Research projects
Biological Catalysis
Wallin G and Åqvist J; The transition state for peptide bond formation reveals the ribosome as a water trap Proc Natl Acad Sci U S A 107, 1888, (2010) [abstract]
Andér, M, Åqvist, J Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors? Biochemistry 48, 3483, (2009) [abstract]
Johansson DGA, Wallin G, Sandberg A, Macao B, Åqvist J and Härd T; 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. 131, 9475, (2009) [abstract]
Almlöf, M., Andér, M., Åqvist, J. Energetics of Codon-Anticodon Recognition on the Small Ribosomal Subunit. Biochemistry 46, 200, (2007)
Thomaeus, A., Carlsson, J., Åqvist, J., Widersten, M. Active Site of Epoxide Hydrolases Revisited: a Non-Canonical Residue in Potato StEH1 Promotes Both Formation and Breakdown of the Alkylenzyme Intermediate. Biochemistry 46, 2466, (2007)
Henriksson, L.M., Unge, T., Carlsson, J., Åqvist, J., Mowbray, S.L., Jones, T.A. Structures of Mycobacterium tuberculosis 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Provide New Insights into Catalysis. J. Biol. Chem. 282, 19905, (2007) [abstract]
Trobro, S., Åqvist, J. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis Mol. Cell 27, 758, (2007)
Trobro, S., Åqvist, J. Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl transfer. Biochemistry 45, 7049, (2006)
Bjelic, S., Åqvist, J. Catalysis and Linear Free Energy Relationships in Aspartic Proteases. Biochemistry 45, 7709, (2006)
Trobro, S., Åqvist, J. Mechanism of Peptide Bond Synthesis on the Ribosome. Proc. Natl. Acad. Sci. U.S.A. 102, 12395, (2005)
Bjelic, S., Åqvist, J. Computational Prediction of Structure, Substrate Binding Mode, Mechanism and Rate for a Malaria Protease with a Novel Type of Active Site. Biochemistry 43, 14521, (2004)
Ion Channels
Andér, M., Luzhkov, V.B., Åqvist, J. Ligand binding to the voltage gated Kv1.5 potassium channel in the open state - docking and computer simulations of a homology model. Biophys. J. 94, 820, (2008)
Luzhkov, V., Almlöf, M., Nervall, M., Åqvist, J. Computational Study of Binding Affinity and Selectivity of the Bacterial Ammonium Transporter AmtB. Biochemistry 45, 10807, (2006)
Österberg, F., Åqvist, J. Exploring Blocker Binding to a Homology Model of the Open hERG K+ Channel using Docking and Molecular Dynamics Methods. FEBS Lett. 579, 2939, (2005)
Luzhkov, V.B., Åqvist, J. Ions and Blockers in Potassium Channels: Insights from Free Energy Simulations. Biochim. Biophys. Acta 1747, 109, (2005)
Luzhkov, V.B., Nilsson, J., Århem, P., Åqvist, J. Computational Modeling of the Open-State Kv1.5 Ion Channel Block by Bupivacaine. Biochim. Biophys. Acta 1652, 35, (2003)
Luzhkov, V.B., Österberg, F., Åqvist J. Structure-Activity Relationship for Extracellular Block of K+ Channels by Tetraalkylammonium Ions. FEBS Lett. 554, 159, (2003)
Methods Development
Almlöf, M., Åqvist, J., Smalås, A.O., Brandsdal, B.O. Probing the Effect of Point Mutations at Protein-Protein Interfaces with Free Energy Calculations. Biophys. J. 90, 433, (2006)
Carlsson, J., Andér, M., Nervall, M., Åqvist, J. Continuum Solvation Models in the Linear Interaction Energy Method. J. Phys. Chem. B 110, 12034, (2006)
Carlsson, J., Åqvist, J. Calculations of Solute and Solvent Entropies from Molecular Dynamics Simulations. Phys. Chem. Chem. Phys. 8, 5385, (2006)
Carlsson, J., Åqvist, J. Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding. J. Phys. Chem. B 109, 6448, (2005)
Almlöf, M., Brandsdal B.O., Åqvist, J. Binding Affinity Prediction with Different Force Fields: Evaluation of the Linear Interaction Energy Method. J. Comput. Chem. 25, 1242, (2004)
Åqvist, J., Wennerström, P., Nervall, M., Bjelic, S., Brandsdal, B.O. Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm. Chem. Phys. Lett. 384, 288, (2004)
Structure-Based Ligand Design
Wallin G, Nervall M, Carlsson J and Åqvist J; Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method J. Chem. Theory Comput. 5, 380, (2009) [abstract]
Nervall, M., Hanspers, P., Carlsson, J., Boukharta, L., Åqvist, J. Predicting binding modes from free energy calculations. J. Med. Chem. 51, 2657, (2008)
Carlsson, J., Boukharta, L., Aqvist, J. 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. 51, 2648, (2008)
Ersmark, K., Nervall, M., Guiterrez de Teran, H., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Gogoll, A., Samuelsson, B., Åqvist, J., Hallberg, A. Macrocyclic Inhibitors of the Malarial Aspartic Proteases Plasmepsin Plm II and IV. Bioorg, Med. Chem. 14, 2197, (2006)
Guiterrez de Teran, H., Nervall, M., Ersmark, K., Liu, P., Janka, L.K., Dunn, B., Hallberg, A., Åqvist, J. Inhibitor Binding to the Plasmepsin IV Aspartic Protease from Plasmodium falciparum. Biochemistry 45, 10529, (2006)
Guiterrez-de-Teran, H., Nervall, M., Dunn, B.M., Clemente, J.C., Åqvist, J. Computational Analysis of Plasmepsin IV Bound to an Allophenylnorstatine Inhibitor. FEBS Lett. 580, 5910, (2006)
Lovmar, M., Nilsson, K., Vimberg, V., Tenson, T., Nervall, M., Ehrenberg, M. The Molecular Mechanism of Peptide-Mediated Erythromycin Resistance. J. Biol. Chem. 281, 6742, (2006)
Ersmark, K., Nervall, M., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Blackman, M.J., Samuelsson, B., Åqvist, J., Hallberg, A. Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations. J. Med. Chem. 48, 6090, (2005)
Ersmark, K., Bjelic, S., Feierberg, I., Hamerlink, E., Hackett, F., Blackman, M.J., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. Potent Inhibitors of the P. falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity. J. Med. Chem. 47, 110, (2004)
Ersmark, K., Feierberg, I., Bjelic, S., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. C2-Symmetric Inhibitors of Plasmodium falciparum Plasmepsin II: Synthesis and Theoretical Predictions. Bioorg. Med. Chem. 11, 3723, (2003)