Mechanical Properties of Super-soft Biomolecular Systems: Application to Twenty Solvated Canonical Amino Acids
DOI:
https://doi.org/10.37155/2972-449X-0101-1Keywords:
Amino acids, Mechanical properties, Soft biomolecules, Solvated structure models, First-principles calculations, Density functional theoryAbstract
Amino acids (AAs) are the basic building blocks of proteins and regulate the body’s metabolism. The mechanical properties of proteins play an essential role in their functionalities in addition to their structure and dynamic properties. They are paramount in understanding the flexibility, rigidity, and ability to resist deformation. It is critical to investigate the mechanical properties of the twenty standard AAs that comprise the protein. Herein, we have developed a computational approach based on a detailed ab initio quantum mechanical method based on density functional theory that can calculate the mechanical properties of strategically designed models of solvated AAs. This de novo approach has been applied to twenty standard amino acids as the first step towards exploring the mechanical properties of super-soft biomolecular systems. The calculated properties include the Young’s modulus, shear modulus, bulk modulus, and Poisson’s ratio under different strains. We have identified AAs with relatively higher/lower compressibility, rigidity, flexibility, stretchability, and hardness based on their mechanical properties. Our findings are valuable as the starting point for future studies on large peptides or small proteins.
References
Xu, Q., H. Deng, X. Li, , et al. Application of amino acids in the structural modification of natural products: A review. Frontiers in Chemistry, 2021, 9, 650569, https://doi.org/10.3389/fchem.2021.650569.
Brosnan, J.T. and M.E. Brosnan. The sulfur-containing amino acids: an overview. The Journal of nutrition, 2006, 136(6), 1636S-1640S, https://doi.org/10.1093/jn/136.6.1636S.
Song, X., B. Dong, X. Kong, et al. A sensitive and selective red fluorescent probe for imaging of cysteine in living cells and animals. Analytical Methods, 2017, 9(12), 1891-1896, https://doi.org/10.1039/C7AY00155J.
Huang, F. and W.M. Nau. A conformational flexibility scale for amino acids in peptides. Angewandte Chemie International Edition, 2003, 42(20), 2269-2272, https://doi.org/10.1002/anie.200250684.
Schwartz, G.W., T. Shauli, M. Linial, et al. Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Scientific Reports, 2019, 9(1), 1-9, https://doi.org/10.1038/s41598-019-53452-3.
Jalab, R., M.A. Saad, I.A. Hussein, et al. Calcite scale inhibition using environmental-friendly amino acid inhibitors: DFT investigation. ACS omega, 2021, 6(47), 32120-32132, https://doi.org/10.1021/acsomega.1c04888.
Brinzei, M., A. Stefaniu, O. Iulian, et al. Density functional theory (DFT) and thermodynamics calculations of amino acids with polar uncharged side chains. Chemistry Proceedings, 2020, 3(1), https://doi.org/10.3390/ecsoc-24-08420.
Dehdab, M., M. Shahraki, and S.M. Habibi-Khorassani. Theoretical study of inhibition efficiencies of some amino acids on corrosion of carbon steel in acidic media: green corrosion inhibitors. Amino acids, 2016, 48(1), 291-306, https://doi.org/10.1007/s00726-015-2090-2.
Frau, J. and D. Glossman-Mitnik. Conceptual DFT descriptors of amino acids with potential corrosion inhibition properties calculated with the latest minnesota density functionals. Frontiers in Chemistry, 2017, 5, 16, https://doi.org/10.3389/fchem.2017.00016.
Fu, J.-j., S.-n. Li, Y. Wang, et al. Computational and electrochemical studies of some amino acid compounds as corrosion inhibitors for mild steel in hydrochloric acid solution. Journal of materials science, 2010, 45, 6255-6265, https://doi.org/10.1007/s10853-010-4720-0.
Kaya, S., B. Tüzün, C. Kaya, et al. Determination of corrosion inhibition effects of amino acids: quantum chemical and molecular dynamic simulation study. Journal of the Taiwan Institute of Chemical Engineers, 2016, 58, 528-535, https://doi.org/10.1016/j.jtice.2015.06.009.
Kol, N., L. Adler-Abramovich, D. Barlam, et al. Self-assembled peptide nanotubes are uniquely rigid bioinspired supramolecular structures. Nano letters, 2005, 5(7), 1343-1346, https://doi.org/10.1021/nl0505896.
