Abstract
Keratin, an alpha-helical protein, is an abundant material that forms the basis of hair and hoof, and is a composite of alpha-helical coiled coils with dense disulfide bonding between helical protein domains. Here, we report a molecular analysis of the mechanics of disulfide bonded alpha-helical protein filaments, focusing on a systematic assessment of structure–property relationships and deformation and failure mechanisms, carried out using a full atomistic explicit water model based on the CHARMM force field, extended here to capture the breaking of disulfide bonds in varied chemical microenvironments. By considering a three-strand alpha-helical model of an assembly of disulfide bonds under an external loading, we demonstrate that weak disulfide cross-link results in a highly cooperative behavior. Strong disulfide bonding resist greater external load, but the cooperative behavior is reduced. We compare the mechanical behavior of the disulfide bonded systems to a molecule with weaker H-bonds between alpha-helix domains. Under mechanical loading, H-bonds between the protein filaments are easily sacrificed and the alpha-helical structure is maintained, but the system has a lower strength. Our atomistic models provide fundamental insight into the effect of disulfide cross-link on mechanical properties of alpha-helix-based protein filament and reveals that the dependence of disulfide bond strength on the chemical microenvironment enables a tunable fiber strength by a factor of ≈2.5.
Similar content being viewed by others
References
Betz, S. F. (1993). Disulfide bonds and the stability of globular proteins. Protein Science, 2(10), 1551–1558.
Hogg, P. J. (2003). Disulfide bonds as switches for protein function. Trends in Biochemical Sciences, 28(4), 210–214.
Wedemeyer, W. J., et al. (2000). Disulfide bonds and protein folding†. Biochemistry, 39(15), 4207–4216.
Sevier, C. S., & Kaiser, C. A. (2002). Formation and transfer of disulphide bonds in living cells. Nature Reviews Molecular Cell Biology, 3(11), 836–847.
Root, B. C., et al. (2009). Design of a heterotetrameric coiled coil. Protein Science, 18(2), 329–336.
Kim, P. S., & Baldwin, R. L. (1990). Intermediates in the folding reactions of small proteins. Annual Review of Biochemistry, 59, 631–660.
Wagschal, K., Tripet, B., Hodges, R. S. (1999). De novo design of a model peptide sequence to examine the effects of single amino acid substitutions in the hydrophobic core on both stability and oligomerization state of coiled-coils. Journal of Molecular Biology, 285(2), 785–803.
Almeida, A. M., Li, R., Gellman, S. H. (2011). Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking. Journal of the American Chemical Society, 134(1), 75–78.
Gong, R., et al. (2009). Engineered human antibody constant domains with increased stability. Journal of Biological Chemistry, 284(21), 14203–14210.
Saerens, D., et al. (2008). Disulfide bond introduction for general stabilization of immunoglobulin heavy-chain variable domains. Journal of Molecular Biology, 377(2), 478–488.
Ciaccio, N. A., & Laurence, J. S. (2009). Effects of disulfide bond formation and protein helicity on the aggregation of activating transcription factor 5. Molecular Pharmaceutics, 6(4), 1205–1215.
Grützner, A., et al. (2009). Modulation of titin-based stiffness by disulfide bonding in the cardiac titin N2-B unique sequence. Biophysical Journal, 97(3), 825–834.
Wang, J., Xu, G., Borchelt, D. R. (2006). Mapping superoxide dismutase 1 domains of non-native interaction: roles of intra- and intermolecular disulfide bonding in aggregation. Journal of Neurochemistry, 96(5), 1277–1288.
Pande, A., Gillot, D., Pande, J. (2009). The cataract-associated R14C mutant of human γD-crystallin shows a variety of intermolecular disulfide cross-links: a Raman spectroscopic study. Biochemistry, 48(22), 4937–4945.
Buehler, M. J., & Yung, Y. C. (2009). Deformation and failure of protein materials in physiologically extreme conditions and disease. Nature Materials, 8(3), 175–188.
Kim, P. S., Berger, B., Wolf, E. (1997). MultiCoil: a program for predicting two-and three-stranded coiled coils. Protein Science, 6(6), 1179–1189.
Parry, D. A. D., Fraser, R. D. B., Squire, J. M. (2008). Fifty years of coiled-coils and α-helical bundles: a close relationship between sequence and structure. Journal of Structural Biology, 163(3), 258–269.
Apostolovic, B., Danial, M., Klok, H. A. (2010). Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials. Chemical Society Reviews, 39(9), 3541–3575.
Pandya, M. J., et al. (2000). Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis. Biochemistry, 39(30), 8728–8734.
Papapostolou, D., et al. (2007). Engineering nanoscale order into a designed protein fiber. Proceedings of the National Academy of Sciences of the United States of America, 104(26), 10853–10858.
Mahmoud, Z. N., et al. (2010). The non-covalent decoration of self-assembling protein fibers. Biomaterials, 31(29), 7468–7474.
Smith, A. M., et al. (2006). Engineering increased stability into self-assembled protein fibers. Advanced Functional Materials, 16(8), 1022–1030.
