Tensile Mechanics of Alanine-Based Helical Polypeptide: Force Spectroscopy versus Computer Simulations

Afrin, Rehana; Takahashi, Ichiro; Shiga, Kazuki; Ikai, Atsushi

doi:10.1016/j.bpj.2008.10.046

Cited by 33 publications

(38 citation statements)

References 53 publications

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“…Therefore various models for the structure of the so-called S form of DNA have been proposed, but so far its nature remains obscured. Single molecule stretching experiments have been carried out also for polypeptide molecules [6][7][8]. Similar diagrams with a typical force-extension plateau have been observed experimentally for synthetical α helices [7] and myosin molecules [6].…”

Section: Introductionmentioning

confidence: 56%

“…Single molecule stretching experiments have been carried out also for polypeptide molecules [6][7][8]. Similar diagrams with a typical force-extension plateau have been observed experimentally for synthetical α helices [7] and myosin molecules [6]. All these studies raise the question on the conformational changes of molecular chains under their stretching.…”

Section: Introductionmentioning

confidence: 62%

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Lattice stretching bistability and dynamic heterogeneity

2012

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A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearestneighbor interaction of a Morse-like potential (required to have a saturation branch) and an harmonic second-neighbor coupling. Under an external stretching applied to the chain ends, the intersite Morse-like potential results in the appearance of a double-well potential within each chain monomer, whereas the interaction between the second neighbors provides a homogeneous bistable (degenerate) ground state, at least within a certain part of the chain. As a result, different conformational changes occur in the chain under the external forcing. The transition regions between these conformations are described as topological solitons. With a strong second-neighbor interaction, the solitons describe the transition between the bistable ground states. However, the key point of the model is the appearance of a heterogenous structure, when the second-neighbor coupling is sufficiently weak. In this case, a part of the chain has short bonds with a single-well potential, whereas the complementary part admits strongly stretched bonds with a double-well potential. This case allows us to explain the existence of a plateau in the force-stretching diagram for DNA and alpha-helix protein. Finally, the soliton dynamics are studied in detail.

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Section: Introductionmentioning

confidence: 56%

Section: Introductionmentioning

confidence: 62%

Lattice stretching bistability and dynamic heterogeneity

2012

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“…This i -th to ( i +4)-th H-bond is also called as α-helical H-bond, whereas the i -th to ( i +3)-th H-bond is named by 3 10 -like helical H-bond[32]. The contour length of the peptide was defined by the distance between C-terminal C α atom and N-terminal C α atom for each one of the peptides.…”

Section: Methodsmentioning

confidence: 99%

A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic α-Helical Peptide HP(2–20) and Its Four Analogues

et al. 2011

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Linear cationic α-helical antimicrobial peptides are referred to as one of the most likely substitutes for common antibiotics, due to their relatively simple structures (≤40 residues) and various antimicrobial activities against a wide range of pathogens. Of those, HP(2–20) was isolated from Helicobacter pylori ribosomal protein. To reveal a mechanical determinant that may mediate the antimicrobial activities, we examined the mechanical properties and structural stabilities of HP(2–20) and its four analogues of same chain length by steered molecular dynamics simulation. The results indicated the following: the resistance of H-bonds to the tensile extension mediated the early extensive stage; with the loss of H-bonds, the tensile force was dispensed to prompt the conformational phase transition; and Young's moduli (N/m2) of the peptides were about 4∼8×109. These mechanical features were sensitive to the variation of the residue compositions. Furthermore, we found that the antimicrobial activity is rigidity-enhanced, that is, a harder peptide has stronger antimicrobial activity. It suggests that the molecular spring constant may be used to seek a new structure-activity relationship for different α-helical peptide groups. This exciting result was reasonably explained by a possible mechanical mechanism that regulates both the membrane pore formation and the peptide insertion.

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“…Specifically, the α-helix consists of an un-stretched rod-like coil and, other than in tensile deformation, imparts increased rigidity and stiffness to protein structures. 29,30 β-sheets, on the other hand, consist of stretched chains hydrogen-bonded into extensive sheets that impart greater flexibility and lower stiffness than the α-helices. 29,30 The data in Figure 6 shows that the cuticle edge has a significant α-helix component and hence greater stiffness than positions further from the edge.…”

Section: Cuticle Surface Approaching the Scale-edgementioning

confidence: 99%

Nanoscale Molecular Characterisation of Hair Cuticles using Integrated AFM-IR

Fellows

Casford

Davies

2020

Preprint

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The nanometre-scale topography and chemical structure of hair cuticles has been investigated by vibrational spectroscopy and imaging in two spectral regions. The combination of Atomic Force Microscopy with a tuneable infrared laser (AFM-IR) circumvents the diffraction limit that has impaired traditional infrared spectroscopy, facilitating surface spectroscopy at ultra-spatial resolution. The variation in protein and lipid content of the cuticle cell surface approaching its edge, as well as the exposed layered structure of the cell at the edge itself, was investigated. Furthermore, the contribution of cystine-related products to the cuticle layers was determined. The variation of protein, lipid and cystine composition in the observed layers, as well as the measured dimensions of each, correspond closely to that of the epicuticle, A-layer, exocuticle and endocuticle layers of the cuticle cell sub-structure. Statement of SignificanceUsing AFM-IR to analyse the nanoscale cuticle features is both significant and novel in the field. Thus far, the great majority of work on the chemical investigation of the structure of hair has been limited to bulk measurements, or subject to the diffraction limit associated with traditional IR spectroscopies and microscopies. AFM-IR circumvents this diffraction limit and allows nanometre-scale, localised chemical investigation with high surface selectivity. While non-chemical investigations, e.g. those using Transmission Election Microscopy, have previously shown cuticles to have a layered substructure, AFM-IR sheds light on significant chemical variations of protein and lipid compositions within such layers, enabling their quantification.

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Tensile Mechanics of Alanine-Based Helical Polypeptide: Force Spectroscopy versus Computer Simulations

Cited by 33 publications

References 53 publications

Lattice stretching bistability and dynamic heterogeneity

Lattice stretching bistability and dynamic heterogeneity

A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic α-Helical Peptide HP(2–20) and Its Four Analogues

Nanoscale Molecular Characterisation of Hair Cuticles using Integrated AFM-IR

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