scholarly journals Molecular Dynamics with the United-Residue Model of Polypeptide Chains. II. Langevin and Berendsen-Bath Dynamics and Tests on Model α-Helical Systems

2005 ◽  
Vol 109 (28) ◽  
pp. 13798-13810 ◽  
Author(s):  
Mey Khalili ◽  
Adam Liwo ◽  
Anna Jagielska ◽  
Harold A. Scheraga
Keyword(s):  
Molecular Dynamics ◽  
Polypeptide Chains

Design and Modeling of a Peptide Based NanoTweezer

2006 ◽  
Author(s):  
Gaurav Sharma ◽  
Kaushal Rege ◽  
Constantinos Mavroidis ◽  
Martin L. Yarmush
Keyword(s):  
Molecular Dynamics ◽  
Coiled Coil ◽  
Computational Results ◽  
Actuation Mechanism ◽  
Electrostatic Charges ◽  
Environmentally Responsive ◽  
Force Profile ◽  
Potential Applications ◽  
Polypeptide Chains ◽  
Molecular Dynamics Results

The design hypothesis, architectures, and preliminary computational results of a peptide based nanoTweezer are presented in this paper. We engineered the α-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoTweezer. The dimeric coiled coil peptide consists of two identical ~4.5 nm long and ~3 nm wide polypeptide chains. The actuation mechanism depends on the modifying electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and therefore, creating the motion of the tweezer. Preliminary molecular dynamics results indicated that pH changes led to a reversible deflection of 1–2 nm with the nanoTweezer. The force profile of the nanoTweezer motion and some potential applications are also discussed.

scholarly journals Intraresidual Correlated Motions in Peptide Chain

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
Javier Carmona-García ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Polypeptide Chain ◽  
Conformational Flexibility ◽  
Peptide Chain ◽  
Atomic Displacements ◽  
Correlated Motions ◽  
Polypeptide Chains

Conformational flexibility of polypeptide chains is mainly driven by changes in the (phi, psi) dihedrals of each residue. Such motions, however, are not completely independent, as certain (anti)correlated motions are favored. In this work, we investigate the correlations between the dihedral displacements of adjacent residues, (Δphi i, Δpsi i+1) and (Δphi i-1, Δpsi i), i.e. interresidual, and within the same residue, (Δphi i, Δpsi i), i.e. intraresidual, by analyzing extensive Molecular Dynamics trajectories of initially extended polyalanine chains in detail. Correlations are evaluated individually at different residue conformations covering the whole (phi, psi)-space. From these we draw maps which clearly show how the coupled motions strongly depend on the conformation, thus unveiling an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. By developing a tailored model, it is also demonstrated that both inter and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements along the whole polypeptide chain.

scholarly journals Intraresidual Correlated Motions in Peptide Chain

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
Javier Carmona-García ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Polypeptide Chain ◽  
Conformational Flexibility ◽  
Peptide Chain ◽  
Atomic Displacements ◽  
Correlated Motions ◽  
Polypeptide Chains

Conformational flexibility of polypeptide chains is mainly driven by changes in the (phi, psi) dihedrals of each residue. Such motions, however, are not completely independent, as certain (anti)correlated motions are favored. In this work, we investigate the correlations between the dihedral displacements of adjacent residues, (Δphi i, Δpsi i+1) and (Δphi i-1, Δpsi i), i.e. interresidual, and within the same residue, (Δphi i, Δpsi i), i.e. intraresidual, by analyzing extensive Molecular Dynamics trajectories of initially extended polyalanine chains in detail. Correlations are evaluated individually at different residue conformations covering the whole (phi, psi)-space. From these we draw maps which clearly show how the coupled motions strongly depend on the conformation, thus unveiling an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. By developing a tailored model, it is also demonstrated that both inter and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements along the whole polypeptide chain.

Insights into amyloid disease from fly models

2014 ◽  
Vol 56 ◽  
pp. 69-83 ◽  
Author(s):  
Ko-Fan Chen ◽  
Damian C. Crowther
Keyword(s):  
Drosophila Melanogaster ◽  
Neurodegenerative Disorders ◽  
Amyloid Β ◽  
Amyloid Β Peptide ◽  
Disease Pathogenesis ◽  
Amyloid Aggregates ◽  
Aβ Amyloid ◽  
Polypeptide Chains ◽  
Amyloid Diseases

The formation of amyloid aggregates is a feature of most, if not all, polypeptide chains. In vivo modelling of this process has been undertaken in the fruitfly Drosophila melanogaster with remarkable success. Models of both neurological and systemic amyloid diseases have been generated and have informed our understanding of disease pathogenesis in two main ways. First, the toxic amyloid species have been at least partially characterized, for example in the case of the Aβ (amyloid β-peptide) associated with Alzheimer's disease. Secondly, the genetic underpinning of model disease-linked phenotypes has been characterized for a number of neurodegenerative disorders. The current challenge is to integrate our understanding of disease-linked processes in the fly with our growing knowledge of human disease, for the benefit of patients.

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