Modelling virus contact mechanics under atomic force imaging conditions

References

• Sloan ED. Fundamental principles and applications of natural gas hydrates. Nature. 2003 Nov;426(6964):353–359. DOI:10.1038/nature02135
   PubMed Web of Science ®Google Scholar
• Greber UF. How cells tune viral mechanics–insights from biophysical measurements of influenza virus. Biophys J. 2014 Jun;106(11):2317–2321. DOI:10.1016/j.bpj.2014.04.025
   PubMed Web of Science ®Google Scholar
• Guerra P, Valbuena A, Querol-Audí J, et al. Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations. Sci Rep. 2017 Dec;7(1):4101. DOI:10.1038/s41598-017-04345-w
   PubMed Web of Science ®Google Scholar
• Zeng C, Hernando-Pérez M, Dragnea B, et al. Contact mechanics of a small icosahedral virus. Phys Rev Lett. 2017 Jul;119(3):Article ID 038102.DOI:10.1103/PhysRevLett.119.038102
   Web of Science ®Google Scholar
• Zeng C, Scott L, Malyutin A, et al. Virus mechanics under molecular crowding. J Phys Chem B. 2021 Feb;125(7):1790–1798. DOI:10.1021/acs.jpcb.0c10947
   PubMed Web of Science ®Google Scholar
• Prevelige PE, Thomas D, King J. Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells. Biophys J. 1993 Mar;64(3):824–835.
   PubMed Web of Science ®Google Scholar
• Zlotnick A, Johnson JM, Wingfield PW, et al. A theoretical model successfully identifies features of hepatitis B virus capsid assembly. Biochemistry. 1999 Nov;38(44):14644–14652.
   PubMed Web of Science ®Google Scholar
• Dragnea B. Watching a virus grow. 2019 Nov. Available from: https://www.pnas.org/content/116/45/22420.short?rss=1.
   Google Scholar
• Zlotnick A. Distinguishing reversible from irreversible virus capsid assembly. J Mol Biol. 2007 Feb;366(1):14–18.
   PubMed Web of Science ®Google Scholar
• Aggarwal A, Rudnick J, Bruinsma RF, et al. Elasticity theory of macromolecular aggregates. Phys Rev Lett. 2012 Oct;109(14):Article ID 148102. DOI:10.1103/PhysRevLett.109.148102
   Web of Science ®Google Scholar
• Zandi R, Reguera D. Mechanical properties of viral capsids. Phys Rev E. 2005 Aug;72(2):Article ID 021917.DOI:10.1103/PhysRevE.72.021917
   Web of Science ®Google Scholar
• Ivanovska IL, de Pablo PJ, Ibarra B, et al. Bacteriophage capsids: tough nanoshells with complex elastic properties. Proc Natl Acad Sci. 2004 May;101(20):7600–7605. DOI:10.1073/pnas.0308198101
   PubMed Web of Science ®Google Scholar
• Michel JP, Ivanovska IL, Gibbons MM, et al. Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. Proc Natl Acad Sci. 2006 Apr;103(16):6184–6189. DOI:10.1073/pnas.0601744103
   PubMed Web of Science ®Google Scholar
• Roos WH. How to perform a nanoindentation experiment on a virus. Methods Mol Biol. 2011 Jan;783:251–264. DOI:10.1007/978-1-61779-282-3_14
   PubMedGoogle Scholar
• Thompson WC, Cattani AJ, Lee O, et al. A laboratory model for virus particle nanoindentation. Biophysicist. 2020 Jan;1(2):DOI:10.35459/tbp.2019.000106
   Google Scholar
• Bruinsma RF, Klug WS. Physics of viral shells. Annu Rev Condens Matter Phys. 2015 Mar;6(1):245–268. DOI:10.1146/annurev-conmatphys-031214-014325
   Web of Science ®Google Scholar
• Gibbons MM, Klug WS. Mechanical modeling of viral capsids. J Mater Sci. 2007 Jul;42(21):8995–9004. DOI:10.1007/s10853-007-1741-4
   Web of Science ®Google Scholar
• Arkhipov A, Roos WH, Wuite GJL, et al. Elucidating the mechanism behind irreversible deformation of viral capsids. Biophys J. 2009 Oct;97(7):2061–2069. DOI:10.1016/j.bpj.2009.07.039
   PubMed Web of Science ®Google Scholar
• Krishnamani V, Globisch C, Peter C, et al. Breaking a virus: identifying molecular level failure modes of a viral capsid by multiscale modeling. Eur Phys J Spec Top. 2016 Jul;1–18. DOI:10.1140/epjst/e2016-60141-2
   Web of Science ®Google Scholar
• Mannige RV, Brooks CL. Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling. Proc Natl Acad Sci. 2009 May;106(21):8531–8536. DOI:10.1073/pnas.0811517106
   PubMed Web of Science ®Google Scholar
• Vliegenthart GA, Gompper G. Mechanical deformation of spherical viruses with icosahedral symmetry. Biophys J. 2006 Aug;91(3):834–841. DOI:10.1529/biophysj.106.081422
   PubMed Web of Science ®Google Scholar
• Ciarlet PG, Piersanti P. Obstacle problems for Koiter's shells. Math Mech Solids. 2019;24:3061–3079.
