A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions

Guàrdia, E.; Martı́, Jordi; García-Tarrés, Lino; Laría, Daniel

doi:10.1016/j.molliq.2004.08.004

Cited by 117 publications

(73 citation statements)

References 20 publications

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“…Although this attenuation in hydrogen bonding may appear insignificant, this difference is nonetheless important for at least two reasons. First, theoretical calculations indicate that, on average, water molecules form ϳ3.5 hydrogen bonds in solutions (40,41). This value is greater than the number of hydrogen bonds coordinating water 1 in the solvent pocket in SET7/9 Y305F (Fig.…”

Section: Discussionmentioning

confidence: 95%

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

Rizzo

Couture

Dirk

et al. 2010

Journal of Biological Chemistry

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SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ⑀-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di-and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ⑀-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ⑀-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.SET domain enzymes represent a family of S-adenosylmethionine (AdoMet) 3 -dependent methyltransferases that catalyze the site-specific methylation of protein lysyl residues in a host of proteins, including histones, transcription factors, chromatin-modifying enzymes, ribosomal subunits, and other substrates (1-3). In many instances, these modifications serve to recruit effector proteins that recognize methyl-lysyl residues in a sequence-dependent fashion (4). In addition, SET domain KMTs exhibit product specificity, defined as their ability to catalyze mono-, di-, or trimethylation of the lysine ⑀-amino group. This specificity is biologically relevant because many methyllysine-binding proteins can discriminate among different degrees of lysine methylation (4). Thus, both the site and degree of lysine methylation are critical to recognition by effector proteins.Structural and functional studies have identified a Phe/Tyr switch in the active site of SET domain KMTs that governs their respective product specificities (5, 6). According to this model, KMTs that possess a tyrosine in the Phe/Tyr switch site are limited to catalyzing lysine monomethylation, whereas enzymes that possess a phenylalanine or another hydrophobic residue in this position display di-or trimethyltransferase activity. Mutational analysis of various SET domain KMTs, including DIM-5 (KMT1) (6), SET7/9 (6), G9A (KMT1C) (5), and SET8 (also known as PR-SET7 and KMT5A) (7,8), has demonstrated that substitutions in the Phe/Tyr switch result in predictable changes in product specificity. Several models have been proposed to explain the mechanism by which the Phe/Tyr switch site governs this specificity, including variations in the diameter of the active site due to the size of Phe/Tyr switch residue and steric hindrance by t...

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Section: Discussionmentioning

confidence: 95%

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

Rizzo

Couture

Dirk

et al. 2010

Journal of Biological Chemistry

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“…More surprising is the distinct elastic response of PBS. Molecular dynamic simulation shows that the hydrogen bond lifetime in water containing alkalai metal and halide ions is only about 20% greater than that of pure water [23] and consequently ionic solutions are not expected to exhibit elasticity at frequencies as low as 5 MHz.…”

Section: Viscoelasticity Of Pbs Solutionmentioning

confidence: 98%

Viscoelastic study of the adsorption of bovine serum albumin on gold and its dependence on pH

Figueira

Jones

2008

Journal of Colloid and Interface Science

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“…51 Only if all three geometrical conditions are fulfilled, we consider molecule 1 as donating a hydrogen bond to molecule 2.…”

Section: Appendix A: Distinguishing Between Liquid and Vapour-like Momentioning

confidence: 99%

Detecting vapour bubbles in simulations of metastable water

González

Menzl

Aragonés

et al. 2014

The Journal of Chemical Physics

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Thermodynamics and kinetics of bubble nucleation: Simulation methodology J. Chem. Phys. 137, 074109 (2012) The investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguish between liquid-and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure. © 2014 AIP Publishing LLC. [http://dx

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A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions

Cited by 117 publications

References 20 publications

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

Viscoelastic study of the adsorption of bovine serum albumin on gold and its dependence on pH

Detecting vapour bubbles in simulations of metastable water

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