Niu, L., X. Chen, S. Allen, et al. Using the bending beam model to estimate the elasticity of diphenylalanine nanotubes. Langmuir, 2007, 23(14), 7443-7446, https://doi.org/10.1021/la7010106.
Dave, D.J., K.D. Parikh, and M.J. Joshi. Vickers Micro-hardness Studies of Amino acids (L-histidine, L-threonien and DL-methionine) doped KDP crystals. in Advanced Materials Research. 2013. Trans Tech Publ.
Ji, W., B. Xue, Z.A. Arnon, et al. Rigid tightly packed amino acid crystals as functional supramolecular materials. ACS nano, 2019, 13(12), 14477-14485, https://doi.org/10.1021/acsnano.9b08217.
Azuri, I., E. Meirzadeh, D. Ehre, et al. Unusually large Young’s moduli of amino acid molecular crystals. Angewandte Chemie International Edition, 2015, 54(46), 13566-13570, https://doi.org/10.1002/anie.201505813.
Matveychuk, Y.V., E.V. Bartashevich, and V.G. Tsirelson. How the H-bond layout determines mechanical properties of crystalline amino acid hydrogen maleates. Crystal Growth & Design, 2018, 18(6), 3366-3375, https://doi.org/10.1021/acs.cgd.8b00067.
Gao, Z. and J.P. Desai. Estimating zero-strain states of very soft tissue under gravity loading using digital image correlation. Medical image analysis, 2010, 14(2), 126-137, https://doi.org/10.1016/j.media.2009.11.002.
Miller, K. How to test very soft biological tissues in extension? Journal of Biomechanics, 2001, 34(5), 651-657, https://doi.org/10.1016/S0021-9290(00)00236-0.
Miller, K. and K. Chinzei. Mechanical properties of brain tissue in tension. Journal of biomechanics, 2002, 35(4), 483-490, https://doi.org/10.1016/S0021-9290(01)00234-2.
Chui, C., E. Kobayashi, X. Chen, et al. Combined compression and elongation experiments and non-linear modelling of liver tissue for surgical simulation. Medical and Biological Engineering and Computing, 2004, 42, 787-798, https://doi.org/10.1007/BF02345212.
Chui, C., E. Kobayashi, X. Chen, et al. Transversely isotropic properties of porcine liver tissue: experiments and constitutive modelling. Medical & biological engineering & computing, 2007, 45, 99-106, https://doi.org/10.1007/s11517-006-0137-y.
Roan, E. and K. Vemaganti. The nonlinear material properties of liver tissue determined from no-slip uniaxial compression experiments. 2007, https://doi.org/10.1115/1.2720928.
Lee, W., A. Ostadi Moghaddam, S. Shen, et al. An optomechanogram for assessment of the structural and mechanical properties of tissues. Scientific reports, 2021, 11(1), 1-12, https://doi.org/10.1038/s41598-020-79602-6.
Serwane, F., A. Mongera, P. Rowghanian, et al. In vivo quantification of spatially varying mechanical properties in developing tissues. Nature methods, 2017, 14(2), 181-186, https://doi.org/10.1038/nmeth.4101.
Yang, L.-Q., P. Sang, Y. Tao, et al. Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. Journal of Biomolecular Structure and Dynamics, 2014, 32(3), 372-393, https://doi.org/10.1080/07391102.2013.770372.
Bao, G. Protein mechanics: a new frontier in biomechanics. Experimental mechanics, 2009, 49, 153-164, https://doi.org/10.1007/s11340-008-9154-0.
Caplan, M.R., E.M. Schwartzfarb, S. Zhang, et al. Effects of systematic variation of amino acid sequence on the mechanical properties of a self-assembling, oligopeptide biomaterial. Journal of Biomaterials Science, Polymer Edition, 2002, 13(3), 225-236, https://doi.org/10.1163/156856202320176493.
Rose, G.D., A.R. Geselowitz, G.J. Lesser, et al. Hydrophobicity of amino acid residues in globular proteins. Science, 1985, 229(4716), 834-838, https://doi.org/10.1126/science.4023714.
