Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of <i>N</i>-Methylacetamide in Aqueous Salt Solutions

Heyda, Jan; Vincent, Jordan C.; Tobias, Douglas J.; Dzubiella, Joachim; Jungwirth, Pavel

doi:10.1021/jp910953w

Cited by 111 publications

(166 citation statements)

References 49 publications

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“…form intermolecular hydrogen bond, which decreases with salt concentration. Our calculated radial distribution functions are very good in agreement with Heyda et al [69], who simulated salt solution of aqueous NMA system with different polarisable and non-polarisable force fields.…”

Section: Translational Diffusion and Structure Of The Solvation Shellsupporting

confidence: 89%

“…Despite these latest advances, much less progress has been made in understanding the detailed interactions of cations and anions with polar and non-polar moieties of proteins. Recently, Jungwirth and co-workers [69] investigated the structure of the solvation shell of ions in aqueous NMA solution in presence of 1 M solutions of NaCl, KCl, KBr and NaBr using both polarisable and non-polarisable force fields. It was found that irrespective of the charge and size; the ionic solutes prefer water than NMA and also observed that in comparison to K + , Na + has a stronger affinity towards carbonyl oxygen of the amide group whereas none of the halide anions show any appreciable attraction for amide hydrogen.…”

Section: Introductionmentioning

confidence: 99%

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Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Pattanayak

Chowdhuri

2013

Molecular Physics

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The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ∼1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation-O NMA radial distribution function decreases whereas the Cl − ৄH NMA radial distribution function increases with ion concentration. On the other hand, the cation-O water and Cl − ৄH water radial distribution function shows very negligible change with respect to ion concentration.We have also calculated NMA-water and water-water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O NMA ৄH water is comparatively slower than the H NMA ৄO water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.

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Section: Translational Diffusion and Structure Of The Solvation Shellsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Pattanayak

Chowdhuri

2013

Molecular Physics

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“…Note the two leftmost oxygen atoms on triglycine are degenerate, as are all the oxygens of the sulfite anion and every alanine monomer. tions (30). This spectrum is generally very similar to that of triglycine without sodium bromide, in that no new features are present.…”

mentioning

confidence: 57%

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Schwartz

Uejio

Duffin

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The authors note that the results of their article indicated that sulfite interacts more directly with the peptide than does bromide. These results do not refute nor contradict the work of Cremer and coworkers involving the interactions of anions with poly(N-isopropylacrylamide) (1). In the case of Cremer's work, a direct Hofmeister series is followed. For triglycine, however, at least a partially reversed Hofmeister series might be expected (2, 3), because this molecule contains a site of positive charge.

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“…This behavior of cations and anions is well documented in simulations of model peptides in salt solutions. 29,32 Anions in both NaCl and NaI solutions interact more strongly with H R (Figure 2b). This preference might be related to the significant difference of solvent accessible areas of the two amide groups (11.1 Å 2 for N R vs 6.3 Å 2 for N L ).…”

Section: Alanine Dipeptide Simulationsmentioning

confidence: 96%

Specific Interactions of Sodium Salts with Alanine Dipeptide and Tetrapeptide in Water: Insights from Molecular Dynamics

2011

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We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space is achieved by the replica exchange method. In agreement with other works, we observe preferential sodium interactions with the peptide carbonyl groups, which are enhanced in the NaI solutions due to the increased affinity of the less hydrophilic iodide anion for the peptide methyl side-chains and terminal blocking groups. These interactions have been associated with a decrease in the helicities of more complex peptides. In our simulations, both salts have a small effect on the dipeptide, but consistently stabilize the intramolecular hydrogen-bonding interactions and "α-helical" conformations of the tetrapeptide. This behavior, and an analysis of the intermolecular interaction energies show that ion-peptide interactions, or changes in the peptide hydration due to salts, are not sufficient determining factors of the peptide conformational preferences. Additional simulations suggest that the observed stabilizing effect is not due to the employed force-field, and that it is maintained in short peptides but is reversed in longer peptides. Thus, the peptide conformational preferences are determined by an interplay of energetic and entropic factors, arising from the peptide sequence and length and the composition of the solution.

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Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of N-Methylacetamide in Aqueous Salt Solutions

Cited by 111 publications

References 49 publications

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Specific Interactions of Sodium Salts with Alanine Dipeptide and Tetrapeptide in Water: Insights from Molecular Dynamics

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