Available online 2 May 2023

Author links open overlay panel, , , , ABSTRACT

Biological particles have evolved to possess mechanical characteristics necessary to carry out their functions. We developed a computational approach to “fatigue testing in silico”, in which constant-amplitude cyclic loading is applied to a particle to explore its mechanobiology. We used this approach to describe dynamic evolution of nanomaterial properties and low-cycle fatigue in the thin spherical encapsulin shell, thick spherical Cowpea Chlorotic Mottle Virus (CCMV) capsid, and thick cylindrical microtubule (MT) fragment over 20 cycles of deformation. Changing structures and force-deformation curves enabled us to describe their damage-dependent biomechanics (strength, deformability, stiffness), thermodynamics (released and dissipated energies, enthalpy, and entropy) and material properties (toughness). Thick CCMV and MT particles experience material fatigue due to slow recovery and damage accumulation over 3–5 loading cycles; thin encapsulin shells show little fatigue due to rapid remodeling and limited damage. The results obtained challenge the existing paradigm: damage in biological particles is partially reversible owing to particle's partial recovery; fatigue crack may or may not grow with each loading cycle and may heal; and particles adapt to deformation amplitude and frequency to minimize the energy dissipated. Using crack size to quantitate damage is problematic as several cracks might form simultaneously in a particle. Dynamic evolution of strength, deformability, and stiffness, can be predicted by analyzing the cycle number (N) dependent damage, d∼(1−exp[−(N/Nf)α]), where α is a power law and Nf is fatigue life. Fatigue testing in silico can now be used to explore damage-induced changes in the material properties of other biological particles.

Statement of Significance

: Biological particles possess mechanical characteristics necessary to perform their functions. We developed “fatigue testing in silico” approach, which employes Langevin Dynamics simulations of constant-amplitude cyclic loading of nanoscale biological particles, to explore dynamic evolution of the mechanical, energetic, and material properties of the thin and thick spherical particles of encapsulin and Cowpea Chlorotic Mottle Virus, and the microtubule filament fragment. Our study of damage growth and fatigue development challenge the existing paradigm. Damage in biological particles is partially reversible as fatigue crack might heal with each loading cycle. Particles adapt to deformation amplitude and frequency to minimize energy dissipation. The evolution of strength, deformability, and stiffness, can be accurately predicted by analyzing the damage growth in particle structure.

Section snippetsINTRODUCTION

Over a number of decades, cell biology research has identified many large macromolecular complexes that occur in the cell [1]. In many cases, especially in eukaryotes, these endogenous structures are complex polymeric assemblies comprised of repeating subunits that evolved to carry out normal specialized enzymatic, structural and/or dynamic functions in the cell (i.e., encapsulin, microtubules, to name a few) [2,3]. Exogenous particles represent another class; virions are a significant example

Self Organized Polymer Model

We used the Self Organized Polymer (SOP) coarse-grained model of the polypeptide chain [67] and Langevin Dynamics simulations. In the native topology-based SOP model, each amino acid is represented by a single interaction center (Cα-atom), and the Cα-Cα covalent bond with the bond distance a= 3.8 Å (peptide bond length). The molecular potential energy of a protein conformation VMOL, specified in terms of the residue coordinates , i= 1, 2, …, M (M is the total number of amino acids), is

Mechanical fatigue measurements in silico

In our recent work [34,35], we developed the computational methodology for performing “indentation experiments in silico” on nanoscale biological particles (Fig. 1C). As is possible in AFM experiments, the direction of applied force can be reversed, and the force amplitude and indentation frequency can be varied, etc. In this study, we extended this methodology to include the “mechanical fatigue testing in silico” capability. The investigator has the ability to switch modes back and forth from

DISCUSSION

Evolution has created complex nanoscale biological particles to carry out a range of sophisticated cellular and extracellular functions. There is a wealth of experimental evidence suggesting that the ability of biological particles to carry out their functions critically depends on their mechanical properties [72]. Nanoreactor encapsulin's (Fig. 1A) primary function is to organize a large number of specific enzymes in its interior to form a highly efficient nanoreactor for carrying out

CONCLUSION

We developed a computational approach to “fatigue testing in silico”, which utilizes the all-atomic and coarse-grained elements of multiscale modeling of the native structures of nanoscale biological particles and the Langevin simulations of their compressive force-induced cyclic deformation. This development enabled us to computationally explore the dynamic evolution of the mechanical, energetic, and material properties of biological soft matter over 20 cycles of repeated indentation for three

Declaration of interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:

Acknowledgments

This work was supported by the NIH grant R01HL148227 (to P.P. and V.B.) and by NSF grant MCB-2027530 (to V.B.)

REFERENCES (101)W.H. Roos et al.Squeezing protein shells: How continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale

Biophys. J.

