An Alpha-Helical Peptide in AOT Micelles Prefers to be Localized at the Water/Headgroup Interface

Tian, Jiang; Garcı́a, Angel E.

doi:10.1016/j.bpj.2009.03.014

Cited by 23 publications

(20 citation statements)

References 26 publications

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“…After encapsulation by the RM, the helical peptide remained at the water/AOT/isooctane interface such that the peptide and AOT head groups shared coordinated water molecules, and the entropy loss of the water is reduced. 46 Our study employs MD calculations to simulate systems approximating those examined by Gai and co-workers, with a focus on elucidating the structure and dynamics of the AOT RM with and without peptide. Our goal is to acquire an atomic-level understanding of the effect that the RM environment (w 0 = 6) has on the conformational folding equilibrium of the alanine-based peptide, AKA 2 (ACE-YGAKAAAA-(KAAAA) n G-NH 2 where n = 2).…”

Section: B the Nature Of A Reverse Micelle Environment In Peptide Comentioning

confidence: 99%

Protein folding in a reverse micelle environment: The role of confinement and dehydration

Martinez

Domı́nguez

Rivera

et al. 2011

The Journal of Chemical Physics

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Characterization of the molecular interactions that stabilize the folded state of proteins including hydrogen bond formation, solvation, molecular crowding, and interaction with membrane environments is a fundamental goal of theoretical biophysics. Inspired by recent experimental studies by Gai and co-workers, we have used molecular dynamics simulations to explore the structure and dynamics of the alanine-rich AKA 2 peptide in bulk solution and in a reverse micelle environment. The simulated structure of the reverse micelle shows substantial deviations from a spherical geometry. The AKA 2 peptide is observed to (1) remain in a helical conformation within a spherically constrained reverse micelle and (2) partially unfold when simulated in an unconstrained reverse micelle environment, in agreement with experiment. While aqueous solvation is found to stabilize the N-and C-termini random coil portions of the peptide, the helical core region is stabilized by significant interaction between the nonpolar surface of the helix and the aliphatic chains of the AOT surfactant. The results suggest an important role for nonpolar peptide-surfactant and peptide-lipid interactions in stabilizing helical geometries of peptides in reverse micelle environments.

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Section: B the Nature Of A Reverse Micelle Environment In Peptide Comentioning

confidence: 99%

Protein folding in a reverse micelle environment: The role of confinement and dehydration

Martinez

Domı́nguez

Rivera

et al. 2011

The Journal of Chemical Physics

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“…However, there are also weaker entropic forces associated with the surfactant and the protein hydration that provide a driving force for binding of the protein to the RM surface. Previous calculations 26 and experiments 14,17 on charged and neutral alpha helical peptides have shown that the peptides have a preference for the RM interface.…”

Section: Discussionmentioning

confidence: 97%

“…29 Experiments in RM are conducted with different solvents. 14,17,18 However, to maintain consistency in the force field and with previous simulations, 26,29,32,33 we use iso-octane as the organic solvent. Simulations are conducted with the parallel molecular dynamics program NAMD.…”

Section: A Simulations Of Ubiquitin-aot Rm Self Assemblymentioning

confidence: 99%

“…The released water will have larger translational and rotational entropy in the center of RM. 26 At low excess salt concentration, both forces apply so that there is a strong bias toward the interface of RM. While in the idealized neutral head group surfactants, the electrostatic attraction force is not present and only the entropy force acts so that the bias toward interface is small.…”

Section: G Potential Of Mean Force Calculationsmentioning

confidence: 99%

“…Self-assembled protein-RM system has been previously studied for an alphahelical peptide by us 26 and a Trp-cage protein by Chaitanya et al 27 In our studies, the reverse micelles are self assembled in the presence of the folded protein, and the dynamics and hydration of the protein are compared with ubiquitin in bulk water. To our knowledge, at this time, our calculations are the longest and most comprehensive simulation studies of self-assembled protein-RM systems.…”

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confidence: 91%

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Simulations of the confinement of ubiquitin in self-assembled reverse micelles

Tian

Garcı́a

2011

The Journal of Chemical Physics

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We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.

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Taste of Sugar at the Membrane: Thermodynamics and Kinetics of the Interaction of a Disaccharide with Lipid Bilayers

Tian

Sethi

Swanson

et al. 2013

Biophysical Journal

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Sugar recognition at the membrane is critical in various physiological processes. Many aspects of sugar-membrane interaction are still unknown. We take an integrated approach by combining conventional molecular-dynamics simulations with enhanced sampling methods and analytical models to understand the thermodynamics and kinetics of a di-mannose molecule in a phospholipid bilayer system. We observe that di-mannose has a slight preference to localize at the water-phospholipid interface. Using umbrella sampling, we show the free energy bias for this preferred location to be just -0.42 kcal/mol, which explains the coexistence of attraction and exclusion mechanisms of sugar-membrane interaction. Accurate estimation of absolute entropy change of water molecules with a two-phase model indicates that the small energy bias is the result of a favorable entropy change of water molecules. Then, we incorporate results from molecular-dynamics simulation in two different ways to an analytical diffusion-reaction model to obtain association and dissociation constants for di-mannose interaction with membrane. Finally, we verify our approach by predicting concentration dependence of di-mannose recognition at the membrane that is consistent with experiment. In conclusion, we provide a combined approach for the thermodynamics and kinetics of a weak ligand-binding system, which has broad implications across many different fields.

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An Alpha-Helical Peptide in AOT Micelles Prefers to be Localized at the Water/Headgroup Interface

Cited by 23 publications

References 26 publications

Protein folding in a reverse micelle environment: The role of confinement and dehydration

Protein folding in a reverse micelle environment: The role of confinement and dehydration

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

Taste of Sugar at the Membrane: Thermodynamics and Kinetics of the Interaction of a Disaccharide with Lipid Bilayers

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