Non-Arrhenius Behavior in the Unfolding of a Short, Hydrophobic α-Helix. Complementarity of Molecular Dynamics and Lattice Model Simulations

2003 ◽  
Vol 125 (21) ◽  
pp. 6573-6580 ◽  
Author(s):  
Olivier Collet ◽  
Christophe Chipot
Keyword(s):  
Molecular Dynamics ◽  
Lattice Model ◽  
Arrhenius Behavior ◽  
Model Simulations ◽  
Α Helix

Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides

2016 ◽  
Vol 35 (9) ◽  
pp. 1923-1935 ◽  
Author(s):  
Bhupesh Goyal ◽  
Anil Kumar ◽  
Kinshuk Raj Srivastava ◽  
Susheel Durani
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Α Helix

scholarly journals Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces

2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Comparative Analysis ◽  
Hot Spots ◽  
Hot Spot ◽  
Accurate Prediction ◽  
Protein Interface ◽  
Alanine Scanning ◽  
Protein Interfaces ◽  
Structural Ensembles ◽  
Α Helix

Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography, and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an α helix-mediated PPI), SIMS/SUMO and GKAP/SHANK-PDZ (both β strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-residues at a topographically novel Affimer/BCL-xL protein-protein interface.

scholarly journals Energetic Self-Folding Mechanism in α-Helixes

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Reasonable Agreement ◽  
Dihedral Angles ◽  
Native Conformation ◽  
Experimental Values ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Large Peptide

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues towards the α<sub>R </sub>conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation, or zipper models, and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.

An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations

2020 ◽  
Vol 22 (48) ◽  
pp. 28055-28073
Author(s):  
Anupamjeet Kaur ◽  
Deepti Goyal ◽  
Bhupesh Goyal
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Helical Conformation ◽  
Aβ Peptide ◽  
Α Helix ◽  
Dynamics Simulations

The molecular dynamics simulations highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptide into helical conformation and destabilized Aβ42 trimer as well as protofibril structures.

Lattice model simulations of the stacking/unstacking behaviour in thylakoid membranes

1990 ◽  
Vol 145 (1) ◽  
pp. 65-81 ◽  
Author(s):  
D. Nicholson ◽  
S.J. Zara ◽  
N.G. Parsonage ◽  
J. Barber
Keyword(s):  
Lattice Model ◽  
Thylakoid Membranes ◽  
Model Simulations

Detailed Microscopic Unfolding Pathways of an α-Helix and a β-Hairpin: Direct Observation and Molecular Dynamics

2014 ◽  
Vol 118 (26) ◽  
pp. 7233-7246 ◽  
Author(s):  
Gouri S. Jas ◽  
Wendy A. Hegefeld ◽  
C. Russell Middaugh ◽  
Carey K. Johnson ◽  
Krzysztof Kuczera
Keyword(s):  
Molecular Dynamics ◽  
Direct Observation ◽  
Α Helix

Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations

2014 ◽  
Vol 54 (7) ◽  
pp. 2093-2104 ◽  
Author(s):  
Jan K. Marzinek ◽  
Peter J. Bond ◽  
Guoping Lian ◽  
Yanyan Zhao ◽  
Lujia Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ligand Binding ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Α Helix
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