Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water.

PubWeight™: 0.96‹?› | Rank: Top 15%

🔗 View Article (PMC 1815233)

Published in Proc Natl Acad Sci U S A on February 13, 2007

Authors

Je-Luen Li1, Roberto Car, Chao Tang, Ned S Wingreen

Author Affiliations

1: Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

Articles cited by this

Generalized Gradient Approximation Made Simple. Phys Rev Lett (1996) 99.29

The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24

Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys Rev B Condens Matter (1990) 12.76

Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett (1985) 7.13

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science (1991) 3.79

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A (2004) 2.71

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry (1991) 2.46

Molecular theory of hydrophobic effects: "She is too mean to have her name repeated.". Annu Rev Phys Chem (2002) 1.83

Peptides with selective affinity for carbon nanotubes. Nat Mater (2003) 1.35

Is water structure around hydrophobic groups clathrate-like? Proc Natl Acad Sci U S A (1995) 1.29

First solvation shell of the Cu(II) aqua ion: evidence for fivefold coordination. Science (2001) 1.27

Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Proteins (2002) 1.23

Theory of hydrophobic interactions. J Biomol Struct Dyn (1998) 1.22

Molecular simulation study of cooperativity in hydrophobic association. Protein Sci (2000) 1.18

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: spectral signatures of hydrogen bond breaking in liquid water. J Chem Phys (2004) 1.12

Solvation: how to obtain microscopic energies from partitioning and solvation experiments. Annu Rev Biophys Biomol Struct (1997) 1.07

Differences between pair and bulk hydrophobic interactions. Proc Natl Acad Sci U S A (1990) 0.99

Ab initio studies on high pressure phases of ice. Phys Rev Lett (1992) 0.91

Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics. J Chem Phys (2005) 0.85

Articles by these authors

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J Phys Condens Matter (2009) 14.22

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell (2004) 8.89

The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci U S A (2004) 6.76

Defining network topologies that can achieve biochemical adaptation. Cell (2009) 5.49

Clinical findings in 111 cases of influenza A (H7N9) virus infection. N Engl J Med (2013) 5.38

Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science (2008) 4.45

Health assessment of cooling fan bearings using wavelet-based filtering. Sensors (Basel) (2012) 3.38

Functionalized single graphene sheets derived from splitting graphite oxide. J Phys Chem B (2006) 3.26

Chemosensing in Escherichia coli: two regimes of two-state receptors. Proc Natl Acad Sci U S A (2006) 3.12

Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol (2009) 3.07

Raman spectra of graphite oxide and functionalized graphene sheets. Nano Lett (2007) 2.83

Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell (2013) 2.69

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. Proc Natl Acad Sci U S A (2011) 2.61

Quantifying the integration of quorum-sensing signals with single-cell resolution. PLoS Biol (2009) 2.40

A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol (2008) 2.33

In vivo residue-specific histone methylation dynamics. J Biol Chem (2009) 2.33

Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell (2012) 2.28

Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones. Proc Natl Acad Sci U S A (2003) 2.19

Precise adaptation in bacterial chemotaxis through "assistance neighborhoods". Proc Natl Acad Sci U S A (2006) 2.13

Cell shape and cell-wall organization in Gram-negative bacteria. Proc Natl Acad Sci U S A (2008) 2.13

The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol Microbiol (2008) 2.11

Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi. Cell (2008) 2.10

Robustness and modular design of the Drosophila segment polarity network. Mol Syst Biol (2006) 2.06

Responding to chemical gradients: bacterial chemotaxis. Curr Opin Cell Biol (2011) 2.00

Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression. EMBO J (2003) 1.99

A curvature-mediated mechanism for localization of lipids to bacterial poles. PLoS Comput Biol (2006) 1.95

Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria. Mol Microbiol (2011) 1.91

Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88

PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution. PLoS Comput Biol (2008) 1.88

Accuracy of direct gradient sensing by single cells. Proc Natl Acad Sci U S A (2008) 1.81

Finding multiple target optimal intervention in disease-related molecular network. Mol Syst Biol (2008) 1.70

Theory of quantum annealing of an Ising spin glass. Science (2002) 1.70

Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment. J Bacteriol (2006) 1.66

Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol (2009) 1.57

Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation. PLoS Comput Biol (2007) 1.56

Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. Mol Cell (2010) 1.52

The effects of atmosphere and calcined temperature on photocatalytic activity of TiO2 nanofibers prepared by electrospinning. Nanoscale Res Lett (2013) 1.43

Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters. Biophys J (2006) 1.43

Hourglass model for a protein-based circadian oscillator. Phys Rev Lett (2006) 1.43

Oxygen-driven unzipping of graphitic materials. Phys Rev Lett (2006) 1.42

α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat Chem Biol (2011) 1.41

Relationship between the transmission of schistosomiasis japonica and the construction of the Three Gorge Reservoir. Acta Trop (2002) 1.39

Information processing and signal integration in bacterial quorum sensing. Mol Syst Biol (2009) 1.39

