Abstract
In this chapter we develop micromechanics-based models of three-dimensional crystallized protein molecules with tetragonal lysozyme as an example system. While certain crystallographic directions exhibit purely elastic behavior, others exhibit elastoplastic response. The yield stress and critical resolved shear stress are observed to be sensitive to temperature and the amount of intracrystalline water. An increase in temperature and the amount of intracrystalline water molecules leads to a decrease in the critical resolved shear stress of the slip systems and makes the crystal softer. The analysis presented here may be applied to other protein crystal systems as well.
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References
Whitesides G M, Boncheva M. Beyond molecules: Self-assembly of mesoscopic and macroscopic components. Proc Natl Acad Sci USA 99: 4769–4774, 2002.
He Y, Ye T, Su M, et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature, 452: 198–202, 2008.
Rothemund P W K. Folding DNA to create nanoscale shapes and patterns. Nature, 440: 2006.
Hanying L, Carter J D. LaBean T H. Nanofabrication by DNA self-assembly. Materialstoday, 12: 24–32, 2009.
Petka W A, Harden J L, McGrath K P, et al. Reversible hydrogels from selfassembling artificial proteins. Science, 281: 389–392, 1998.
Holmes T C, Delacalle S, Su X, Rich A, et al. Extensive neurite outgrowth and active neuronal synapses on peptide scaffolds. Proc Natl Acad Sci USA, 97: 6728–6733, 2000.
Ghadiri M R, Tirrell D A. Chemistry at the crossroads. Curr Opin Chem Biol, 4: 661–662, 2000.
Fernandez-Lopez S, Kim H S, Choi E C, et al. Antibacterial agents based on the cyclic D, L-alphapeptide architecture. Nature, 412: 452–455, 2001.
Aggeli A, Nyrkova I A, Bell M, et al. Hierarchical self-assembly of chiral rodlike molecules as a model for peptide beta-sheet tapes, ribbons, fibrils, and fibers. Proc Natl Acad Sci USA, 98: 11857–11862, 2001.
Marini D M, Hwang W, Lauffenburger D A, et al. Left handed helical ribbon intermediates in the self-assembly of a beta-sheet peptide. Nano Letters, 2: 295–299, 2002.
Caplan M R, Moore P N, Zhang S, et al. Self-assembly of a beta-sheet protein governed by relief of electrostatic repulsion relative to van der Waals attraction. Biomacromolecules, 1: 627–631, 2000.
Vauthey S, Santoso S, Gong H, et al. Molecular self assembly of surfactantlike peptides to form nanotubes and nanovesicles. Proc Natl Acad Sci USA, 99: 5355–5360, 2002.
Santoso S, Hwang W, Hartman H, et al. Self-assembly of surfactant-like peptides with variable glycine tails to form nanotubes and nanovesicles. Nano Letters, 2: 687–691, 2002.
Marsh E N, DeGrado W F. Noncovalent self-assembly of a heterotetrameric diiron protein. Proc Natl Acad Sci USA, 99: 5150–5154, 2002.
Moffet D A, Case M A, House J C, et al. Carbon monoxide binding by de novo heme proteins derived from designed combinatorial libraries. J Am Chem Soc, 123: 2109–2115, 2001.
Nowak A P, Breedveld V, Pakstis L, et al. Rapidly recovering hydrogel scaffolds from selfassembling diblock copolypeptide amphiphiles. Nature, 417: 424–428, 2002.
Whaley S R, English D S, Hu E L, et al. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature, 405: 665–668, 2000.
Lee SW, Mao C, Flynn C E, et al. Ordering of quantum dots using genetically engineered viruses. Science, 296: 892–895, 2002.
Hartgerink J D, Beniash E, Stupp S I. Self-assembly and mineralization of peptide-amphiphile nanofibers. Science, 294: 1684–1687, 2001.
Hartgerink J D, Beniash E, Stupp S I. Peptide-amphiphile nanofibers: a versatile scaffold for the preparation of self-assembling materials. Proc Natl Acad Sci USA, 99: 5133–5138, 2002.
Szela S, Avtges P, Valluzzi R, et al. Reduction-oxidation control of beta-sheet assembly in genetically engineered silk. Biomacromolecules, 1: 534–542, 2000.
Zhou Y, Wu S, Conticello V P. Genetically directed synthesis and spectroscopic analysis of a protein polymer derived from a flagelliform silk sequence. Biomacromolecules, 2: 111–125, 2001.
