karplus, A. M. Belcher, W. Hwang, and M. J. Lang. Kinesin’s cover-neck bundle folds forward to generate force. Proc. Natl Acad. Sci. USA 105:9247–19252, 2008.
Kolahi, K. S., and M. R. Mofrad. Molecular mechanics of filamin’s rod domain. Biophys. J. 94:1075–1083, 2008.
Kong, F., A. J. García, A. P. Mould, M. J. Humphries, and C. Zhu. Demonstration of catch bonds between an integrin and its ligand. J. Cell Biol. 185:1275–1284, 2009.
Konstantopoulos, K., W. D. Hanley, and D. Wirtz. Receptor–ligand binding: ‘catch’ bonds finally caught. Curr. Biol. 13:R611–R613, 2003.
Lee, S. E., S. Chunsrivirot, R. D. Kamm, and M. R. Mofrad. Molecular dynamics study of talin–vinculin binding. Biophys. J. 95:2027–2036, 2008.
Lee, S. E., R. D. Kamm, and M. R. Mofrad. Force-induced activation of talin and its possible role in focal adhesion mechanotransduction. J. Biomech. 40:2096–2106, 2007.
Lee, J. H., et al. Artificially engineered magnetic nanoparticles for ultra-sensitive molecular imaging. Nat. Med. 13:95–99, 2007.
Lehoux, S., Y. Castier, and A. Tedgui. Molecular mechanisms of the vascular responses to haemodynamic forces. J. Intern. Med. 259:381–392, 2006.
Lou, J. Z., and C. Zhu. Flow induces loop-to-beta-hairpin transition on the beta-switch of platelet glycoprotein Ib alpha. Proc. Natl Acad. Sci. USA 105:13847–13852, 2008.
Marszalek, P. E., et al. Mechanical unfolding intermediates in titin modules. Nature 402:100–103, 1999.
Martin, B., B. N. Giepmans, S. R. Adams, and R. Y. Tsien. Mammalian cell-based optimization of the biarsenical-binding tetracysteine motif for improved fluorescence and affinity. Nat. Biotechnol. 23:1308–1314, 2005.
Meng, F., T. M. Suchyna, and F. Sachs. A fluorescence energy transfer-based mechanical stress sensor for specific proteins in situ. FEBS J. 275:3072–3087, 2008.
Mertz, D., C. Vogt, J. Hemmerlé, J. Mutterer, V. Ball, J. C. Voegel, P. Schaaf, and P. Lavalle. Mechanotransductive surfaces for reversible biocatalysis activation. Nat. Mater. 8:731–735, 2009.
Mofrad, M. R., J. Golji, N. A. Abdul Rahim, and R. D. Kamm. Force-induced unfolding of the focal adhesion targeting domain and the influence of paxillin binding. Mech. Chem. Biosyst. 1:253–265, 2004.
Nayak, G. D., H. S. Ratnayaka, R. J. Goodyear, and G. P. Richardson. Development of the hair bundle and mechanotransduction. Int. J. Dev. Biol. 51:597–608, 2007.
Neuman, K. C. L., T. Lionnet, and J.-F. Allemand. Single-molecule micromanipulation techniques. Annu. Rev. Mater. Res. 37:33–67, 2007.
Ng, L. G., A. J. Grodzinsky, J. D. Sandy, A. H. K. Plaas, and C. Ortiz. Individual aggrecan molecules and their constituent glycosaminoglycans visualized via atomic force microscopy. J. Structural Biol. 143:242–257, 2003.
Oberhauser, A. F., C. Badilla-Fernandez, M. Carrion-Vazquez, and J. M. Fernandez. The mechanical hierarchies of fibronectin observed with single-molecule AFM. J. Mol. Biol. 319:433–447, 2002.
O’Hare, H. M., K. Johnsson, and A. Gautier. Chemical probes shed light on protein function. Curr. Opin. Struct. Biol. 17:488–494, 2007.
Parekh, A., and A. M. Weaver. Regulation of cancer invasiveness by the physical extracellular matrix environment. Cell Adh. Migr. 3:288–292, 2009.
Park, T. J., et al. Protein nanopatterns and biosensors using gold binding polypeptide as a fusion partner. Anal. Chem. 78:7197–7205, 2006.
Pfister, B. J., T. P. Weihs, M. Betenbaugh, and G. Bao. An in vitro uniaxial stretch model for axonal injury. Ann. Biomed. Eng. 31:589–598, 2003.
Puchner, E. M., A. Alexandrovich, A. L. Kho, U. Hensen, L. V. Schäfer, B. Brandmeier, F. Gräter, H. Grubmüller, H. E. Gaub, and M. Gautel. Mechanoenzymatics of titin kinase. Proc. Natl Acad. Sci. USA 105:13385–13390, 2008.
Rief, M., M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276:1109–1112, 1997.
Santangelo, P., N. Nitin, and G. Bao. Nanostructured probes for RNA detection in living cells. Ann. Biomed. Eng. 34:39–50, 2006.
Siedlecki, C. A., et al. Shear-dependent changes in the three-dimensional structure of human von Willebrand factor. Blood 88:2939–2950, 1996.
