Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations

Diana Lousa, M. Cianci, J. Helliwell, Peter Halling, A Baptista, Claudio Soares

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals.(1) To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl– and Cs+ ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs+ can be used to find the binding sites of cations like Na+ and K+, which, unlike Cs+, have physiological and biotechnological roles. The Na+Cl– is more stable than the Cs+Cl– ion pair, decreasing the probability of interaction between Cl– and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium.
LanguageEnglish
Pages5838–5848
Number of pages11
JournalJournal of Physical Chemistry B
Volume116
Issue number20
Early online date30 Apr 2012
DOIs
Publication statusPublished - 2012

Fingerprint

Subtilisin
Acetonitrile
acetonitrile
Molecular dynamics
Ions
molecular dynamics
Computer simulation
ions
simulation
interactions
Cesium
cesium ions
enzymes
Cations
chlorides
Enzymes
proteins
Positive ions
cations
Subtilisins

Keywords

  • chloride ions
  • cesium ions
  • molecular dynamics simulations
  • acetonitrile soaked crystal

Cite this

Lousa, Diana ; Cianci, M. ; Helliwell, J. ; Halling, Peter ; Baptista, A ; Soares, Claudio. / Interaction of counterions with subtilisin in acetonitrile : insights from molecular dynamics simulations. In: Journal of Physical Chemistry B. 2012 ; Vol. 116, No. 20. pp. 5838–5848.
@article{e45a113f0a38443b8683faded2626ec0,
title = "Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations",
abstract = "A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals.(1) To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl– and Cs+ ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs+ can be used to find the binding sites of cations like Na+ and K+, which, unlike Cs+, have physiological and biotechnological roles. The Na+Cl– is more stable than the Cs+Cl– ion pair, decreasing the probability of interaction between Cl– and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium.",
keywords = "chloride ions, cesium ions, molecular dynamics simulations, acetonitrile soaked crystal",
author = "Diana Lousa and M. Cianci and J. Helliwell and Peter Halling and A Baptista and Claudio Soares",
year = "2012",
doi = "10.1021/jp303008g",
language = "English",
volume = "116",
pages = "5838–5848",
journal = "Journal of Physical Chemistry B",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "20",

}

Interaction of counterions with subtilisin in acetonitrile : insights from molecular dynamics simulations. / Lousa, Diana; Cianci, M.; Helliwell, J.; Halling, Peter; Baptista, A; Soares, Claudio.

In: Journal of Physical Chemistry B, Vol. 116, No. 20, 2012, p. 5838–5848.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Interaction of counterions with subtilisin in acetonitrile

T2 - Journal of Physical Chemistry B

AU - Lousa, Diana

AU - Cianci, M.

AU - Helliwell, J.

AU - Halling, Peter

AU - Baptista, A

AU - Soares, Claudio

PY - 2012

Y1 - 2012

N2 - A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals.(1) To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl– and Cs+ ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs+ can be used to find the binding sites of cations like Na+ and K+, which, unlike Cs+, have physiological and biotechnological roles. The Na+Cl– is more stable than the Cs+Cl– ion pair, decreasing the probability of interaction between Cl– and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium.

AB - A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals.(1) To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl– and Cs+ ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs+ can be used to find the binding sites of cations like Na+ and K+, which, unlike Cs+, have physiological and biotechnological roles. The Na+Cl– is more stable than the Cs+Cl– ion pair, decreasing the probability of interaction between Cl– and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium.

KW - chloride ions

KW - cesium ions

KW - molecular dynamics simulations

KW - acetonitrile soaked crystal

UR - http://www.scopus.com/inward/record.url?scp=84862279541&partnerID=8YFLogxK

U2 - 10.1021/jp303008g

DO - 10.1021/jp303008g

M3 - Article

VL - 116

SP - 5838

EP - 5848

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

SN - 1520-6106

IS - 20

ER -