Qin, Z., et al. (2012). Structural, mechanical and functional properties of intermediate filaments from the atomistic to the cellular scales. In S. Li & B. Sun (Eds.), Advances in cell mechanics (pp. 117–166). Berlin: Springer.
Goldman, R. D., et al. (2008). Intermediate filaments: versatile building blocks of cell structure. Current Opinion in Cell Biology, 20(1), 28–34.
de Guzman, R. C., et al. (2011). Mechanical and biological properties of keratose biomaterials. Biomaterials, 32(32), 8205–8217.
Carmofonseca, M., & Davidferreira, J. F. (1990). Interactions of intermediate filaments with cell structures. Electron Microscopy Reviews, 3(1), 115–141.
Feughelman, M. (2002). Natural protein fibers. Journal of Applied Polymer Science, 83(3), 489–507.
Oxenham, W. (1989). The mechanics of wool structures R. Postle, G. A. Carnaby and S. de Jong, Ellis Horwood, Chichester, 1988. pp. 462, price £59.50. ISBN 0-7458-0322-9. British. Polymer Journal, 21(3), 279–279.
Chou, S. F., & Overfelt, R. A. (2011). Tensile deformation and failure of North American porcupine quills. Materials Science & Engineering C-Materials for Biological Applications, 31(8), 1729–1736.
Seshadri, I. P., & Bhushan, B. (2008). In situ tensile deformation characterization of human hair with atomic force microscopy. Acta Materialia, 56(4), 774–781.
Fudge, D. S., & Gosline, J. M. (2004). Molecular design of the α-keratin composite: insights from a matrix-free model, hagfish slime threads. Proceedings of the Royal Society of London. Series B: Biological Sciences, 271(1536), 291–299.
Guthold, M., et al. (2007). A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers. Cell Biochemistry and Biophysics, 49(3), 165–181.
Bertram, J. E., & Gosline, J. M. (1987). Functional design of horse hoof keratin: the modulation of mechanical properties through hydration effects. Journal of Experimental Biology, 130(1), 121–136.
Guzman, C., et al. (2006). Exploring the mechanical properties of single vimentin intermediate filaments by atomic force microscopy. Journal of Molecular Biology, 360(3), 623–630.
Smith, T. A., & Parry, D. A. D. (2008). Three-dimensional modelling of interchain sequence similarities and differences in the coiled-coil segments of keratin intermediate filament heterodimers highlight features important in assembly. Journal of Structural Biology, 162(1), 139–151.
Akkermans, R. L. C., & Warren, P. B. (2004). Multiscale modelling of human hair. Philosophical Transactions of the Royal Society of London, Series A: Mathematical, Physical and Engineering Sciences, 362(1821), 1783–1793.
Knopp, B., Jung, B., Wortmann, F. J. (1997). Modeling of the transition temperature for the helical denaturation of alpha-keratin intermediate filaments. Macromolecular Theory and Simulations, 6(1), 1–12.
Danciulescu, C., Nick, B., Wortmann, F.-J. (2004). Structural stability of wild type and mutated α-keratin fragments: molecular dynamics and free energy calculations. Biomacromolecules, 5(6), 2165–2175.
Qin, Z., Kreplak, L., Buehler, M. J. (2009). Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments. PLoS ONE, 4(10), e7294.
Humphrey, W., Dalke, A., Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14, 6.
Plimpton, S. (1995). Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117(1), 1–19.
MacKerell, A. D., et al. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B, 102(18), 3586–3616.
Wiita, A. P., et al. (2006). Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques. Proceedings of the National Academy of Sciences of the United States of America, 103(19), 7222–7227.
Qin, Z., Kreplak L., Buehler, M.J. (2009) Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments. PLoS ONE 4(10): e7294.
Ackbarow, T., Keten, S., Buehler, M. J. (2009). A multi-timescale strength model of alpha-helical protein domains. Journal of Physics-Condensed Matter, 21, 035111.
Ackbarow, T., et al. (2007). Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of α-helical and β-sheet protein domains. Proceedings of the National Academy of Sciences, 104(42), 16410–16415.
Yoon, G., Na, S., Eom, K. (2012) Loading device effect on protein unfolding mechanics. Journal of Chemical Physics 137(2).
Maitra, A., & Arya, G. (2011). Influence of pulling handles and device stiffness in single-molecule force spectroscopy. Physical Chemistry Chemical Physics, 13(5), 1836–1842.
Chou, C.-C., & Buehler, M. J. (2011). Bond energy effects on strength, cooperativity and robustness of molecular structures. Interface Focus, 1(5), 734–743.
Buehler, M. J. (2007) Molecular nanomechanics of nascent bone: fibrillar toughening by mineralization. Nanotechnology 18, 295102.
Buehler, M. J., & Ackbarow, T. (2008). Nanomechanical strength mechanisms of hierarchical biological materials and tissues. Computer Methods in Biomechanics and Biomedical Engineering, 11(6), 595–607.
Acknowledgments
This work was supported by AFOSR and ARO-MURI.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Chou, CC., Buehler, M.J. Molecular Mechanics of Disulfide Bonded Alpha-Helical Protein Filaments. BioNanoSci. 3, 85–94 (2013). https://doi.org/10.1007/s12668-012-0065-2
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12668-012-0065-2