   Web of Science ®Google Scholar
• Ciarlet PG, Piersanti P. A confinement problem for a linearly elastic Koiter's shell. C R Math. 2019;357:221–230.
   Web of Science ®Google Scholar
• Ciarlet PG, Mardare C, Piersanti P. Un problème de confinement pour une coque membranaire linéairement élastique de type elliptique. C R Math. 2018;356(10):1040–1051.
   Web of Science ®Google Scholar
• Ciarlet PG, Mardare C, Piersanti P. An obstacle problem for elliptic membrane shells. Math Mech Solids. 2019;24(5):1503–1529.
   Web of Science ®Google Scholar
• Piersanti P. On the improved interior regularity of the solution of a fourth order elliptic problem modelling the displacement of a linearly elastic shallow shell subject to an obstacle. Asymptot Anal. 2021;127:1–21.
   Web of Science ®Google Scholar
• Piersanti P, Shen X. Numerical methods for static shallow shells lying over an obstacle. Numer Algorithms. 2020;85623–652.
   PubMed Web of Science ®Google Scholar
• Piersanti P. A time-dependent obstacle problem in linearised elasticity. Nonlinear Anal. 2020;192:Article ID 111660.
   Web of Science ®Google Scholar
• Piersanti P, White K, Dragnea B, et al. A three-dimensional discrete model for approximating the deformation of a viral capsid subjected to lying over a flat surface. In preparation. Preprint arxiv. https://arxiv.org/abs/2202.05625
   Google Scholar
• Baclayon M, Wuite GJL, Roos WH. Imaging and manipulation of single viruses by atomic force microscopy. Soft Matter. 2010;6(21):5273–5285. DOI:10.1039/b923992h
   Web of Science ®Google Scholar
• Calo A, Eleta-Lopez A, Ondarcuhu T, et al. Nanoscale wetting of single viruses. Molecules. 2021 Aug;26(17):5184.DOI:10.3390/molecules26175184
   PubMed Web of Science ®Google Scholar
• Cartagena A, Hernando-Pérez M, Carrascosa JL, et al. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy. Nanoscale. 2013;5(11):4729. DOI:10.1039/c3nr34088k
   PubMed Web of Science ®Google Scholar
• Kuznetsov YG, McPherson A. Atomic force microscopy investigation of viruses. Methods Mol Biol. 2011 Apr;736(4):171–195.
   PubMedGoogle Scholar
• Castellanos M, Pérez R, Carrasco C, et al. Mechanical elasticity as a physical signature of conformational dynamics in a virus particle. Proc Natl Acad Sci. 2012 Jul;109(30):12028–12033. DOI:10.1073/pnas.1207437109
   PubMed Web of Science ®Google Scholar
• Kononova O, Snijder J, Brasch M, et al. Structural transitions and energy landscape for cowpea chlorotic mottle virus capsid mechanics from nanomanipulation in vitro and in silico. Biophys J. 2013 Oct;105(8):1893–1903. DOI:10.1016/j.bpj.2013.08.032
   PubMed Web of Science ®Google Scholar
• Mateu MG. Mechanical properties of viruses analyzed by atomic force microscopy: a virological perspective. Virus Res. 2012 Sep;168(1–2):1–22. DOI:10.1016/j.virusres.2012.06.008
   PubMed Web of Science ®Google Scholar
• Pang H-B, Hevroni L, Kol N, et al. Virion stiffness regulates immature HIV-1 entry. Retrovirology. 2013 Jan;10:4.DOI:10.1186/1742-4690-10-4
   PubMed Web of Science ®Google Scholar
• Snijder J, Reddy VS, May ER, et al. Integrin and defensin modulate the mechanical properties of adenovirus. J Virol. 2013 Mar;87(5):2756–2766. DOI:10.1128/JVI.02516-12
   PubMed Web of Science ®Google Scholar
• Kiselev AP. Geometry. Book I. Planimetry. Sumizdat; 2006.
   Google Scholar
• Temam R, Miranville A. Mathematical modeling in continuum mechanics. 2nd ed. Cambridge: Cambridge University Press; 2005.
   Google Scholar
• Quarteroni A, Saleri F, Gervasio P. Scientific computing with MATLAB and octave. Berlin: Springer-Verlag; 2010. (Texts in computational science and engineering; vol. 2).
   Google Scholar
• Strang G. Linear algebra and its applications. 2nd ed. New York: Academic Press; 1980.
   Google Scholar
• Ekeland I, Temam R. Convex analysis and variational problems. english ed. Translated from the French. Philadelphia (PA): Society for Industrial and Applied Mathematics (SIAM); 1999. (Classics in applied mathematics; vol. 28).
   Google Scholar
• Duvaut G, Lions J-L. Inequalities in mechanics and physics. Berlin: Springer; 1976.
   Google Scholar
• Sun W, Yuan Y-X. Optimization theory and methods: nonlinear programming. New York: Springer; 2006. (Springer optimization and its applications; vol. 1).
   Google Scholar
• Somorjai GA. Introduction to surface chemistry and catalysis. New York: John Wiley & Sons; 1994.
   Google Scholar