Zhou C Z, Confalonieri F, Jacquet M, et al. Silk fibroin: Structural implications of a remarkable amino acid sequence. Proteins, 44: 119–122, 2001.
Zhang S, Marini D M, Hwang W, et al. Design of nanostructured biological materials through self-assembly of peptides and proteins. Current Opinion in Chemical Biology, 6: 865–871, 2002.
Sarikaya M, tamerler C, Jen A Y, et al. Molecular biomimetics: Nanotechnology through biology. Nature, 2: 577–585, 2003.
Malek K. Solute transport in orthorhombic lysozyme crystals: A molecular simulation study. Biotechnol. Lett., 29: 1865–1873, 2007.
Eddaoudi M, Kim J, Rosi N, et al. Systematic design of pore size and functionality in isoreticular MOFs and their application in methane storage. Science, 295: 469, 2002.
St Clair N, Shenoy B, Jacob J D, et al. Cross-linked proteins for vaccine delivery. Proc. Natl. Acad. Sci. USA, 96: 9469–9474, 1999.
Blundell T L, Jhoti H, Abell C. High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Discov, 1: 45–54, 2003.
Vilenchik L Z, Griffith J P, St Clair N L, et al. Protein crystals as novel microporous materials. J. Am. Chem. Soc., 120: 4290–4294, 1998.
Margolin A L, Navia M A. Protein crystals as novel catalytic materials. Angew Chem Int Ed, 40: 2204–2222, 2001.
Cvetkovic A, Picioreanu C, Straathof A J J, et al. Quantification of binary diffusion in protein crystals. J. Phys. Chem. B, 109: 10561–10566, 2005.
Daniel R M. The upper limits of enzyme thermal stability. Enzyme and Microbial Technology, 19: 74–79, 1996.
Pechenov S, Shenoy B, Yang M X, et al. Injectable controlled release formulations incorporating protein crystals. Control Release, 96: 149–158, 2004.
Margolin A L, Navia M A. Protein crystals as novel catalytic materials. Angew. Chem., Int. Ed. Engl., 40: 2204–2222, 2001.
Tait S, White E T, Litster J D. Mechanical characterization of protein crystals. Part. Part. Syst. Charact., 25: 266, 2008.
Tachibana M, Kobayashi Y, Shimazu T, et al. Growth and mechanical properties of lysozyme crystals. Journal of Crystal Growth, 198/199: 661–664, 1999.
Zamiri A, De S. Modeling the mechanical response of tetragonal lysozyme crystals. Langmuir, 26: 4251–4257, 2001.
Gilman J J. Micromechanics of Flow in Solids. McGraw-Hill, New York, 195, 1962.
Koizumi H, Tachibana M, Kawamoto H, et al. Temperature dependence of microhardness of tetragonal hen-egg-white lysozyme single crystals. Philosophical Magazine, 84: 2961–2968, 2004.
Koizumi H, Tachibana M, Kojima K. Elastic constants in tetragonal hen eggwhite lysozyme crystals containing large amount of water. Phys. Rev E, 79: 061917, 2009.
Speziale S, Jiang F, Caylor C L, et al. Sound velocity and elasticity of tetragonal lysozyme crystals by Brillouin spectroscopy. Biophys. J., 85: 3202, 2003.
Koizumi, H, Kawamoto, H, Tachibana M, et al. Effect of intracrystalline water on micro-Vickers hardness in tetragonal hen egg-white lysozyme single crystals. J. Phys. D: Appl. Phys., 41: 074019, 2008.
Tachibana M, Koizumi H, Kojima K. Effect of intracrystalline water on longitudinal sound velocity in tetragonal hen-egg-white lysozyme crystals. Phys. Rev. E, 69: 051921, 2004.
Harata K, Muraki M, Jigami Y. Role of Arg115 in the catalytic action of human lysozyme: X-ray structure of His115 and Glu115 mutants. J. Mol. Biol., 233: 524, 1993.
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© 2012 Higher Education Press, Beijing and Springer-Verlag Berlin Heidelberg
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Zamiri, A.R., De, S. (2012). Micromechanics of 3D Crystallized Protein Structures. In: Advances in Soft Matter Mechanics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19373-6_7
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DOI: https://doi.org/10.1007/978-3-642-19373-6_7
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