(2010)

A. Evilevitch et al.Effects of salts on internal DNA pressure and mechanical properties of phage capsids

J. Mol. Biol.

(2011)

J. Snijder et al.Probing the impact of loading rate on the mechanical properties of viral nanoparticles

Micron

(2012)

M. Marchetti et al.Atomic force microscopy observation and characterization of single virions and virus-like particles by nano-indentation

Curr. Opin. Virol.

(2016)

E. Kliuchnikov et al.Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules’ Growth, Catastrophe, Shortening, and Rescue

Comput. Struct. Biotechnol. J.

(2022)

E. Nogales et al.High-resolution model of the microtubule

Cell

(1999)

N. Kol et al.A stiffness switch in human immunodeficiency virus

Biophys. J.

(2007)

P.J. de PabloAtomic force microscopy of virus shells

Semin. Cell Dev. Biol.

(2018)

P.K. Purohit et al.Forces during bacteriophage DNA packaging and ejection

Biophys. J.

(2005)

K.H. Downing et al.Tubulin and microtubule structure

Curr. Opin. Cell Biol.

(1998)

M. Dogterom et al.Microtubule organization in vitro

Curr. Opin. Cell Biol.

(2013)

J.B. BancroftThe self-assembly of spherical plant viruses

Adv. Virus Res.

(1970)

A. Zlotnick et al.Mechanism of capsid assembly for an icosahedral plant virus

Virology

(2000)

F. Maksudov et al.Fluctuating nonlinear spring theory: Strength, deformability, and toughness of biological nanoparticles from theoretical reconstruction of force-deformation spectra

Acta Biomater

(2021)

B.D. Wilts et al.Swelling and softening of the cowpea chlorotic mottle virus in response to pH shifts

Biophys. J.

(2015)

O. Kononova et al.Structural transitions and energy landscape for cowpea chlorotic mottle virus capsid mechanics from nanomanipulation in vitro and in silico

Biophys. J.

(2013)

J. Snijder et al.V. Barsegov, others, Assembly and mechanical properties of the cargo-free and cargo-loaded bacterial nanocompartment encapsulin

Biomacromolecules

(2016)

F. Maksudov et al.Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves

Acta Biomater

(2021)

W. Li et al.Fibrin fiber stiffness is strongly affected by fiber diameter, but not by fibrinogen glycation

Biophys. J.

(2016)

N.E. Kurland et al.Measurement of nanomechanical properties of biomolecules using atomic force microscopy

Micron

(2012)

B. Alberts

Molecular biology of the cell

(2017)

C.A. McHugh et al.others, A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress

EMBO J

(2014)

C. Garcin et al.Microtubules in cell migration

Essays Biochem

(2019)

E.W. Nester et al.Nester's microbiology: a human perspective

(2016)

K. Saunders et al.Exploiting plant virus-derived components to achieve in planta expression and for templates for synthetic biology applications

New Phytol

(2013)

A. Trache et al.Atomic force microscopy (AFM)

Curr. Protoc. Microbiol.

(2008)

M. Krieg et al.Atomic force microscopy-based mechanobiology

Nat. Rev. Phys.

(2019)

Y. Guo et al.AFM nanoindentation experiments on protein shells: A protocol

(2019)

Q. Peng et al.Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: evidence for a kinetic partitioning mechanism

Proc. Natl. Acad. Sci. USA

(2008)

R. Afrin et al.Pretransition and progressive softening of bovine carbonic anhydrase II as probed by single molecule atomic force microscopy

Protein Sci

(2005)

A. Parra et al.Nanomechanical properties of globular proteins: lactate oxidase

Langmuir

(2007)

T. Watanabe-Nakayama et al.High-speed atomic force microscopy reveals strongly polarized movement of clostridial collagenase along collagen fibrils

Sci. Rep.

(2016)

S.S. Wijeratne et al.Atomic force microscopy reveals distinct protofilament-scale structural dynamics in depolymerizing microtubule arrays

Proc. Natl. Acad. Sci. USA

(2022)

I. Boyton et al.Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages

ACS Omega

(2021)

I. Rousso et al.Applications of Atomic Force Microscopy in HIV-1 Research

Viruses

(2022)

M. Hernando-Pérez et al.Direct measurement of phage Φ29 stiffness provides evidence of internal pressure

Small

(2012)

I.L. Ivanovska et al.Discrete fracture patterns of virus shells reveal mechanical building blocks

Proc. Natl. Acad. Sci. USA

(2011)

J.P. Michel 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. USA.

(2006)

W.S. Klug et al.Failure of viral shells

Phys. Rev. Lett.

(2006)

P.K. Purohit et al.Mechanics of DNA packaging in viruses

Proc. Natl. Acad. Sci. USA

(2003)

View full text

© 2023 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.