Simulation of the bis‐(penicillamine) enkephalin in ammonium chloride solution: A comparison with sodium chloride

Marlow, Gail E.; Pettitt, B. Montgomery

doi:10.1002/bip.10292

Cited by 4 publications

(6 citation statements)

References 55 publications

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“…More recent MD simulation studies that are 10 ns long also support a bent model with close head to tail arrangement and a 2 f 5 hydrogen bond at neutral pH. 16 Simulations in the presence of different salts or ionic cosolvents, such as NaCl and NH 4 Cl, [22][23][24][25] detail interactions between the positively charged N terminus and many Clions. The study suggests that the conformation of the peptide is sensitive to the precise anion that interacts singly with the negatively charged C terminus.…”

Section: Introductionmentioning

confidence: 90%

“…Simulations in the presence of different salts or ionic cosolvents, such as NaCl and NH 4 Cl, − detail interactions between the positively charged N terminus and many Cl - ions. The study suggests that the conformation of the peptide is sensitive to the precise anion that interacts singly with the negatively charged C terminus . In general, simulation studies indicate a bent form for the peptide even in aqueous solution though the details of the bend may vary.…”

Section: Introductionmentioning

confidence: 99%

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Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation

et al. 2005

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The morphogenic opiate pentapeptide leucine-enkephalin (lenk) in a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer is studied using NMR spectroscopy and molecular dynamics simulation. Contrary to the frequent assumption that the peptide attains a single fixed conformation in the presence of membranes, we find that the lenk molecule is flexible, switching between specific bent conformations. The constraints to the orientation of the aromatic rings that are identified by the NMR experiment are found by the MD simulation to be related to the depth of the peptide in the bilayer. The motion of the N-H vectors of the peptide bonds with respect to the magnetic field direction as observed by MD largely explain the magnitude of the observed residual dipolar coupling (RDC), which are much reduced over the static (15)N-(1)H coupling. The measured RDCs are nevertheless significantly larger than the predicted ones, possibly due the absence of long-time motions in the simulations. The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms.

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Section: Introductionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation

et al. 2005

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“…To avoid these difficulties, we adopted the ionprotein distance as a parameter for the quantitation of the ions' locations. A similar parameter was used for the studies of ion distributions in the vicinity of peptides (36)(37)(38)(39).…”

Section: Contacts Between the Ions And The Proteinmentioning

confidence: 99%

“…Therefore, statistical analysis of ion distributions around the surface of such proteins would be meaningless. However, when only a small number of ions is present in the solution, their dynamics can be studied directly by monitoring the distance between each ion and the protein, or certain moieties on its surface, as reported by Pettit and coworkers (36)(37)(38)(39).…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of a Protein Surface: Ion-Residues Interactions

Friedman

Nachliel

Gutman

2005

Biophysical Journal

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Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

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“…Furthermore, analysis of the thermodynamics of denaturation provides estimated total numbers of bound cosolvent molecules that can vary widely depending on the binding model used for the analysis. − In principle, computer simulations of peptides or proteins in different solvent environments can provide atomic level detail of the interactions between cosolvent molecules and proteins. However, most previous studies have provided only qualitative descriptions of the effects of different cosolvents − and do not relate the observations to thermodynamic changes. Here, we describe how quantitative thermodynamic information can be obtained from molecular dynamics (MD) simulations, which can then be used to compare directly with the experimental thermodynamic data and therefore provide insights into the action of different cosolvents.…”

Section: Introductionmentioning

confidence: 99%

A Combined Simulation and Kirkwood−Buff Approach to Quantify Cosolvent Effects on the Conformational Preferences of Peptides in Solution

Aburi

Smith

2004

J. Phys. Chem. B

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A molecular dynamics study of the effects of salt on the conformational preferences of leucine enkephalin (LE) in water has been performed to outline a general approach for quantifying the effects of a cosolvent on a biomolecular equilibrium in solution using molecular simulation. The simulations of LE suggest that the peptide exists as a mixture of folded and unfolded conformations in pure water, and a potential of mean force calculation indicates the population of the folded form to be 53±3%. The addition of 2 M salt reduces the population of the folded form to 12±5%. A combination of the simulation data and Kirkwood−Buff theory is used to determine the preferential interactions of the cosolvent with the peptide and to reproduce the population changes indicated by the potential of mean force calculations. The results demonstrate the potential of a combined simulation and Kirkwood−Buff approach for quantifying simulation data in an effort to understand the effects of cosolvents on the thermodynamics of biomolecules in solution, especially for systems where potential of mean force calculations are unfeasible.

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Simulation of the bis‐(penicillamine) enkephalin in ammonium chloride solution: A comparison with sodium chloride

Cited by 4 publications

References 55 publications

Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation

Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation

Molecular Dynamics of a Protein Surface: Ion-Residues Interactions

A Combined Simulation and Kirkwood−Buff Approach to Quantify Cosolvent Effects on the Conformational Preferences of Peptides in Solution

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