Impact of β-Sheet Conformations on the Mechanical Response of Protein in Biocomposites
22 Nov 2006-Materials and Manufacturing Processes (Taylor & Francis Group)-Vol. 21, Iss: 7, pp 676-682
TL;DR: Comparative study of the stress-deformation characteristics of these two structures with almost similar number of amino acids have been extracted from one single spinach protein: Ferredoxin Reductase (1FNR).
Abstract: Proteins in biological nanocomposites play an important role in their mechanical response. Proteins in nacre, the inner layer of seashells, have been shown to have exceptional mechanical properties. One of the important nacre proteins, Lustrin-A, has abundance of polypeptides in zig-zag conformation called β-sheets. β-sheets of protein when present close to each other in multiple numbers could take the shape of a planar β-sheath like structure or a β-barrel to form a domain. In natural proteins both these types of structures are commonly found. However, the conformation of β-sheets in Lustrin-A is not known at this time. Effort has been made through this work to study the mechanical response of these β-planar sheath and β-barrel structures when subjected to external loads. Comparative study of the stress-deformation characteristics of these two types of structures has been made. Both these structures with almost similar number of amino acids have been extracted from one single spinach protein: Ferredoxin ...
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TL;DR: This review focuses on the hierarchical architecture, macroscopic and microscopic deformation and fracture behavior, as well as toughening mechanisms in nacre and summarizes recent progress in the fabrication of materials inspired by nacre taking into consideration its mechanical properties.
131 citations
TL;DR: This study has used molecular dynamics and steered molecular dynamics to study directional dependence of deformation response of collagen with respect to the hydroxyapatite surface, and simulations indicate that the mechanics of collagen pulled in different directions with Respect to hydroxyAPatite is significantly different.
58 citations
TL;DR: These simulations give important information about the molecular mechanics of collagen and are also useful for the development of novel biomimetic artificial implant materials.
Abstract: Bone is a widely studied structure due to its important function in the human body and also for its unique mechanical properties, which depend upon several factors, such as, its hierarchal structure, its constituents, degree of interactions between different constituents, etc. The major constituents of bone are collagen and hydroxyapatite (HAP). In this work, the load-carrying behavior of collagen is evaluated using steered molecular dynamics simulations. It is observed that the mineral HAP influences the load-deformation behavior of collagen. The collagen molecule (tropocollagen) requires more energy to deform when it is in close proximity of HAP. The reasons for a typical load-deformation behavior are also analyzed. It is observed that with stretching of the tropocollagen, first hydrogen bonds between the tropocollagen chains break, as a result of which more water molecules start interacting with chains. HAP significantly alters the interaction between tropocollagen and water. The load-carrying behavior of tropocollagen at different loading rates is also analyzed by pulling collagen at different velocities. These simulations give important information about the molecular mechanics of collagen and are also useful for the development of novel biomimetic artificial implant materials.
52 citations
TL;DR: In this paper, the deformation behavior of the organic polymer matrix of the biocomposite nacre structure in abalone shell was investigated by in situ straining during transmission electron microscopy (TEM).
Abstract: The deformation behavior of the organic polymer matrix of the biocomposite nacre structure in abalone shell was investigated by in situ straining during transmission electron microscopy (TEM). We observed strong adhesion to mineral plates and high ductility of the organic matrix, confirming a crack-bridging toughening mechanism. In addition, direct observation of reversible mechanical behavior was made in the viscoelastic reformation of matrix ligaments after failure. Crystalline β-sheet structures identified through electron diffraction suggested the presence of protein structures similar to spider or cocoon silk, and the reversible mechanism was attributed to hydration-induced unfolding and refolding of domains in these silklike proteins. This work provides further insight into the molecular and nanoscale behavior of nacre organic matrix and its contribution to bulk mechanical performance.
41 citations
TL;DR: The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers and the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations.
Abstract: The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers. Here, the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations. Our simulations indicate that energy required for unfolding protein in the proximity of mineral aragonite is several times higher than that for isolated protein in the absence of the mineral. Here, we present details of specific mechanisms which result in higher energy for protein unfolding in the proximity of mineral. At the early stage of pulling, peaks in the load-displacement (LD) plot at mineral proximity are quantitatively correlated to the interaction energy between atoms involved in the latching phenomenon of amino acid side chain to aragonite surface. Water plays an important role during mineral and protein interaction and water molecules closer to the mineral surface are highly oriented and remain rigidly attached as the protein strand is pulled. Also, the high magnitude of load for a given displacement originates from attractive interactions between the protein, protein-bound water, and mineral. This study provides an insight into mineral-protein interactions that are predominant in biological nanocomposites and also provides guidelines towards design of biomimetic nanocomposites.
21 citations
Cites methods from "Impact of β-Sheet Conformations on ..."
...In our previous work, [21] we have used steered molecular dynamics to understand the deformational behavior of the beta barrel and beta planar sheet structures in proteins....
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References
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TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
46,130 citations
"Impact of β-Sheet Conformations on ..." refers methods in this paper
...VMD [27] is used for all interactive studies CHARMm force field [28] has been used, the parameters for which are obtained from standard CHARMm parameter file par_22_pro [29]....
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TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
14,725 citations
"Impact of β-Sheet Conformations on ..." refers methods in this paper
...VMD [27] is used for all interactive studies CHARMm force field [28] has been used, the parameters for which are obtained from standard CHARMm parameter file par_22_pro [29]....
[...]
TL;DR: The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...
13,164 citations
"Impact of β-Sheet Conformations on ..." refers methods in this paper
...VMD [27] is used for all interactive studies CHARMm force field [28] has been used, the parameters for which are obtained from standard CHARMm parameter file par_22_pro [29]....
[...]
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
Abstract: Modularly invariant equations of motion are derived that generate the isothermal–isobaric ensemble as their phase space averages. Isotropic volume fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one‐dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
4,282 citations
"Impact of β-Sheet Conformations on ..." refers methods in this paper
...Then the temperature is raised to 300K, using Langevian method [30, 31]....
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TL;DR: In this paper, a new method for performing molecular dynamics simulations under constant pressure is presented, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical "ringing" of the volume associated with the piston mass.
Abstract: A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical ‘‘ringing’’ of the volume associated with the piston mass. In this way it is similar to the ‘‘weak coupling algorithm’’ developed by Berendsen and co‐workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.
3,799 citations
"Impact of β-Sheet Conformations on ..." refers methods in this paper
...Then the temperature is raised to 300K, using Langevian method [30, 31]....
[...]