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α-Helical stabilization by side chain shielding of backbone hydrogen bonds
TLDR
The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds, which can be directly correlated with a higher probability of hydrogen bond formation. Expand
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
TLDR
These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core, and integrates water expulsion effects into the funnel energy landscape theory of protein folding. Expand
The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study.
TLDR
The conformational ensembles of the Abeta40 and Abeta42 peptide monomers are characterized by using a combination of molecular dynamics and measured scalar data from NMR experiments to confirm the existence of structured regions within the otherwise flexible Abeta peptides. Expand
Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes
TLDR
A mechanism for the spontaneous translocation of the Tat peptides across a lipid membrane is proposed and explains how key ingredients, such as the cooperativity among the peptides, the large positive charge, and specifically the arginine amino acids, contribute to the uptake. Expand
Exploring the energy landscape of a β hairpin in explicit solvent
We studied the energy landscape of the peptide Ace‐GEWTYDDATKTFTVTE‐Nme, taken from the C‐terminal fragment (41–56) of protein G, in explicit aqueous solution by a highly parallel replica‐exchangeExpand
On the free energy of ionic hydration
The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory.Expand
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
TLDR
The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. Expand
Cosolvent effects on protein stability.
TLDR
The development of a model for TMAO is presented that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins. Expand
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
TLDR
This work uses the replica exchange molecular dynamics method to sample the conformational phase space of two α-helical peptides, A21 and the Fs, by using two different classical potentials and both water models, and finds that the potential of mean force in the ϕψ plane is markedly different in the two solvents. Expand
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
TLDR
The folding mechanism of a three-helix bundle protein is studied at atomic resolution, including effects of explicit water, and the kinetic bottlenecks for folding can be determined from the thermal ensembles of structures on the free energy barriers, provided the kinetically determined transition-state ensembled are similar to those determined fromfree energy barriers. Expand
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