Published in Structure on February 05, 2013
Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria. Proc Natl Acad Sci U S A (2013) 0.93
Photocycle of Exiguobacterium sibiricum rhodopsin characterized by low-temperature trapping in the IR and time-resolved studies in the visible. J Phys Chem B (2013) 0.78
Microcompartments and protein machines in prokaryotes. J Mol Microbiol Biotechnol (2013) 0.77
Stable closure of the cytoplasmic half-channel is required for efficient proton transport at physiological membrane potentials in the bacteriorhodopsin catalytic cycle. Biochemistry (2014) 0.76
Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin. PLoS One (2013) 0.76
Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form. PLoS One (2014) 0.76
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem (2003) 15.88
Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium. Biophys J (1975) 12.68
Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science (1999) 3.83
Aspartic acids 96 and 85 play a central role in the function of bacteriorhodopsin as a proton pump. EMBO J (1989) 3.36
Role of aspartate-96 in proton translocation by bacteriorhodopsin. Proc Natl Acad Sci U S A (1989) 3.22
Aspartic acid-96 is the internal proton donor in the reprotonation of the Schiff base of bacteriorhodopsin. Proc Natl Acad Sci U S A (1989) 3.06
Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution. Science (1998) 2.89
Molecular mechanism of vectorial proton translocation by bacteriorhodopsin. Nature (2000) 2.88
Replacement of aspartic acid-96 by asparagine in bacteriorhodopsin slows both the decay of the M intermediate and the associated proton movement. Proc Natl Acad Sci U S A (1989) 2.64
Bacteriorhodopsin. Annu Rev Physiol (2004) 2.61
A defective proton pump, point-mutated bacteriorhodopsin Asp96----Asn is fully reactivated by azide. EMBO J (1989) 2.53
Closing in on bacteriorhodopsin: progress in understanding the molecule. Annu Rev Biophys Biomol Struct (1999) 2.39
Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature (2005) 2.31
Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base. Biochemistry (1991) 2.06
Proton transfers in the bacteriorhodopsin photocycle. Biochim Biophys Acta (2005) 1.90
Acid-base equilibrium of the Schiff base in bacteriorhodopsin. Biochemistry (1982) 1.88
Bacteriorhodopsin's intramolecular proton-release pathway consists of a hydrogen-bonded network. Biochemistry (1998) 1.69
Controlling the pKa of the bacteriorhodopsin Schiff base by use of artificial retinal analogues. Proc Natl Acad Sci U S A (1986) 1.62
Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin. J Mol Biol (2000) 1.61
What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. Biophys J (2003) 1.53
The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins (2006) 1.49
Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment. Biophys J (2004) 1.41
Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol (2003) 1.38
Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Biophys J (2001) 1.36
Proton binding within a membrane protein by a protonated water cluster. Proc Natl Acad Sci U S A (2005) 1.36
pH-induced structural changes in bacteriorhodopsin studied by Fourier transform infrared spectroscopy. Biophys J (1994) 1.31
Proton transfer reactions across bacteriorhodopsin and along the membrane. Biochim Biophys Acta (2000) 1.31
Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography. EMBO J (2000) 1.30
In situ determination of transient pKa changes of internal amino acids of bacteriorhodopsin by using time-resolved attenuated total reflection Fourier-transform infrared spectroscopy. Proc Natl Acad Sci U S A (1999) 1.28
Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle. J Mol Biol (2003) 1.24
Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proc Natl Acad Sci U S A (2007) 1.15
Proton transfer via a transient linear water-molecule chain in a membrane protein. Proc Natl Acad Sci U S A (2011) 1.15
Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle. Proc Natl Acad Sci U S A (2000) 1.14
Substitution of membrane-embedded aspartic acids in bacteriorhodopsin causes specific changes in different steps of the photochemical cycle. Biochemistry (1989) 1.03
Coupling of the reisomerization of the retinal, proton uptake, and reprotonation of Asp-96 in the N photointermediate of bacteriorhodopsin. Biochemistry (2001) 0.98
Water molecules and hydrogen-bonded networks in bacteriorhodopsin--molecular dynamics simulations of the ground state and the M-intermediate. Biophys J (2005) 0.98
The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochim Biophys Acta (2008) 0.96
Structural snapshots of conformational changes in a seven-helix membrane protein: lessons from bacteriorhodopsin. Curr Opin Struct Biol (2009) 0.95
Proton translocation by bacteriorhodopsin in the absence of substantial conformational changes. J Mol Biol (2002) 0.94
Directional proton transfer in membrane proteins achieved through protonated protein-bound water molecules: a proton diode. Angew Chem Int Ed Engl (2010) 0.94
Water structural changes in the L and M photocycle intermediates of bacteriorhodopsin as revealed by time-resolved step-scan Fourier transform infrared (FTIR) spectroscopy. Biochemistry (2007) 0.92
Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212. Biochemistry (1999) 0.91
Active internal waters in the bacteriorhodopsin photocycle. A comparative study of the L and M intermediates at room and cryogenic temperatures by infrared spectroscopy. Biochemistry (2008) 0.89
How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation. Biophys J (2004) 0.88
Time-resolved X-ray diffraction reveals movement of F helix of D96N bacteriorhodopsin during M-MN transition at neutral pH. Biophys J (2002) 0.88
Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein. Proteins (2005) 0.88
Subsecond proton-hole propagation in bacteriorhodopsin. Biophys J (2003) 0.85
Membrane-protein stability in a phospholipid-based crystallization medium. J Struct Biol (2006) 0.84
Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin. Photochem Photobiol (2007) 0.83
The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophys J (2003) 0.80
Structural changes in the N and N' states of the bacteriorhodopsin photocycle. Biophys J (2009) 0.80
Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin. J Phys Chem B (2006) 0.76
An integrated pipeline for de novo assembly of microbial genomes. PLoS One (2012) 8.97
SPARX, a new environment for Cryo-EM image processing. J Struct Biol (2006) 4.66
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
Mauve assembly metrics. Bioinformatics (2011) 2.25
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc Natl Acad Sci U S A (2007) 1.99
Automatic particle selection: results of a comparative study. J Struct Biol (2004) 1.82
Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution. J Mol Biol (2003) 1.75
Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins (2004) 1.74
Model-based deconvolution of genome-wide DNA binding. Bioinformatics (2007) 1.70
Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol (2009) 1.62
Practical factors affecting the performance of a thin-film phase plate for transmission electron microscopy. Ultramicroscopy (2008) 1.60
Two-stage folding of HP-35 from ab initio simulations. J Mol Biol (2007) 1.59
Design of a microfabricated, two-electrode phase-contrast element suitable for electron microscopy. Ultramicroscopy (2006) 1.49
Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Biochemistry (2005) 1.48
Polarization effects in molecular mechanical force fields. J Phys Condens Matter (2009) 1.41
Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future. J Struct Biol (2008) 1.37
Convergence of replica exchange molecular dynamics. J Chem Phys (2005) 1.35
A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res (2006) 1.35
Stroboscopic image capture: reducing the dose per frame by a factor of 30 does not prevent beam-induced specimen movement in paraffin. Ultramicroscopy (2006) 1.35
Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations. J Am Chem Soc (2007) 1.30
Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J Phys Chem B (2007) 1.28
Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J Comput Chem (2006) 1.26
Improved sampling methods for molecular simulation. Curr Opin Struct Biol (2007) 1.26
The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations. J Mol Biol (2008) 1.22
Statistical characterization of salt bridges in proteins. Proteins (2005) 1.21
Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers (2003) 1.18
A method for the alignment of heterogeneous macromolecules from electron microscopy. J Struct Biol (2008) 1.16
Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability. J Phys Chem B (2011) 1.12
Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent. J Am Chem Soc (2005) 1.11
New-generation amber united-atom force field. J Phys Chem B (2006) 1.11
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One (2012) 1.07
Ligand entry and exit pathways in the beta2-adrenergic receptor. J Mol Biol (2009) 1.07
Experimental characterization and mitigation of specimen charging on thin films with one conducting layer. Microsc Microanal (2004) 1.06
IRF-1 and miRNA126 modulate VCAM-1 expression in response to a high-fat meal. Circ Res (2012) 1.04
Chromophore channeling in the G-protein coupled receptor rhodopsin. J Am Chem Soc (2007) 1.04
Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. Biophys J (2005) 1.04
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res (2008) 1.03
Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies. J Phys Chem B (2011) 1.02
The parallelization of SPIDER on distributed-memory computers using MPI. J Struct Biol (2006) 1.01
Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys J (2004) 1.00
Concerted perturbation observed in a hub network in Alzheimer's disease. PLoS One (2012) 1.00
Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal Peptide. Biophys J (2008) 0.99
Restoration of weak phase-contrast images recorded with a high degree of defocus: the "twin image" problem associated with CTF correction. Ultramicroscopy (2008) 0.98
Modeling chemical bonding effects for protein electron crystallography: the transferable fragmental electrostatic potential (TFESP) method. Acta Crystallogr A (2002) 0.97
