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

Wilkins, Ryan Scott; Lund, Bjarte Aarmo; Isaksen, Geir Villy; Åqvist, Johan et al.

Ingår i Journal of Chemical Theory and Computation, s. 451-458, 2024

• DOI för Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations
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Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

Oanca, Gabriel; Åqvist, Johan

Ingår i Journal of Chemical Theory and Computation, s. 2582-2591, 2024

• DOI för Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?
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Computational design of the temperature optimum of an enzyme reaction

van der Ent, Florian; Skagseth, Susann; Lund, Bjarte A.; Socan, Jaka et al.

Ingår i Science Advances, 2023

• DOI för Computational design of the temperature optimum of an enzyme reaction
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Efficient Empirical Valence Bond Simulations with GROMACS

Oanca, Gabriel; van der Ent, Florian; Åqvist, Johan

Ingår i Journal of Chemical Theory and Computation, s. 6037-6045, 2023

• DOI för Efficient Empirical Valence Bond Simulations with GROMACS
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Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

Koenekoop, Lucien; Åqvist, Johan

Ingår i Molecular biology and evolution, 2023

• DOI för Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction
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Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"

Åqvist, Johan

Ingår i ACS Catalysis, s. 10007-10009, 2023

• DOI för Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"
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Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

Åqvist, Johan; van der Ent, Florian

Ingår i Journal of Chemical Theory and Computation, s. 6345-6353, 2022

• DOI för Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding
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Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

Åqvist, Johan

Ingår i ACS Catalysis, s. 1452-1460, 2022

• DOI för Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme
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Structure and Mechanism of a Cold-Adapted Bacterial Lipase

van der Ent, Florian; Lund, Bjarte A.; Svalberg, Linn; Purg, Miha et al.

Ingår i Biochemistry, s. 933-942, 2022

• DOI för Structure and Mechanism of a Cold-Adapted Bacterial Lipase
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The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

Koenekoop, Lucien; van der Ent, Florian; Purg, Miha; Åqvist, Johan

Ingår i Biochemistry, s. 514-522, 2022

• DOI för The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

Majellaro, María; Jespers, Willem; Crespo, Abel; Núñez, María J. et al.

Ingår i Journal of Medicinal Chemistry, s. 458-480, 2021

• DOI för 3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

Jespers, Willem; Heitman, Laura H.; IJzerman, Adriaan P.; Sotelo, Eddy et al.

Ingår i PloS Computational Biology, 2021

• DOI för Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations
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Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

Reddy Vanga, Sudarsana; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

Ingår i Frontiers in Molecular Biosciences, 2021

• DOI för Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors
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Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

Guo, Xiaohu; Söderholm, Annika; Kanchugal Puttaswamy, Sandesh; Isaksen, Geir V et al.

Ingår i eLIFE, 2021

• DOI för Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family
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Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer a Sub-zero Temperatures

Machado, Teresa F. G.; Purg, Miha; Åqvist, Johan; da Silva, Rafael G.

Ingår i Biochemistry, s. 2186-2194, 2021

• DOI för Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer a Sub-zero Temperatures

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

Socan, Jaka; Purg, Miha; Åqvist, Johan

Ingår i Nature Communications, 2020

• DOI för Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme
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Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry

Machado, Teresa F. G.; Purg, Miha; McMahon, Stephen A.; Read, Benjamin J. et al.

Ingår i ACS Catalysis, s. 15019-15032, 2020

• DOI för Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry
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Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists

Vasile, Silvana; Hallberg, Anders; Sallander, Jessica; Hallberg, Mathias et al.

Ingår i Biomolecules, 2020

• DOI för Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists
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Hidden conformational states and strange temperature optima in enzyme catalysis

Åqvist, Johan; Sočan, Jaka; Purg, Miha

Ingår i Biochemistry, s. 3844-3855, 2020

• DOI för Hidden conformational states and strange temperature optima in enzyme catalysis
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Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

Barlow, Nicholas; Reddy Vanga, Sudarsana; Sävmarker, Jonas; Sandström, Anja et al.

Ingår i RSC Medicinal chemistry, s. 234-244, 2020

• DOI för Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors

Engen, Karin; Reddy Vanga, Sudarsana; Lundbäck, Thomas; Agalo, Faith et al.

Ingår i ChemistryOpen, s. 325-337, 2020

• DOI för Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors
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X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A(2A) Adenosine Receptor Antagonists

Jespers, Willem; Verdon, Gregory; Azuaje, Jhonny; Majellaro, Maria et al.

Ingår i Angewandte Chemie International Edition, s. 16536-16543, 2020

• DOI för X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A(2A) Adenosine Receptor Antagonists

A Series of Analogues to the AT₂R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode

Isaksson, Rebecka; Lindman, Jens; Wannberg, Johan; Sallander, Jessica et al.

Ingår i ChemistryOpen, s. 114-125, 2019

• DOI för A Series of Analogues to the AT₂R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode
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Free energy calculations of RNA interactions

Lind, Christoffer; Esguerra, Mauricio; Jespers, Willem; Satpati, Priyadarshi et al.

Ingår i Methods, s. 85-95, 2019

• DOI för Free energy calculations of RNA interactions

Inhibition of translation termination by small molecules targeting ribosomal release factors

Ge, Xueliang; Oliveira, Ana; Hjort, Karin; Bergfors, Terese et al.