Dipolar correlations and the dielectric permittivity of water. Phys Rev Lett (2007) 1.37

Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. Science (2003) 1.37

Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell (2013) 1.34

Accurate and efficient method for many-body van der Waals interactions. Phys Rev Lett (2012) 1.34

Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis. EMBO J (2010) 1.32

Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines. Proc Natl Acad Sci U S A (2009) 1.31

The liquid-liquid transition in supercooled ST2 water: a comparison between umbrella sampling and well-tempered metadynamics. Faraday Discuss (2013) 1.30

Variable sizes of Escherichia coli chemoreceptor signaling teams. Mol Syst Biol (2008) 1.29

Lipid localization in bacterial cells through curvature-mediated microphase separation. Biophys J (2008) 1.25

Thermal robustness of signaling in bacterial chemotaxis. Cell (2011) 1.23

Nuclear quantum effects in water. Phys Rev Lett (2008) 1.22

Toward an atomistic model for predicting transcription-factor binding sites. Proteins (2004) 1.22

Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol Syst Biol (2011) 1.19

A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol Biol Cell (2013) 1.19

Maximum likelihood and the single receptor. Phys Rev Lett (2009) 1.18

Dynamic simulations on the arachidonic acid metabolic network. PLoS Comput Biol (2007) 1.14

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: spectral signatures of hydrogen bond breaking in liquid water. J Chem Phys (2004) 1.12

Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules. Proc Natl Acad Sci U S A (2010) 1.12

Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell. Biophys J (2010) 1.11

Achieving optimal growth through product feedback inhibition in metabolism. PLoS Comput Biol (2010) 1.10

Dynamic studies of scaffold-dependent mating pathway in yeast. Biophys J (2006) 1.08

Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 1.08

Self-organized periodicity of protein clusters in growing bacteria. Phys Rev Lett (2008) 1.08

Dynamics of cooperativity in chemical sensing among cell-surface receptors. Phys Rev Lett (2011) 1.08

Growth-induced instability in metabolic networks. Phys Rev Lett (2007) 1.08

Quantum chemical evaluation of protein control over heme ligation: CO/O2 discrimination in myoglobin. J Phys Chem B (2005) 1.08

Min-protein oscillations in round bacteria. Phys Biol (2004) 1.04

Limits of sensing temporal concentration changes by single cells. Phys Rev Lett (2010) 1.04

Chemotaxis receptor complexes: from signaling to assembly. PLoS Comput Biol (2007) 1.04

Exponential sensitivity of noise-driven switching in genetic networks. Phys Biol (2008) 1.04

X-ray absorption signatures of the molecular environment in water and ice. Phys Rev Lett (2010) 1.02

Antidiabetic and antioxidant effects and phytochemicals of mulberry fruit (Morus alba L.) polyphenol enhanced extract. PLoS One (2013) 1.02

Precision and kinetics of adaptation in bacterial chemotaxis. Biophys J (2010) 1.02

Electronic structure and reactivity of isomeric oxo-Mn(V) porphyrins: effects of spin-state crossing and pKa modulation. Inorg Chem (2006) 1.02

Modular mass spectrometric tool for analysis of composition and phosphorylation of protein complexes. PLoS One (2007) 1.02

Rationalizing translation attenuation in the network architecture of the unfolded protein response. Proc Natl Acad Sci U S A (2008) 1.02

Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix. Proteins (2002) 1.00

Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins (2002) 1.00

Filament depolymerization can explain chromosome pulling during bacterial mitosis. PLoS Comput Biol (2011) 0.99

A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli. Proc Natl Acad Sci U S A (2010) 0.98

Weight matrices for protein-DNA binding sites from a single co-crystal structure. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.98

Flexibility of alpha-helices: results of a statistical analysis of database protein structures. J Mol Biol (2003) 0.97

Hydrogen bonds and van der waals forces in ice at ambient and high pressures. Phys Rev Lett (2011) 0.97

Unexpected one-pot method to synthesize spiro[fluorene-9,9'-xanthene] building blocks for blue-light-emitting materials. Org Lett (2006) 0.97

Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model. PLoS One (2013) 0.97

Controlling the nonequilibrium interlayer exchange coupling in asymmetric magnetic tunnel junctions. Phys Rev Lett (2009) 0.96

Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Protein Sci (2004) 0.96

How can vaccines against influenza and other viral diseases be made more effective? PLoS Biol (2010) 0.96

Why are water-hydrophobic interfaces charged? J Am Chem Soc (2008) 0.96

Sensitivity to visual motion in amblyopic macaque monkeys. Vis Neurosci (2006) 0.95

Accuracy of direct gradient sensing by cell-surface receptors. Prog Biophys Mol Biol (2009) 0.93

Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant. Biophys J (2005) 0.93

Design principles of the yeast G1/S switch. PLoS Biol (2013) 0.92

Flexibility of beta-sheets: principal component analysis of database protein structures. Proteins (2004) 0.92