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Effect of the Structural Water on the Mechanical Properties of Collagen-like Microfibrils: A Molecular Dynamics Study

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Abstract

The objective of this paper is to investigate the role played by the structural water on the intermolecular sliding between collagen-like 1QSU peptides in a microfibril under deformation. Three modes of deformation are used to generate intermolecular sliding: forced axial stretching (case I) or sliding (case II) of a central peptide monomer (while other surrounding monomers are fixed); and cantilever bending (case III) under a terminal lateral load. The force–displacement curve of each deformation mode is derived using a module called Steered Molecular Dynamics (SMD) in a molecular dynamics package NAMD under the CHARMM22 force field. Each calculation is carried out twice, one in the presence of structural water, one without. It is found that the structural water is a weak “lubricant” in forced axial stretching (case I), but it functions as a “glue” in forced axial sliding (case II) and cantilever bending (case III). A change in the pulling speed does not significantly alter the force–displacement behavior in axial stretching (case I) and sliding (case II), but it does in cantilever bending (case III). The additional resistance contributed by the structural water is attributed to the additional energy cost in breaking the water-mediated hydrogen bonds (water bridges).

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Abbreviations

AFM:

atomic force microscopy

BFP:

biomembrane force probes

1CGD:

protein databank ID of the collagen-like, alanine replacement peptide, also called Gly→Ala.

1QSU:

protein databank ID of the collagen-like, EKG replacement peptide

BPTI:

bovine pancreatic trypsin inhibitor

CHARMM:

Chemistry at HARvard Molecular Mechanics

CHEM3D:

name of a commercial molecular modeling package

CPU:

central processing unit

EKG:

glutamate-lysine-glycine

GLU:

three letter code for glutamate (E)

GLY:

three letter code for glycine (G)

GROMACS:

name of an open-access molecular dynamics package using GROMOS96 force field

GROMOS96:

name of a force field with open access, GROMOS stands for “GROningen MOlecular Simulation”

LOT:

laser optical tweezers

LYS:

three letter code for lysine (K)

MD:

molecular dynamics

MM:

molecular mechanics

NAMD:

Not Another Molecular Dynamics

NMR:

nuclear magnetic resonance

PDB:

protein data bank

RATTLE:

name of an algorithm to apply constraints in MD

RMSD:

root mean square deviation

SMD:

steered molecular dynamics

SPC/E:

name of a configurational model of the water molecule

TIP3P:

name of a configurational model of the water molecule

VMD:

visual molecular dynamics

WAXD:

wide angle X-ray diffraction

X-PLOR :

name of a software used in X-ray crystallography and NMR

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Acknowledgment

The authors acknowledge the financial supports from Rutgers, State University of New Jersey. The authors also thank Virginia Dare for proofreading a final version of this paper.

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  1. Bone Mechanics Laboratory, Department of Mechanical & Aerospace Engineering, Rutgers, State University of New Jersey, 98 Brett Road, Piscataway, NJ, 08854, USA

    Dajun Zhang, Uday Chippada & Kenneth Jordan

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  1. Dajun Zhang
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  2. Uday Chippada
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Correspondence to Dajun Zhang.

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Zhang, D., Chippada, U. & Jordan, K. Effect of the Structural Water on the Mechanical Properties of Collagen-like Microfibrils: A Molecular Dynamics Study. Ann Biomed Eng 35, 1216–1230 (2007). https://doi.org/10.1007/s10439-007-9296-8

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  • DOI: https://doi.org/10.1007/s10439-007-9296-8

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