Search Results - "Aqvist, Johan"

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

“…Despite advances in computational design of protein structures, it has proven very difficult to design efficient enzyme catalysts by such approaches. One of…”
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Reply to Comment on: “Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme” by Åqvist, Johan

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Cold Adaptation of Triosephosphate Isomerase by Åqvist, Johan

“…The main problem for enzymes from psychrophilic species, which need to work near the freezing point of liquid water, is the exponential decay of reaction rates…”
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Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction by Koenekoop, Lucien, Åqvist, Johan

“…Abstract Cold-adapted enzymes from psychrophilic and psychrotolerant species are characterized by a higher catalytic activity at low temperature than their…”
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Computational Analysis of Heat Capacity Effects in Protein–Ligand Binding by Koenekoop, Lucien, Åqvist, Johan

“…Heat capacity effects in protein–ligand binding as measured by calorimetric experiments have recently attracted considerable attention, particularly in the…”
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Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots? by Oanca, Gabriel, Åqvist, Johan

“…Computer simulations of the temperature dependence of enzyme reactions using the empirical valence bond (EVB) method have proven to give very accurate results…”
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Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme by Sočan, Jaka, Purg, Miha, Åqvist, Johan

“…Cold-adapted enzymes from psychrophilic species show the general characteristics of being more heat labile, and having a different balance between enthalpic…”
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Efficient Empirical Valence Bond Simulations with GROMACS by Oanca, Gabriel, van der Ent, Florian, Åqvist, Johan

“…We describe a protocol to perform empirical valence bond (EVB) simulations using GROMACS software. EVB is a fast and reliable method that allows one to…”
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Principles of start codon recognition in eukaryotic translation initiation by Lind, Christoffer, Åqvist, Johan

“…Selection of the correct start codon during initiation of translation on the ribosome is a key event in protein synthesis. In eukaryotic initiation, several…”
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Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding by Åqvist, Johan, van der Ent, Florian

“…It has been suggested that heat capacity changes in enzyme catalysis may be the underlying reason for temperature optima that are not related to unfolding of…”
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Chemical reaction mechanisms in solution from brute force computational Arrhenius plots by Kazemi, Masoud, Åqvist, Johan

“…Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic…”
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Entropy and Enzyme Catalysis by Åqvist, Johan, Kazemi, Masoud, Isaksen, Geir Villy, Brandsdal, Bjørn Olav

“…The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed…”
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Enzyme surface rigidity tunes the temperature dependence of catalytic rates by Isaksen, Geir Villy, Åqvist, Johan, Brandsdal, Bjørn Olav

“…The structural origin of enzyme adaptation to low temperature, allowing efficient catalysis of chemical reactions even near the freezing point of water,…”
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Free Energy Calculations for Protein-Ligand Binding Prediction by Jespers, Willem, Åqvist, Johan, Gutiérrez-de-Terán, Hugo

“…Computational prediction of protein-ligand binding involves initial determination of the binding mode and subsequent evaluation of the strength of the…”
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Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis by Åqvist, Johan, Sočan, Jaka, Purg, Miha

“…The existence of temperature optima in enzyme catalysis that occur before protein melting sets in can be described by different types of kinetic models. Such…”
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The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization by Koenekoop, Lucien, van der Ent, Florian, Purg, Miha, Åqvist, Johan

“…The structural principles of enzyme cold adaptation are of fundamental interest both for understanding protein evolution and for biotechnological applications…”
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Computation of enzyme cold adaptation by Åqvist, Johan, Isaksen, Geir Villy, Brandsdal, Bjørn Olav

“…Earth has several environments that are potentially hostile to life. The survival of organisms has required the expression of proteins that are adapted to…”
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Origin of the omnipotence of eukaryotic release factor 1 by Lind, Christoffer, Oliveira, Ana, Åqvist, Johan

“…Termination of protein synthesis on the ribosome requires that mRNA stop codons are recognized with high fidelity. This is achieved by specific release factor…”
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Force Field Independent Metal Parameters Using a Nonbonded Dummy Model by Duarte, Fernanda, Bauer, Paul, Barrozo, Alexandre, Amrein, Beat Anton, Purg, Miha, Åqvist, Johan, Kamerlin, Shina Caroline Lynn

“…The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both…”
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Structure-Based Energetics of mRNA Decoding on the Ribosome by Satpati, Priyadarshi, Sund, Johan, Åqvist, Johan

“…The origin of high fidelity in bacterial protein synthesis on the ribosome remains a fundamental unsolved problem despite available three-dimensional…”
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