Published in J Am Chem Soc on March 17, 2010
In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. J Am Chem Soc (2011) 1.20
Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J (2013) 1.19
Simplified bacterial "pore" channel provides insight into the assembly, stability, and structure of sodium channels. J Biol Chem (2011) 1.11
Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol (2011) 1.02
Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys J (2012) 0.94
Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. J Gen Physiol (2014) 0.94
Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion. Nat Commun (2014) 0.92
Determining peptide partitioning properties via computer simulation. J Membr Biol (2010) 0.86
Computational modeling of membrane proteins. Proteins (2014) 0.83
Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer. J Phys Chem B (2011) 0.81
3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys J (2014) 0.80
Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80
Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices. J Chem Theory Comput (2014) 0.80
Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol (2015) 0.79
Assembly and Stability of α-Helical Membrane Proteins. Soft Matter (2012) 0.79
More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. J Chem Phys (2014) 0.77
Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem (2011) 0.76
Membrane binding and insertion of a pHLIP peptide studied by all-atom molecular dynamics simulations. Int J Mol Sci (2013) 0.76
Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide. Nat Commun (2016) 0.75
The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. J Chem Theory Comput (2012) 0.75
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. J Comput Chem (2017) 0.75
Transmembrane helices containing a charged arginine are thermodynamically stable. Eur Biophys J (2017) 0.75
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
The genetic basis for bacterial mercury methylation. Science (2013) 2.87
Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr Biol (2003) 2.28
Membrane damage by human islet amyloid polypeptide through fibril growth at the membrane. Proc Natl Acad Sci U S A (2008) 2.25
Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. J Chem Phys (2007) 2.23
Is the first hydration shell of lysozyme of higher density than bulk water? Proc Natl Acad Sci U S A (2002) 2.19
Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by (2)H NMR. Biophys J (2002) 2.01
Tilt angles of transmembrane model peptides in oriented and non-oriented lipid bilayers as determined by 2H solid-state NMR. Biophys J (2004) 1.98
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A (2011) 1.96
Nonbilayer lipids affect peripheral and integral membrane proteins via changes in the lateral pressure profile. Biochim Biophys Acta (2004) 1.94
Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry (2003) 1.92
Structural mechanism of the recovery stroke in the myosin molecular motor. Proc Natl Acad Sci U S A (2005) 1.66
Lateral diffusion of membrane proteins. J Am Chem Soc (2009) 1.65
Translational hydration water dynamics drives the protein glass transition. Biophys J (2003) 1.63
Islet amyloid polypeptide-induced membrane leakage involves uptake of lipids by forming amyloid fibers. FEBS Lett (2004) 1.59
Snorkeling of lysine side chains in transmembrane helices: how easy can it get? FEBS Lett (2003) 1.57
Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides. Biochemistry (2002) 1.54
On the orientation of a designed transmembrane peptide: toward the right tilt angle? J Am Chem Soc (2007) 1.54
How protein transmembrane segments sense the lipid environment. Biochemistry (2007) 1.50
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc Natl Acad Sci U S A (2011) 1.50
Influence of flanking residues on tilt and rotation angles of transmembrane peptides in lipid bilayers. A solid-state 2H NMR study. Biochemistry (2005) 1.45
Principal components of the protein dynamical transition. Phys Rev Lett (2003) 1.43
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation. J Am Chem Soc (2003) 1.42
Sphingomyelin is much more effective than saturated phosphatidylcholine in excluding unsaturated phosphatidylcholine from domains formed with cholesterol. FEBS Lett (2003) 1.37
SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallogr D Biol Crystallogr (2002) 1.36
Self-association of transmembrane alpha-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch. J Biol Chem (2005) 1.36
Structural basis of cellulosome efficiency explored by small angle X-ray scattering. J Biol Chem (2005) 1.32
Transbilayer movement of phospholipids in biogenic membranes. Biochemistry (2004) 1.32
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. J Am Chem Soc (2008) 1.30
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J (2007) 1.30
Phospholipid flop induced by transmembrane peptides in model membranes is modulated by lipid composition. Biochemistry (2003) 1.28
Hydrophobic mismatch between helices and lipid bilayers. Biophys J (2003) 1.28
Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2010) 1.26
Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel. Proc Natl Acad Sci U S A (2013) 1.25
The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane alpha-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry (2002) 1.22
The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure (2007) 1.22
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem (2002) 1.21
In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. J Am Chem Soc (2011) 1.20
Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett (2004) 1.20
Orientation and dynamics of transmembrane peptides: the power of simple models. Eur Biophys J (2009) 1.18
Mechanism of primary proton transfer in bacteriorhodopsin. Structure (2004) 1.17
Recent insights in islet amyloid polypeptide-induced membrane disruption and its role in beta-cell death in type 2 diabetes mellitus. Exp Diabetes Res (2008) 1.15
Influence of lipids on membrane assembly and stability of the potassium channel KcsA. FEBS Lett (2002) 1.15
A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophys J (2007) 1.15
Stability of KcsA tetramer depends on membrane lateral pressure. Biochemistry (2004) 1.12
Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins (2005) 1.12
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys J (2005) 1.10
The alpha helix dipole: screened out? Structure (2005) 1.09
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J (2002) 1.09
The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. J Mol Biol (2006) 1.08
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc Natl Acad Sci U S A (2007) 1.07
Membrane interaction of the glycosyltransferase MurG: a special role for cardiolipin. J Bacteriol (2003) 1.06
Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy. Biophys J (2009) 1.05
Importance of hydrophobic matching for spontaneous insertion of a single-spanning membrane protein. Biochemistry (2002) 1.05
Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study. J Phys Chem B (2007) 1.05
Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination. J Am Chem Soc (2002) 1.05
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J Phys Chem B (2005) 1.05
Role of histone tails in structural stability of the nucleosome. PLoS Comput Biol (2011) 1.04
Bacterial reaction centers purified with styrene maleic acid copolymer retain native membrane functional properties and display enhanced stability. Angew Chem Int Ed Engl (2014) 1.04
Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnol Biofuels (2012) 1.04
A molecular mechanics force field for biologically important sterols. J Comput Chem (2005) 1.03
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J Chem Phys (2011) 1.03
Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide. Biophys J (2010) 1.02
Domain formation in phosphatidylcholine bilayers containing transmembrane peptides: specific effects of flanking residues. Biochemistry (2002) 1.01
Transmembrane peptides stabilize inverted cubic phases in a biphasic length-dependent manner: implications for protein-induced membrane fusion. Biophys J (2005) 1.00
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J (2012) 1.00
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. Biochemistry (2006) 0.99
Neutron frequency windows and the protein dynamical transition. Biophys J (2004) 0.98
Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys J (2010) 0.98
Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins (2007) 0.98
Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J Comput Chem (2010) 0.98
Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.96
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A (2011) 0.96
Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc (2009) 0.95
Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophys J (2008) 0.95
Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke. J Mol Biol (2006) 0.95
Interaction of the K+ channel KcsA with membrane phospholipids as studied by ESI mass spectrometry. FEBS Lett (2003) 0.95
Protein self-assembly and lipid binding in the folding of the potassium channel KcsA. Biochemistry (2008) 0.95
Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein. J Am Chem Soc (2012) 0.95
Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys J (2012) 0.94
Detection and identification of stable oligomeric protein complexes in Escherichi coli inner membranes: a proteomics approach. J Biol Chem (2005) 0.94
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proc Natl Acad Sci U S A (2007) 0.94
Lattice dynamics of a protein crystal. Phys Rev Lett (2007) 0.93
Influence of hydrophobic mismatch and palmitoylation on the association of transmembrane alpha-helical peptides with detergent-resistant membranes. FEBS Lett (2002) 0.93
A synergistic effect between cholesterol and tryptophan-flanked transmembrane helices modulates membrane curvature. Biochemistry (2005) 0.93
Simulation analysis of the temperature dependence of lignin structure and dynamics. J Am Chem Soc (2011) 0.93
Peptide partitioning properties from direct insertion studies. Biophys J (2010) 0.92
Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase. J Mol Biol (2011) 0.92
2,2,2-Trifluoroethanol changes the transition kinetics and subunit interactions in the small bacterial mechanosensitive channel MscS. Biophys J (2007) 0.92
Phosphatidic acid plays a special role in stabilizing and folding of the tetrameric potassium channel KcsA. FEBS Lett (2007) 0.92
Sterols have higher affinity for sphingomyelin than for phosphatidylcholine bilayers even at equal acyl-chain order. Biophys J (2011) 0.92
Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions. J Phys Chem B (2008) 0.91
Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity. J Biol Chem (2011) 0.91
Enzyme activity and flexibility at very low hydration. Biophys J (2005) 0.91
Small alcohols destabilize the KcsA tetramer via their effect on the membrane lateral pressure. Biochemistry (2004) 0.90
Ruthenium-decorated lipid vesicles: light-induced release of [Ru(terpy)(bpy)(OH2)]2+ and thermal back coordination. J Am Chem Soc (2010) 0.90