Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

Journal Article · Mon Dec 14 00:00:00 EST 2009 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.3268703· OSTI ID:21559821

Carnevale, V ^[1]; Raugei, S ^[2]

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1. Department of Chemistry, Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323 (United States)
2. International School for Advanced Studies (SISSA) and CNR-INFM Democritos, Via Beirut 2, Trieste I-34014 Italy, Trieste (Italy)

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

• OSTI ID: 21559821
• Journal Information: Journal of Chemical Physics, Vol. 131, Issue 22; Other Information: DOI: 10.1063/1.3268703; (c) 2009 American Institute of Physics; ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY
ACETYLATION
AFFINITY
AQUEOUS SOLUTIONS
BIOCHEMISTRY
BIOPHYSICS
CHARGE DENSITY
CHARGE EXCHANGE
DNA
INTERACTIONS
LYSINE
MOLECULAR DYNAMICS METHOD
MOLECULAR STRUCTURE
PROTEINS
RELIABILITY
SHELLS
SIMULATION
SOLUTES
SOLVATION
WATER
ACYLATION
AMINO ACIDS
CALCULATION METHODS
CARBOXYLIC ACIDS
CHEMICAL REACTIONS
CHEMISTRY
DISPERSIONS
HOMOGENEOUS MIXTURES
HYDROGEN COMPOUNDS
MIXTURES
NUCLEIC ACIDS
ORGANIC ACIDS
ORGANIC COMPOUNDS
OXYGEN COMPOUNDS
PHYSICS
SOLUTIONS