Roach, P., D. Farrar, and C.C. Perry. Interpretation of protein adsorption: surface-induced conformational changes. Journal of the American Chemical Society, 2005, 127(22), 8168-8173, https://doi.org/10.1021/ja042898o.
de Jesus, A.J. and T.W. Allen. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. Biochimica et Biophysica Acta (BBA)-Biomembranes, 2013, 1828(2), 864-876, https://doi.org/10.1016/j.bbamem.2012.09.009.
Hocky, G.M., J.L. Baker, M.J. Bradley, et al. Cations stiffen actin filaments by adhering a key structural element to adjacent subunits. The Journal of Physical Chemistry B, 2016, 120(20), 4558-4567, https://doi.org/10.1021/acs.jpcb.6b02741.
Schepers, A.V., C. Lorenz, and S. Köster. Tuning intermediate filament mechanics by variation of pH and ion charges. Nanoscale, 2020, 12(28), 15236-15245, https://doi.org/10.1039/D0NR02778B.
Protein Structure. Available from: https://www.nature.com/scitable/topicpage/protein-structure-14122136/. [cited 20 March, 2023]
Berg, J.M., Tymoczko, John L., Stryer, Lubert. Biochemistry. Fifth Edition ed.: W.H. Freeman and company.
Hammarström, P. and U. Carlsson. Is the unfolded state the Rosetta Stone of the protein folding problem? Biochemical and biophysical research communications, 2000, 276(2), 393-398, https://doi.org/10.1006/bbrc.2000.3360.
Fersht, A.R. Nucleation mechanisms in protein folding. Current opinion in structural biology, 1997, 7(1), 3-9, https://doi.org/10.1016/S0959-440X(97)80002-4.
He, X., T. Zhu, X. Wang, et al. Fragment quantum mechanical calculation of proteins and its applications. Accounts of chemical research, 2014, 47(9), 2748-2757, https://doi.org/10.1021/ar500077t.
Kim, S., J. Chen, T. Cheng, et al. PubChem 2023 update. Nucleic Acids Research, 2023, 51(D1), D1373-D1380, https://doi.org/10.1093/nar/gkac956.
Martínez, L., R. Andrade, E.G. Birgin, et al. PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of computational chemistry, 2009, 30(13), 2157-2164, https://doi.org/10.1002/jcc.21224.
VASP-Vienna Ab initio Simulation Package. Available from: https://www.vasp.at/. [cited 1 November, 2022]
Perdew, J.P., K. Burke, and M. Ernzerhof. Generalized gradient approximation made simple. Physical review letters, 1996, 77(18), 3865, https://doi.org/10.1103/PhysRevLett.77.3865.
Kresse, G. and D. Joubert. From ultrasoft pseudopotentials to the projector augmented-wave method. Physical review b, 1999, 59(3), 1758, https://doi.org/10.1103/PhysRevB.59.1758.
Ching, W.-Y., L. Poudel, S. San, et al. Interfacial interaction between suolunite crystal and silica binding peptide for novel bioinspired cement. ACS Combinatorial Science, 2019, 21(12), 794-804, https://doi.org/10.1021/acscombsci.9b00131.
Adhikari, P., N. Li, P. Rulis, et al. Deformation behavior of an amorphous zeolitic imidazolate framework–from a supersoft material to a complex organometallic alloy. Physical Chemistry Chemical Physics, 2018, 20(46), 29001-29011, https://doi.org/10.1039/C8CP05610B.
San, S., N. Li, Y. Tao, et al. Understanding the atomic and electronic origin of mechanical property in thaumasite and ettringite mineral crystals. Journal of the American Ceramic Society, 2018, 101(11), 5177-5187, https://doi.org/10.1111/jace.15774.
Baral, K., P. Adhikari, and W.Y. Ching. Ab initio Modeling of the Electronic Structures and Physical Properties of a‐Si1− xGexO2 Glass (x= 0 to 1). Journal of the American Ceramic Society, 2016, 99(11), 3677-3684, https://doi.org/10.1111/jace.14386.
Adhikari, P., Shafei, L., San, S., et al. Origin of the existence of inter‐granular glassy films in β‐Si3N4. Journal of the American Ceramic Society, 2020, 103(2), 737-743, https://doi.org/10.1111/jace.16818.
Nielsen, O. and R.M. Martin. First-principles calculation of stress. Physical Review Letters, 1983, 50(9), 697, https://doi.org/10.1103/PhysRevLett.50.697.