Silver, F. H., and L. M. Siperko. Mechanosensing and mechanochemical transduction: how is mechanical energy sensed and converted into chemical energy in an extracellular matrix? Crit. Rev. Biomed. Eng. 31:255–331, 2003.
Sims, P. A., and X. S. Xie. Probing dynein and kinesin stepping with mechanical manipulation in a living cell. Chemphyschem 10:1511–1516, 2009.
Smith, M. L., et al. Force-induced unfolding of fibronectin in the extracellular matrix of living cells. PLoS Biol. 5:e268, 2007.
Spetzler, D., et al. Recent developments of bio-molecular motors as on-chip devices using single molecule techniques. Lab Chip 7:1633–1643, 2007.
Strick, T. R., J. F. Allemand, D. Bensimon, and V. Croquette. Stress-induced structural transitions in DNA and proteins. Annu. Rev. Biophys. Biomol. Struct. 29:523–543, 2000.
Suchyna, T., and F. Sachs. Mechanical and electrical properties of membranes from dystrophic and normal mouse muscle. J. Physiol. 581:369–387, 2007.
Sundberg, M., et al. Actin filament guidance on a chip: toward high-throughput assays and lab-on-a-chip applications. Langmuir 22:7286–7295, 2006.
Suri, S. S., H. Fenniri, and B. Singh. Nanotechnology-based drug delivery systems. J. Occup. Med. Toxicol. 2:16, 2007.
Thomas, W. E. Catch bonds in adhesion. Annu. Rev. Biomed. Eng. 10:39–57, 2008.
Tschumperlin, D. J., et al. Mechanotransduction through growth-factor shedding into the extracellular space. Nature 429:83–86, 2004.
Tzakos, A. G., C. R. Grace, P. J. Lukavsky, and R. Riek. NMR techniques for very large proteins and RNAs in solution. Annu. Rev. Biophys. Biomol. Struct. 35:319–342, 2006.
Usami, S., H. H. Chen, Y. H. Zhao, S. Chien, and R. Skalak. Design and construction of a linear shear-stress flow chamber. Ann. Biomed. Eng. 21:77–83, 1993.
Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112:467, 2003.
van den Heuvel, M. G. L., and C. Dekker. Motor proteins at work for nanotechnology. Science 317:333–336, 2007.
Vogel, V. Mechanotransduction involving multimodular proteins: converting force into biochemical signals. Annu. Rev. Biophys. Biomol. Struct. 35:459–488, 2006.
Vogel, V., and M. Sheetz. Local force and geometry sensing regulate cell functions. Nat. Rev. Mol. Cell Biol. 7:265–275, 2006.
Williams, J. M., V. Rayan, D. R. Sumner, and E. J. Thonar. The use of intra-articular Na-hyaluronate as a potential chondroprotective device in experimentally induced acute articular cartilage injury and repair in rabbits. J. Orthop. Res. 21:305–311, 2003.
Willig, K. I., S. O. Rizzoli, V. Westphal, R. Jahn, and S. W. Hell. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 440:935–939, 2006.
World, C. J., G. Garin, and B. Berk. Vascular shear stress and activation of inflammatory genes. Curr. Atheroscler. Rep. 8:240–244, 2006.
Yago, T., J. Lou, T. Wu, J. Yang, J. J. Miner, L. Coburn, J. A. López, M. A. Cruz, J.-F. Dong, L. V. McIntire, R. M. McEver, and C. Zhu. Platelet glycoprotein Iba forms catch bonds with human WT vWF but not with type 2B von Willebrand Disease vWF. J. Clin. Invest. 118:3195–3207, 2008.
Yefimov, S., E. van der Giessen, P. R. Onck, and S. J. Marrink. Mechanosensitive membrane channels in action. Biophys. J. 94:2994–3002, 2008.
Yuan, C., A. Chen, P. Kolb, and V. T. Moy. Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. Biochemistry 39:10219–10223, 2000.
Zaman, M. H., and M. R. Kaazempur-Mofrad. How flexible is alpha-actinin’s rod domain? Mech. Chem. Biosyst. 1:291–302, 2004.
Zhu, C., G. Bao, and N. Wang. Cell mechanics: mechanical response, cell adhesion, and molecular deformation. Annu. Rev. Biomed. Eng. 2:189–226, 2000.
Zhu, C., and R. P. McEver. Catch bonds: physical models and biological functions. Mol. Cell. Biomech. 2:91–104, 2005.
Acknowledgments
This work was supported by NIH as a Program of Excellence in Nanotechnology (UO1HL80711-05 to GB), by NIH Grants R01GM076689-01 (RDK), R01AR033236-26 (AJG), R01GM087677-01A1 (WH), R01AI44902 (CZ) and R01AI38282 (CZ), and by NSF Grant CMMI-0645054 (WT), CBET-0829205 (MRKM) and CAREER-0955291 (MRKM).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bao, G., Kamm, R.D., Thomas, W. et al. Molecular Biomechanics: The Molecular Basis of How Forces Regulate Cellular Function. Cel. Mol. Bioeng. 3, 91–105 (2010). https://doi.org/10.1007/s12195-010-0109-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12195-010-0109-z