Published in J Am Chem Soc on July 11, 2014
Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science (2014) 2.67
Site-specific infrared probes of proteins. Annu Rev Phys Chem (2015) 0.96
Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res (2015) 0.94
Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proc Natl Acad Sci U S A (2014) 0.90
Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation. Biophys J (2015) 0.81
Transition States and transition state analogue interactions with enzymes. Acc Chem Res (2015) 0.78
Oriented electric fields as future smart reagents in chemistry. Nat Chem (2016) 0.78
Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase. Biochemistry (2016) 0.77
Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes. PLoS One (2015) 0.77
Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions. PLoS Genet (2016) 0.76
Protein rethreading: A novel approach to protein design. Sci Rep (2016) 0.75
Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B (2016) 0.75
Simple Method to Introduce an Ester Infrared Probe into Proteins. Protein Sci (2016) 0.75
Quantified electrostatic preorganization in enzymes using the geometry of the electron charge density. Chem Sci (2017) 0.75
Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study. Struct Dyn (2017) 0.75
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput (2008) 34.90
Canonical dynamics: Equilibrium phase-space distributions. Phys Rev A Gen Phys (1985) 26.82
Development and testing of a general amber force field. J Comput Chem (2004) 23.29
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
The dynamic energy landscape of dihydrofolate reductase catalysis. Science (2006) 7.55
Intrinsic motions along an enzymatic reaction trajectory. Nature (2007) 5.53
Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry (1997) 5.46
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. J Chem Theory Comput (2008) 4.56
Relating protein motion to catalysis. Annu Rev Biochem (2006) 4.50
Electrostatic basis for enzyme catalysis. Chem Rev (2006) 4.35
Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry (1987) 4.29
Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci U S A (2002) 3.98
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science (2011) 3.19
Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry (2001) 2.77
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins (2010) 2.69
Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry (1997) 2.61
Free-energy landscape of enzyme catalysis. Biochemistry (2008) 2.52
Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32
Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc (2003) 2.30
Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc Natl Acad Sci U S A (2005) 2.05
Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry (1991) 1.86
Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry (2005) 1.68
Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. J Am Chem Soc (2006) 1.68
Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry (2011) 1.60
Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. J Am Chem Soc (2010) 1.46
Interaction of dihydrofolate reductase with methotrexate: ensemble and single-molecule kinetics. Proc Natl Acad Sci U S A (2002) 1.43
Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. J Phys Chem Lett (2011) 1.36
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proc Natl Acad Sci U S A (2012) 1.29
Nitrile groups as vibrational probes: calculations of the CN infrared absorption line shape of acetonitrile in water and tetrahydrofuran. J Phys Chem B (2008) 1.21
Nitrile and thiocyanate IR probes: molecular dynamics simulation studies. J Chem Phys (2008) 1.19
Calculations of the electric fields in liquid solutions. J Phys Chem B (2013) 1.13
Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy. J Phys Chem B (2012) 1.10
Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc Natl Acad Sci U S A (2013) 1.09
Cyanylated Cysteine: A Covalently Attached Vibrational Probe of Protein-Lipid Contacts. J Phys Chem Lett (2010) 1.08
A method of preparation and purification of (4R)-deuterated-reduced nicotinamide adenine dinucleotide phosphate. Anal Biochem (1994) 1.03
Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. Proc Natl Acad Sci U S A (2011) 1.02
Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics. Biochemistry (2009) 1.02
A solvatochromic model calibrates nitriles' vibrational frequencies to electrostatic fields. J Am Chem Soc (2012) 1.01
Resolving the complex role of enzyme conformational dynamics in catalytic function. Proc Natl Acad Sci U S A (2012) 0.99
Ultraviolet spectroscopic evidence for decreased motion of the active site tyrosine residue of delta 5-3-ketosteroid isomerase by steroid binding. Biochemistry (1995) 0.99
Infrared probes for studying the structure and dynamics of biomolecules. Chem Rev (2013) 0.99
Redesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering. Protein Eng (1999) 0.90
Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water. J Phys Chem Lett (2010) 0.90
Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates. Nat Chem (2013) 0.90
Crucial role of protein flexibility in formation of a stable reaction transition state in an α-amylase catalysis. J Am Chem Soc (2012) 0.87
Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. J Am Chem Soc (2012) 0.86
Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase. Proteins (2012) 0.84
Solvatochromic effects in the electronic absorption and nuclear magnetic resonance spectra of hypericin in organic solvents and in lipid bilayers. Photochem Photobiol (2001) 0.81
A perspective on enzyme catalysis. Science (2003) 5.15
Relating protein motion to catalysis. Annu Rev Biochem (2006) 4.50
Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci U S A (2002) 3.98
DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry (2004) 3.71
Allosteric regulation and catalysis emerge via a common route. Nat Chem Biol (2008) 3.62
Ketamine-associated ulcerative cystitis: a new clinical entity. Urology (2007) 3.56
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science (2011) 3.19
Reversible compartmentalization of de novo purine biosynthetic complexes in living cells. Science (2008) 2.98
On-chip manipulation of single microparticles, cells, and organisms using surface acoustic waves. Proc Natl Acad Sci U S A (2012) 2.91
Surface sites for engineering allosteric control in proteins. Science (2008) 2.82
An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science (2007) 2.82
Design and evolution of new catalytic activity with an existing protein scaffold. Science (2006) 2.71
Free-energy landscape of enzyme catalysis. Biochemistry (2008) 2.52
Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc Natl Acad Sci U S A (2006) 2.37
Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis. J Am Chem Soc (2004) 2.21
Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates. Biochemistry (2002) 2.09
Colloidal-quantum-dot photovoltaics using atomic-ligand passivation. Nat Mater (2011) 2.08
Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc Natl Acad Sci U S A (2005) 2.05
Proton-coupled electron transfer in soybean lipoxygenase. J Am Chem Soc (2004) 2.01
Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects. J Am Chem Soc (2007) 1.80
Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proc Natl Acad Sci U S A (2007) 1.76
The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci U S A (2004) 1.76
Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry (2004) 1.72
Regulation of polymerase exchange between Poleta and Poldelta by monoubiquitination of PCNA and the movement of DNA polymerase holoenzyme. Proc Natl Acad Sci U S A (2008) 1.71
Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry (2005) 1.68
Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome. Nat Chem Biol (2009) 1.68
The 10/66 Dementia Research Group's fully operationalised DSM-IV dementia computerized diagnostic algorithm, compared with the 10/66 dementia algorithm and a clinician diagnosis: a population validation study. BMC Public Health (2008) 1.60
Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry (2011) 1.60
Effects of a distal mutation on active site chemistry. Biochemistry (2006) 1.59
Effect of mutation on enzyme motion in dihydrofolate reductase. J Am Chem Soc (2003) 1.57
Coupled motions in enzyme catalysis. Curr Opin Chem Biol (2010) 1.49
Watching Hydrogen Bonds Break: A Transient Absorption Study of Water. J Phys Chem A (2004) 1.44
Interaction of dihydrofolate reductase with methotrexate: ensemble and single-molecule kinetics. Proc Natl Acad Sci U S A (2002) 1.43
The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase. Philos Trans R Soc Lond B Biol Sci (2006) 1.39
Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J Am Chem Soc (2012) 1.37
Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2. J Biol Chem (2010) 1.36
The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication. Mol Cell (2006) 1.35
Boron-containing inhibitors of synthetases. Chem Soc Rev (2011) 1.32
Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli. Nat Protoc (2007) 1.31
Calculation of vibronic couplings for phenoxyl/phenol and benzyl/toluene self-exchange reactions: implications for proton-coupled electron transfer mechanisms. J Am Chem Soc (2006) 1.31
The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. Proc Natl Acad Sci U S A (2006) 1.29
Biochemistry. Enzyme motions inside and out. Science (2006) 1.27
Analysis of kinetic isotope effects for proton-coupled electron transfer reactions. J Phys Chem A (2009) 1.26
Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions. J Chem Phys (2005) 1.24