Ingår i Scientific Reports, 2019

• DOI för Inhibition of translation termination by small molecules targeting ribosomal release factors
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Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair

Kumar, Amit; Åqvist, Johan; Satpati, Priyadarshi

Ingår i ACS Omega, s. 15539-15548, 2019

• DOI för Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair
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QligFEP: an automated workflow for small molecule free energy calculations in Q

Jespers, Willem; Esguerra, Mauricio; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

Ingår i Journal of Cheminformatics, 2019

• DOI för QligFEP: an automated workflow for small molecule free energy calculations in Q
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QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

Jespers, Willem; Isaksen, Geir V; Andberg, Tor A H; Vasile, Silvana et al.

Ingår i Journal of Chemical Theory and Computation, s. 5461-5473, 2019

• DOI för QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

Towards Rational Computational Engineering of Psychrophilic Enzymes

Socan, Jaka; Isaksen, Geir Villy; Brandsdal, Björn Olav; Åqvist, Johan

Ingår i Scientific Reports, 2019

• DOI för Towards Rational Computational Engineering of Psychrophilic Enzymes
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Catalytic Adaptation of Psychrophilic Elastase

Socan, Jaka; Kazemi, Masoud; Isaksen, Geir Villy; Brandsdal, Bjorn Olav et al.

Ingår i Biochemistry, s. 2984-2993, 2018

• DOI för Catalytic Adaptation of Psychrophilic Elastase

Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Ge, Xueliang; Mandava, Chandra Sekhar; Lind, Christoffer; Åqvist, Johan et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 4649-4654, 2018

• DOI för Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y-₂ Receptor

Xu, Bo; Vasile, Silvana; Østergaard, Søren; Paulsson, Johan F. et al.

Ingår i Molecular Pharmacology, s. 323-334, 2018

• DOI för Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y-₂ Receptor
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Mechanistic alternatives for peptide bond formation on the ribosome

Kazemi, Masoud; Socan, Jaka; Himo, Fahmi; Åqvist, Johan

Ingår i Nucleic Acids Research, s. 5345-5354, 2018

• DOI för Mechanistic alternatives for peptide bond formation on the ribosome
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Molecular mechanisms in the selectivity of nonsteroidal anti-inflammatory drugs

Shamsudin, Yasmin; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

Ingår i Biochemistry, s. 1236-1248, 2018

• DOI för Molecular mechanisms in the selectivity of nonsteroidal anti-inflammatory drugs

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Bauer, Paul; Barrozo, Alexandre; Purg, Miha; Amrein, Beat Anton et al.

Ingår i SoftwareX, s. 388-395, 2018

• DOI för Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations
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Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides

Reddy Vanga, Sudarsana; Sävmarker, Jonas; Ng, Leelee; Larhed, Mats et al.

Ingår i ACS Omega, s. 4509-4521, 2018

• DOI för Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides
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A close-up view of codon selection in eukaryotic initiation

Lind, Christoffer; Esguerra, Mauricio; Åqvist, Johan

Ingår i RNA Biology, s. 815-819, 2017

• DOI för A close-up view of codon selection in eukaryotic initiation

Cold Adaptation of Triosephosphate Isomerase

Åqvist, Johan

Ingår i Biochemistry, s. 4169-4176, 2017

• DOI för Cold Adaptation of Triosephosphate Isomerase

Effect of Nitrogen Atom Substitution in A(3) Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

Azuaje, Jhonny; Jespers, Willem; Yaziji, Vicente; Mallo, Ana et al.

Ingår i Journal of Medicinal Chemistry, s. 7502-7511, 2017

• DOI för Effect of Nitrogen Atom Substitution in A(3) Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

Origin of the omnipotence of eukaryotic release factor 1

Lind, Christoffer; Oliveira, Ana; Åqvist, Johan

Ingår i Nature Communications, 2017

• DOI för Origin of the omnipotence of eukaryotic release factor 1
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Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations

Shamsudin, Yasmin; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

Ingår i Biochemistry, s. 1911-1920, 2017

• DOI för Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations

Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors

Jespers, Willem; Oliveira, Ana; Prieto-Diaz, Ruben; Majellaro, Maria et al.

Ingår i Molecules, 2017

• DOI för Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors
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The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site

Nohr, Anne Cathrine; Jespers, Willem; Shehata, Mohamed A.; Floryan, Leonard et al.

Ingår i Scientific Reports, 2017

• DOI för The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site
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Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Björn Olav

Ingår i Biochemistry, s. 306-312, 2017

• DOI för Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures

Diwakarla, Shanti; Nylander, Erik; Grönbladh, Alfhild; Vanga, Sudarsana Reddy et al.

Ingår i ACS Chemical Neuroscience, s. 1383-1392, 2016

• DOI för Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures

Binding to and Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Macrocyclic Disulfides Enhances Spine Density

Diwakarla, Shanti; Nylander, Erik; Grönbladh, Alfhild; Reddy Vanga, Sudarsana et al.

Ingår i Molecular Pharmacology, s. 413-424, 2016

• DOI för Binding to and Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Macrocyclic Disulfides Enhances Spine Density

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase

Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Björn Olav

Ingår i Biochemistry, s. 2153-2162, 2016

• DOI för Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase

Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis

Aqvist, Johan; Kamerlin, Shina C. L.

Ingår i ACS Catalysis, s. 1737-1743, 2016

• DOI för Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis
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Enzyme catalysis by entropy without Circe effect

Kazemi, Masoud; Himo, Fahmi; Åqvist, Johan

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 2406-2411, 2016

• DOI för Enzyme catalysis by entropy without Circe effect

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Björn Olav

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 7822-7827, 2016

• DOI för Enzyme surface rigidity tunes the temperature dependence of catalytic rates