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Towards Rational Computational Engineering of Psychrophilic Enzymes

Scientific reports, 2019-12, Vol.9 (1), p.19147-19147, Article 19147

2019

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Enzyme catalysis by entropy without Circe effect

Proceedings of the National Academy of Sciences - PNAS, 2016-03, Vol.113 (9), p.2406-2411

2016

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Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations

Journal of chemical theory and computation, 2024-01, Vol.20 (1), p.451-458

2024

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Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

Nature communications, 2013-12, Vol.4 (1), p.2940-2940, Article 2940

2013

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Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels

Biophysical journal, 2014-05, Vol.106 (9), p.1859-1863

2014

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A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis

Molecular cell, 2007-09, Vol.27 (5), p.758-766

2007

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transition state for peptide bond formation reveals the ribosome as a water trap

Proceedings of the National Academy of Sciences - PNAS, 2010-02, Vol.107 (5), p.1888-1893

2010

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Structure and Mechanism of a Cold-Adapted Bacterial Lipase

Biochemistry (Easton), 2022-05, Vol.61 (10), p.933-942

2022

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Reply to Comment on: “Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme”

ACS catalysis, 2023-08, Vol.13 (15), p.10007-10009

Åqvist, Johan

2023

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Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

ACS catalysis, 2022-01, Vol.12 (2), p.1452-1460

Åqvist, Johan

2022

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Mechanism of Peptide Bond Synthesis on the Ribosome

Proceedings of the National Academy of Sciences - PNAS, 2005-08, Vol.102 (35), p.12395-12400

2005

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Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations

The journal of physical chemistry. B, 2009-07, Vol.113 (30), p.10255-10260

2009

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Catalysis and Linear Free Energy Relationships in Aspartic Proteases

Biochemistry (Easton), 2006-06, Vol.45 (25), p.7709-7723

2006

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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

Journal of medicinal chemistry, 2008-05, Vol.51 (9), p.2648-2656

2008

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Cold Adaptation of Triosephosphate Isomerase

Biochemistry (Easton), 2017-08, Vol.56 (32), p.4169-4176

Åqvist, Johan

2017

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Mechanism of the Translation Termination Reaction on the Ribosome

Biochemistry (Easton), 2009-12, Vol.48 (47), p.11296-11303

2009

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Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009152-e1009152

2021

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pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

Proceedings of the National Academy of Sciences - PNAS, 2011-01, Vol.108 (1), p.79-84

2011

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Exploring blocker binding to a homology model of the open hERG K + channel using docking and molecular dynamics methods

FEBS letters, 2005-05, Vol.579 (13), p.2939-2944

2005

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Comment on "The mechanism for activation of GTP hydrolysis on the ribosome"

Science (American Association for the Advancement of Science), 2011-07, Vol.333 (6038), p.37; author reply 37-37

2011

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A close-up view of codon selection in eukaryotic initiation

RNA biology, 2017-07, Vol.14 (7), p.815-819

2017

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Ion permeation mechanism of the potassium channel

Nature (London), 2000-04, Vol.404 (6780), p.881-884

2000

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Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl Transfer

Biochemistry (Easton), 2006-06, Vol.45 (23), p.7049-7056

2006

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Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

Nature communications, 2020-05, Vol.11 (1), p.2644-2644, Article 2644

2020

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Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding

The journal of physical chemistry. B, 2005-04, Vol.109 (13), p.6448-6456

2005

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Towards Rational Computational Engineering of Psychrophilic Enzymes

Enzyme catalysis by entropy without Circe effect

Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels

A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis

transition state for peptide bond formation reveals the ribosome as a water trap

Structure and Mechanism of a Cold-Adapted Bacterial Lipase

Reply to Comment on: “Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme”

Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

Mechanism of Peptide Bond Synthesis on the Ribosome

Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations

Catalysis and Linear Free Energy Relationships in Aspartic Proteases

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

Cold Adaptation of Triosephosphate Isomerase

Mechanism of the Translation Termination Reaction on the Ribosome

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations

pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

Exploring blocker binding to a homology model of the open hERG K + channel using docking and molecular dynamics methods

Comment on "The mechanism for activation of GTP hydrolysis on the ribosome"

A close-up view of codon selection in eukaryotic initiation

Ion permeation mechanism of the potassium channel

Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl Transfer

Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding

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