Published in Proc Natl Acad Sci U S A on January 11, 2010
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol (2014) 1.31
A two-step chemical mechanism for ribosome-catalysed peptide bond formation. Nature (2011) 0.99
Different substrate-dependent transition states in the active site of the ribosome. Nature (2011) 0.96
Computational studies of molecular machines: the ribosome. Curr Opin Struct Biol (2012) 0.96
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits. EMBO J (2010) 0.91
Entropy-driven mechanism of an E3 ligase. Biochemistry (2011) 0.88
Heavy water reduces GFP expression in prokaryotic cell-free assays at the translation level while stimulating its transcription. Biomed Res Int (2013) 0.77
A Role for the 2' OH of peptidyl-tRNA substrate in peptide release on the ribosome revealed through RF-mediated rescue. Chem Biol (2012) 0.77
Peptide Bond Formation Mechanism Catalyzed by Ribosome. J Am Chem Soc (2015) 0.76
Natural isotopic signatures of variations in body nitrogen fluxes: a compartmental model analysis. PLoS Comput Biol (2014) 0.75
A close-up view of codon selection in eukaryotic initiation. RNA Biol (2017) 0.75
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature (2005) 3.18
The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell (2004) 3.18
Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat Struct Mol Biol (2004) 2.53
Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell (2005) 2.49
The ribosome as an entropy trap. Proc Natl Acad Sci U S A (2004) 2.40
Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci U S A (2008) 2.11
Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc Natl Acad Sci U S A (2001) 2.06
Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol Cell (2002) 1.91
The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis. Chem Biol (2008) 1.79
Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A (2005) 1.76
Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature (2001) 1.71
The kinetics of ribosomal peptidyl transfer revisited. Mol Cell (2008) 1.70
Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat Struct Mol Biol (2006) 1.58
The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA (2006) 1.53
Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem (2008) 1.42
Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2'-OH to activity. Nucleic Acids Res (2003) 1.31
Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451. Nucleic Acids Res (2005) 1.29
What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry (2005) 1.23
Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J Biol Chem (2005) 1.23
Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA. J Am Chem Soc (2006) 1.20
The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA (2003) 1.13
Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry (2006) 1.11
The rate enhancement produced by the ribosome: an improved model. Biochemistry (2007) 1.11
Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry (2005) 1.09
Molecular aspects of the ribosomal peptidyl transferase. Biochem Soc Trans (2002) 1.06
Role of ribosomal protein L27 in peptidyl transfer. Biochemistry (2008) 1.03
The transition state for formation of the peptide bond in the ribosome. Proc Natl Acad Sci U S A (2006) 0.97
An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction. Chem Biol (2008) 0.97
Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed. J Chem Theory Comput (2009) 0.94
The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism. J Am Chem Soc (2006) 0.86
Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A (2005) 1.76
A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol Cell (2007) 1.61
Free energy calculations and ligand binding. Adv Protein Chem (2003) 1.39
Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B (2005) 1.36
The catalytic power of ketosteroid isomerase investigated by computer simulation. Biochemistry (2002) 1.31
Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase. Biochemistry (2007) 1.27
Resolving the energy paradox of chaperone/usher-mediated fibre assembly. Biochem J (2005) 1.25
Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry (2006) 1.15
Principles of stop-codon reading on the ribosome. Nature (2010) 1.13
Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry (2006) 1.11
Probing the effect of point mutations at protein-protein interfaces with free energy calculations. Biophys J (2005) 1.09
Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem (2007) 1.07
Catalysis and linear free energy relationships in aspartic proteases. Biochemistry (2006) 1.07
Role of ribosomal protein L27 in peptidyl transfer. Biochemistry (2008) 1.03
Binding affinity prediction with different force fields: examination of the linear interaction energy method. J Comput Chem (2004) 1.02
Cold adaptation of enzyme reaction rates. Biochemistry (2008) 1.02
Calculations of solute and solvent entropies from molecular dynamics simulations. Phys Chem Chem Phys (2006) 0.99
Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J Med Chem (2008) 0.96
Energetics of activation of GTP hydrolysis on the ribosome. Nat Commun (2013) 0.96
Energetics of codon-anticodon recognition on the small ribosomal subunit. Biochemistry (2007) 0.95
Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction. J Am Chem Soc (2009) 0.95
Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model. Biophys J (2007) 0.95
Toward a consensus model of the HERG potassium channel. ChemMedChem (2010) 0.95
Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry (2004) 0.93
Mechanism of the translation termination reaction on the ribosome. Biochemistry (2009) 0.93
Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods. FEBS Lett (2005) 0.91
Absolute hydration entropies of alkali metal ions from molecular dynamics simulations. J Phys Chem B (2009) 0.90
Structure-based energetics of mRNA decoding on the ribosome. Biochemistry (2014) 0.88
Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions. FEBS Lett (2003) 0.87
Continuum solvation models in the linear interaction energy method. J Phys Chem B (2006) 0.87
Force field independent metal parameters using a nonbonded dummy model. J Phys Chem B (2014) 0.87
Linear interaction energy: method and applications in drug design. Methods Mol Biol (2012) 0.87
Predicting binding modes from free energy calculations. J Med Chem (2008) 0.86
Mutagenesis and homology modeling of the Tn21 integron integrase IntI1. Biochemistry (2009) 0.83
Computer simulations of structure-activity relationships for HERG channel blockers. Biochemistry (2011) 0.82
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity. J Med Chem (2004) 0.82
Active site of epoxide hydrolases revisited: a noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate. Biochemistry (2007) 0.82
Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine. Biochim Biophys Acta (2003) 0.81
Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome. Chemistry (2014) 0.81
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin. Proteins (2006) 0.80
C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions. Bioorg Med Chem (2003) 0.80
Phe369(7.38) at human 5-HT(7) receptors confers interspecies selectivity to antagonists and partial agonists. Br J Pharmacol (2009) 0.79
Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor. FEBS Lett (2006) 0.79
Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum. Biochemistry (2006) 0.78
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations. J Med Chem (2005) 0.77
alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases. Bioorg Med Chem (2009) 0.77
Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors? Biochemistry (2009) 0.77
Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions. J Am Chem Soc (2002) 0.77
Mutagenesis and computational modeling of human G-protein-coupled receptor Y2 for neuropeptide Y and peptide YY. Biochemistry (2013) 0.76
Comparative analysis of putative agonist-binding modes in the human A1 adenosine receptor. Chembiochem (2004) 0.76
Molecular dynamics study of heparin based coatings. Biomaterials (2008) 0.75
Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. Eur J Pharm Sci (2004) 0.75