Yao, H., L. Ouyang, and W.Y. Ching. Ab initio calculation of elastic constants of ceramic crystals. Journal of the American Ceramic Society, 2007, 90(10), 3194-3204, https://doi.org/10.1111/j.1551-2916.2007.01931.x.
Voigt, W., Lehrbuch der kristallphysik (mit ausschluss der kristalloptik), edited by bg teubner and jw edwards, leipzig berlin. Ann Arbor, Mich, 1928.
Reuß, A., Berechnung der fließgrenze von mischkristallen auf grund der plastizitätsbedingung für einkristalle. ZAMM‐Journal of Applied Mathematics and Mechanics/Zeitschrift für Angewandte Mathematik und Mechanik, 1929, 9(1), 49-58.
Hill, R. The elastic behaviour of a crystalline aggregate. Proceedings of the Physical Society. Section A, 1952, 65(5), 349, https://doi.org/10.1088/0370-1298/65/5/307.
Papadopoulou, A., J. Laucks, and S. Tibbits. Auxetic materials in design and architecture. Nature Reviews Materials, 2017, 2(12), 1-3, https://doi.org/10.1038/natrevmats.2017.78.
Stavroulakis, G., Auxetic behaviour: appearance and engineering applications. Physica status solidi (b), 2005, 242(3), 710-720, https://doi.org/10.1002/pssb.200460388.
Mott, P. and C. Roland. Limits to Poisson’s ratio in isotropic materials. Physical review B, 2009, 80(13), 132104, https://doi.org/10.1103/PhysRevB.80.132104.
Javanmardi, Y., H. Colin-York, N. Szita, et al. Quantifying cell-generated forces: Poisson’s ratio matters. Communications physics, 2021, 4(1), 237, https://doi.org/10.1038/s42005-021-00740-y.
Raveh Tilleman, T., M. Tilleman, and H. Neumann. The elastic properties of cancerous skin: Poisson’s ratio and Young’s modulus. Israel Medical Association Journal, 2004, 6(2), 753-755.
Silicone Rubber. Available from: https://www.azom.com/properties.aspx?ArticleID=920.
What Is Bulk Modulus? Available from: https://www.thoughtco.com/bulk-modulus-definition-and-examples-4175476. [cited 10 March, 2023];
Hoek, E. and J.D. Bray. Rock slope engineering. 1981: CRC press.
Pariseau, W.G., Design analysis in rock mechanics. 2017: CRC Press.
Shear modulus. Available from: https://en.wikipedia.org/wiki/Shear_modulus#cite_note-Spanos-6. [cited 10 March, 2023];
Spanos, P. Cure system effect on low temperature dynamic shear modulus of natural rubber. in 2001 Technical Meeting of the American Chemical Society, Rubber Division. 2001.
Medium Density Fiberboard (MDF). Available from: https://www.makeitfrom.com/material-properties/Medium-Density-Fiberboard-MDF. [cited 10 March, 2023].
Rho, J.Y., R.B. Ashman, and C.H. Turner. Young's modulus of trabecular and cortical bone material: ultrasonic and microtensile measurements. Journal of biomechanics, 1993, 26(2), 111-119, https://doi.org/10.1016/0021-9290(93)90042-D.
Tian, Y., B. Xu, and Z. Zhao. Microscopic theory of hardness and design of novel superhard crystals. International Journal of Refractory Metals and Hard Materials, 2012, 33, 93-106, https://doi.org/10.1016/j.ijrmhm.2012.02.021.
Adhikari, P., A.M. Wen, R.H. French, et al. Electronic structure, dielectric response and surface charge distribution of RGD (1FUV) peptide. Scientific reports, 2014, 4(1), 5605, https://doi.org/10.1038/srep05605.
Adhikari, P., R. Podgornik, B. Jawad, et al. First-Principles Simulation of Dielectric Function in Biomolecules. Materials, 2021, 14(19), 5774, https://doi.org/10.3390/ma14195774.
Adhikari, P. and W.-Y. Ching. Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein. RSC advances, 2020, 10(65), 39831-39841, https://doi.org/10.1039/D0RA08222H.
Ching, W.-Y. and P. Rulis. Electronic Structure Methods for Complex Materials: The orthogonalized linear combination of atomic orbitals. 2012: OUP Oxford.
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