High-throughput film-densitometry: an efficient approach to generate large data sets. J Struct Biol (2005) 0.96
Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water. J Comput Chem (2004) 0.96
Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. J Chem Phys (2008) 0.95
Down-regulation of energy metabolism in Alzheimer's disease is a protective response of neurons to the microenvironment. J Alzheimers Dis (2012) 0.93
Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptapeptide from human beta2-microglobulin: implication for the protofibril structure. J Mol Biol (2005) 0.93
The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J (2005) 0.92
A giant protease with a twist: the TPP II complex from Drosophila studied by electron microscopy. EMBO J (2002) 0.92
A binary segmentation approach for boxing ribosome particles in cryo EM micrographs. J Struct Biol (2004) 0.90
Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: principles of ion pumping. Biophys J (2003) 0.90
Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals. J Struct Biol (2012) 0.89
The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier. J Chem Phys (2008) 0.89
A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. Nucleic Acids Res (2012) 0.88
Disulfide linkage and structure of highly stable yeast-derived virus-like particles of murine polyomavirus. J Biol Chem (2014) 0.88
Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris. J Struct Biol (2007) 0.88
Design of a hybrid double-sideband/single-sideband (schlieren) objective aperture suitable for electron microscopy. Ultramicroscopy (2011) 0.88
Experimental evaluation of support vector machine-based and correlation-based approaches to automatic particle selection. J Struct Biol (2011) 0.88
Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions for protein structure prediction. J Mol Model (2005) 0.88
Probing the stability-limiting regions of an antibody single-chain variable fragment: a molecular dynamics simulation study. Protein Eng Des Sel (2011) 0.88
The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J Chem Phys (2004) 0.88
Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts. Biophys J (2006) 0.87
The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. J Chem Phys (2011) 0.87
Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environ Microbiol (2014) 0.87
Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes. J Phys Chem B (2012) 0.87
Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations. J Phys Chem B (2006) 0.86
Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A (2009) 0.86
Further insights into the mode of action of the lipoglycopeptide telavancin through global gene expression studies. Antimicrob Agents Chemother (2012) 0.86
Crystallization of membrane proteins from media composed of connected-bilayer gels. Biopolymers (2002) 0.85
Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A. J Phys Chem B (2005) 0.85
Membrane-protein stability in a phospholipid-based crystallization medium. J Struct Biol (2006) 0.84
iBIG: an integrative network tool for supporting human disease mechanism studies. Genomics Proteomics Bioinformatics (2013) 0.84
Crystal structures of bR(D85S) favor a model of bacteriorhodopsin as a hydroxyl-ion pump. FEBS Lett (2004) 0.84
Characteristic transformation of blood transcriptome in Alzheimer's disease. J Alzheimers Dis (2013) 0.83
Functional networking of human divergently paired genes (DPGs). PLoS One (2013) 0.83
Molecular architecture and assembly mechanism of Drosophila tripeptidyl peptidase II. Proc Natl Acad Sci U S A (2005) 0.83
Trends in template/fragment-free protein structure prediction. Theor Chem Acc (2010) 0.83
Regulatory multidimensionality of gas vesicle biogenesis in Halobacterium salinarum NRC-1. Archaea (2011) 0.83
Alzheimer's disease drug candidates stabilize A-β protein native structure by interacting with the hydrophobic core. Biophys J (2011) 0.82
[Sero-epidemiology of six viruses natural infection in Tupaia belangeri chinensis]. Dongwuxue Yanjiu (2011) 0.82
In vitro activity of telavancin and occurrence of vancomycin heteroresistance in isolates from patients enrolled in phase 3 clinical trials of hospital-acquired pneumonia. Diagn Microbiol Infect Dis (2012) 0.82
Folding network of villin headpiece subdomain. Biophys J (2010) 0.82
Electron microscopy of biological macromolecules: bridging the gap between what physics allows and what we currently can get. Microsc Microanal (2004) 0.82
The surface of evaporated carbon films is an insulating, high-bandgap material. J Struct Biol (2011) 0.82
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. BMC Bioinformatics (2012) 0.81
Ranking TEM cameras by their response to electron shot noise. Ultramicroscopy (2013) 0.81
Disseminated Penicillium marneffei infection in acquired immunodeficiency syndrome: a case report. Chin Med J (Engl) (2005) 0.81
Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. J Chem Phys (2009) 0.80
[The problem of public health service delivery insufficiency of disease prevention and control system of China]. Wei Sheng Yan Jiu (2005) 0.80
Specificity of anion binding in the substrate pocket of bacteriorhodopsin. Biochemistry (2004) 0.80