Inhibition of HIV budding by a genetically selected cyclic peptide targeting the Gag-TSG101 interaction. ACS Chem Biol (2008) 1.23
Microtubule-assisted mechanism for functional metabolic macromolecular complex formation. Proc Natl Acad Sci U S A (2010) 1.23
Evolution of cyclic peptide protease inhibitors. Proc Natl Acad Sci U S A (2011) 1.20
Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase. J Phys Chem B (2010) 1.16
Identification of a novel boron-containing antibacterial agent (AN0128) with anti-inflammatory activity, for the potential treatment of cutaneous diseases. Bioorg Med Chem Lett (2006) 1.16
GPCRs regulate the assembly of a multienzyme complex for purine biosynthesis. Nat Chem Biol (2011) 1.15
Formation and dissociation of intra-intermolecular hydrogen-bonded solute-solvent complexes: chemical exchange two-dimensional infrared vibrational echo spectroscopy. J Am Chem Soc (2006) 1.14
Theoretical analysis of mechanistic pathways for hydrogen evolution catalyzed by cobaloximes. Inorg Chem (2011) 1.14
Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. Proc Natl Acad Sci U S A (2004) 1.14
Tunable, pulsatile chemical gradient generation via acoustically driven oscillating bubbles. Lab Chip (2013) 1.13
Hybrid quantum/classical path integral approach for simulation of hydrogen transfer reactions in enzymes. J Chem Phys (2006) 1.12
Replication clamps and clamp loaders. Cold Spring Harb Perspect Biol (2013) 1.10
Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc Natl Acad Sci U S A (2013) 1.09
The application of a minicircle substrate in the study of the coordinated T4 DNA replication. J Biol Chem (2003) 1.08
Preorganization and protein dynamics in enzyme catalysis. Chem Rec (2002) 1.08
Collaborative coupling between polymerase and helicase for leading-strand synthesis. Nucleic Acids Res (2012) 1.08
Evolution of highly active enzymes by homology-independent recombination. Proc Natl Acad Sci U S A (2005) 1.08
An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex. Biochemistry (2006) 1.07
Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. J Am Chem Soc (2014) 1.07
A systematic method for identifying small-molecule modulators of protein-protein interactions. Proc Natl Acad Sci U S A (2004) 1.07
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry (2011) 1.07
Mechanism of strand displacement synthesis by DNA replicative polymerases. Nucleic Acids Res (2012) 1.07
FamClash: a method for ranking the activity of engineered enzymes. Proc Natl Acad Sci U S A (2004) 1.06
Assembly of the bacteriophage T4 helicase: architecture and stoichiometry of the gp41-gp59 complex. J Biol Chem (2002) 1.06
Hydrogen tunneling in enzymes and biomimetic models. Chem Rev (2013) 1.06
Regulation of Rad6/Rad18 Activity During DNA Damage Tolerance. Annu Rev Biophys (2015) 1.06
Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. Biochemistry (2005) 1.05
Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation. Biochemistry (2006) 1.05
Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid. Biochemistry (2003) 1.05
Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. J Mol Biol (2003) 1.04
Artificial photosynthesis and solar fuels. Acc Chem Res (2009) 1.04
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation. J Phys Chem B (2011) 1.04
Single-molecule mechanical identification and sequencing. Nat Methods (2012) 1.04
RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue. Nat Commun (2013) 1.03
Proton-coupled electron transfer in a model for tyrosine oxidation in photosystem II. J Am Chem Soc (2003) 1.03
IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J (2006) 1.02
Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics. Biochemistry (2009) 1.02
RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins. J Biol Chem (2008) 1.02
On the solution structure of the T4 sliding clamp (gp45). Biochemistry (2004) 1.02
Role of a solvent-exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase. Protein Sci (2003) 1.01
Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridyl complexes. J Am Chem Soc (2002) 1.01
Assembly of the bacteriophage T4 primosome: single-molecule and ensemble studies. Proc Natl Acad Sci U S A (2005) 1.01
Direct observation of stalled fork restart via fork regression in the T4 replication system. Science (2012) 1.01
Discovery of antibacterial cyclic peptides that inhibit the ClpXP protease. Protein Sci (2007) 1.00
Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations. J Am Chem Soc (2010) 1.00
Dissociative properties of the proteins within the bacteriophage T4 replisome. J Biol Chem (2003) 0.99
The oligomeric T4 primase is the functional form during replication. J Biol Chem (2005) 0.99
A clamp-like biohybrid catalyst for DNA oxidation. Nat Chem (2013) 0.98
The T4 phage UvsW protein contains both DNA unwinding and strand annealing activities. J Biol Chem (2006) 0.98