Simulations of the bis-penicillamine enkephalin in sodium chloride solution: A parameter study

Marlow, Gail E.; Pettitt, Bernard

doi:10.1002/1097-0282(2001)60:2<134::aid-bip1009>3.0.co;2-m

Cited by 8 publications

(29 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…60 Yet and , the RDF capture the interactions between ions and protein backbone and side-chains and have been used to characterize the attraction between ions and the protein surface. 18,30,[61][62][63] To make sure that the attraction of ions to the protein surface is not a geometrical Analysis of the X-ray coordinates of alkali metal ions and halides bound to proteins was carried out by using the PDBeMotif search tool 53 ( Figure 5). Alkali metal ions bind preferentially to side chains of glu and asp residues, and less often to polar residues such as ser, asn or thr.…”

Section: Gross Interactions Between the Protein And The Ionsmentioning

confidence: 99%

“…Computer simulations, and in particular molecular dynamics (MD) have provided an atomistic view of ionbinding to proteins, see e.g.,. [17][18][19][20] Moreover, classical force-fields with fixed partial charges are constantly under ongoing development, with recent contributions dealing with calcium, 21 alkali metal ions, [22][23][24][25] halides, 22,24 heavy metal ions 26 and lanthanide ions. 27 Over the recent years, several studies have aimed at an understanding of the specificity of salts to the protein surface.…”

Section: Table Of Contents Graphics Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Ions and the Protein Surface Revisited: Extensive Molecular Dynamics Simulations and Analysis of Protein Structures in Alkali-Chloride Solutions

Friedman

2011

J. Phys. Chem. B

View full text Add to dashboard Cite

Proteins interact with ions in various ways. The surface of proteins has an innate capability to bind ions, and is also influenced by the screening of the electrostatic potential owing to the presence of salts in the bulk solution. Alkali metal ions and chlorides interact with the protein surface, but such interactions are relatively weak and often transient. In this paper, computer simulations and analysis of protein structures are used to characterize the interactions between ions and the protein surface. The results show that the ion-binding properties of protein residues are highly variable. For example, alkali metal ions are more often associated with aspartate residues than with glutamates, whereas chlorides are most likely to be located near arginines. When comparing NaCl and KCl solutions, it was found that certain surface residues attract the anion more strongly in NaCl. This study demonstrates that proteinsalt interactions should be accounted for in the planning and execution of experiments and simulations involving proteins, particularly if subtle structural details are sought after.

show abstract

Section: Gross Interactions Between the Protein And The Ionsmentioning

confidence: 99%

Section: Table Of Contents Graphics Introductionmentioning

confidence: 99%

Ions and the Protein Surface Revisited: Extensive Molecular Dynamics Simulations and Analysis of Protein Structures in Alkali-Chloride Solutions

Friedman

2011

J. Phys. Chem. B

View full text Add to dashboard Cite

show abstract

“…Possible implications of this behavior for the design of molecules with pharmaceutical potential are also discussed. The interaction of the chloride anion with the peptide in the presence of the ammonium cation is compared to the interactions observed in a previous simulation of DPDPE where chloride was present with a sodium counterion 45…”

Section: Introductionmentioning

confidence: 99%

“…DPDPE is large enough to exhibit some degree of secondary structure, yet small enough to allow substantial conformational sampling. DPDPE has been studied by NMR,34–36 x‐ray crystallography,37 molecular modeling and mechanics,25, 34, 36, 38–42 and molecular dynamics 26, 43–45…”

Section: Introductionmentioning

confidence: 99%

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

Marlow

Pettitt

2002

Biopolymers

Self Cite

View full text Add to dashboard Cite

In order to quantify specific ion effects, a simulation study of bis(penicllamine) enkephalin, also known as DPDPE, has been performed in aqueous ammonium chloride solution and has been compared to a previous simulation of DPDPE in aqueous sodium chloride solution. Global thermodynamics have been calculated for a model system and the solution environment around DPDPE has been characterized. Associations of ions with DPDPE have been investigated. The observed differences between sodium chloride solution and ammonium chloride solution suggest that individual cations affect the solvation and peptide binding properties of a given anion.

show abstract

“…Non-polarizable forcefields have been used routinely and successfully to study proteins and other macromolecules, typically in NaCl or KCl solutions [27][28][29][30][31][32][33][34][35] . Interestingly, using energy decomposition analysis (EDA) we have recently found out that polarization contributes 29% of the interaction free energy between Li + and firstshell water molecules and as much as 23-25% of the same interaction for Na + .…”

Section: Introductionmentioning

confidence: 99%

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

Ahlstrand

Schpector

Friedman

2017

The Journal of Chemical Physics

View full text Add to dashboard Cite

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions is available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields, and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1 M). In addition, quantummechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li + and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved, but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

show abstract

Simulations of the bis-penicillamine enkephalin in sodium chloride solution: A parameter study

Cited by 8 publications

References 72 publications

Ions and the Protein Surface Revisited: Extensive Molecular Dynamics Simulations and Analysis of Protein Structures in Alkali-Chloride Solutions

Ions and the Protein Surface Revisited: Extensive Molecular Dynamics Simulations and Analysis of Protein Structures in Alkali-Chloride Solutions

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

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

Contact Info

Product

Resources

About