Using all-atom simulations in explicit solvent to study aggregation of amphipathic peptides into amyloid-like fibrils

2021 ◽  
pp. 118283
Author(s):  
Sharareh Jalali ◽  
Yanxing Yang ◽  
Farbod Mahmoudinobar ◽  
Shaneen M. Singh ◽  
Bradley Nilsson ◽  
...  
Keyword(s):  
Amphipathic Peptides ◽  
Explicit Solvent

scholarly journals Synthetic Amphipathic Peptides Resembling Apolipoproteins Stimulate the Release of Human Placental Lactogen

1989 ◽  
Vol 264 (16) ◽  
pp. 9215-9219
Author(s):  
E V Jorgensen ◽  
G M Anantharamaiah ◽  
J P Segrest ◽  
J T Gwynne ◽  
S Handwerger
Keyword(s):  
Placental Lactogen ◽  
Human Placental Lactogen ◽  
Amphipathic Peptides

scholarly journals Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

2021 ◽  
Vol 22 (3) ◽  
pp. 1364
Author(s):  
V. V. Krishnan ◽  
Timothy Bentley ◽  
Alina Xiong ◽  
Kalyani Maitra
Keyword(s):  
Principal Component ◽  
Md Simulations ◽  
Conformational Space ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Small Peptides ◽  
Conformational Ensembles ◽  
Solution State ◽  
Peptide Motifs ◽  
Explicit Solvent

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

scholarly journals A method for validating the accuracy of NMR protein structures

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicholas J. Fowler ◽  
Adnan Sljoka ◽  
Mike P. Williamson
Keyword(s):  
Secondary Structure ◽  
Crystal Structures ◽  
Protein Structures ◽  
Random Coil ◽  
Local Rigidity ◽  
Correlation Score ◽  
Nmr Structures ◽  
Explicit Solvent ◽  
Structure Ensemble ◽  
Better Than

AbstractWe present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

scholarly journals Study of membrane deformations induced by Hepatitis C protein NS4B and its terminal amphipathic peptides

2021 ◽  
Vol 1863 (3) ◽  
pp. 183537
Author(s):  
Malika Ouldali ◽  
Karine Moncoq ◽  
Agnès de la Croix de la Valette ◽  
Ana A. Arteni ◽  
Jean-Michel Betton ◽  
...  
Keyword(s):  
Hepatitis C ◽  
C Protein ◽  
Amphipathic Peptides ◽  
Membrane Deformations

scholarly journals Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

2014 ◽  
Vol 82 (7) ◽  
pp. 1319-1331 ◽  
Author(s):  
Garrett B. Goh ◽  
Benjamin S. Hulbert ◽  
Huiqing Zhou ◽  
Charles L. Brooks
Keyword(s):  
Molecular Dynamics ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Constant Ph Molecular Dynamics

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol

2010 ◽  
Vol 6 (6) ◽  
pp. 1871-1883 ◽  
Author(s):  
Alok Juneja ◽  
Jorge Numata ◽  
Lennart Nilsson ◽  
Ernst Walter Knapp
Keyword(s):  
Polyethylene Glycol ◽  
Explicit Solvent
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