Publications

Software


Q6 | CADEE | Micelle Maker

Crystal Structures


Crystal structures deposited with our work (PDB IDs): 4UFN, 4UFO, 4UFP, 4UHB, 4Y9S, 4Q1U.

2017


88. M. Kaltenbach, J. R. Burke, M. Dindo, A. Pabis, F. S. Munsberg, A. Rabin, S. C. L. Kamerlin, J. P. Noel and D. S. Tawfik. Evolution of chalcone isomerase from a non-catalytic ancestor. bioRxiv 2017, Pre-print. DOI: 10.1101/174128 Manuscript PDF


87. M. Purg, M. Elias and S. C. L. Kamerlin. Similar active sites and mechanisms do not lead to cross-promiscuity in organophosphate hydrolysis: Implications for biotherapeutic engineering. J. Am. Chem. Soc. Just AcceptedPublisher’s PDF


86. A. Pabis, V. Risso, J. M. Sanchez-Ruiz and S. C. L. Kamerlin. Cooperativity and flexibility in enzyme evolution. Curr. Opin. Struct. Biol. 2018, 48, 83. Publisher’s PDF


85. Q. Liao, A. Pabis, B. Strodel and S. C. L. Kamerlin. Extending the nonbonded cationic dummy model to account for ion-induced dipole interactions. J. Phys. Chem. Lett. 2017, 8, 5408. Publisher’s PDF


84. D. Petrović, D. Frank, S. C. L. Kamerlin, K. Hoffmann and B. Strodel. Shuffling active site sub-state populations impacts catalytic activity: The case of glucose oxidase ACS Catal. 2017, 7, 6188. Publisher’s PDF


83. A. Pabis, N. H. Williams and S. C. L. Kamerlin. Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer. Org. Biomol. Chem. 2017, 15, 7308. Publisher’s Page


82. S. N. Maximoff, S. C. L. Kamerlin and J. Florián. DNA polymerase λ active site favors a mutagenic mispair between the enol form of deoxyguanosine triphosphate substrate and the keto form of thymidine template: A free energy perturbation study. J. Phys. Chem. B 2017, 121, 7813. Publisher’s Page


81. D. M. Krüger and S. C. L. Kamerlin. Micelle Maker: An online tool for generating equilibrated micelles as direct input for molecular dynamics simulations. ACS Omega 2017, 2, 4524. Publisher’s PDF | Webserver


80. Y. Kulkarni, Q. Liao, D. Petrovic, D. M. Krüger, B. Strodel, T. Amyes, J. Richard and S. C. L. Kamerlin. Enzyme architecture: Modeling the operation of a hydrophobic clamp in catalysis by triosephosphate isomerase. J. Am. Chem. Soc. 2017, 139, 10514. Publisher’s PDF


79. V. A. Risso, S. Martinez Rodriguez, A. M. Candel, D. M. Krüger, D. Pantoja-Uceda, M. Ortega-Muñoz, F. Santoyo-Gonzalez, E. A. Gaucher, S. C. L. Kamerlin, M. Bruit, J. A. Gavira and J. M. Sanchez-Ruiz. De novo active sites for resurrected Precambrian enzymes. Nat. Commun. 2017, 8, 16113. Publisher’s PDF


78. B. Braîda and  S. C. L. Kamerlin. Preface to a special issue on valence bond theory. Comp. Theor. Chem. A. 2017, 1116, 1. Publisher’s Page


77. S. Zhan, D. Mårtensson, M. Purg, S. C. L. Kamerlin and M. Ahlquist. Capturing the role of explicit solvent in the dimerization of RuV(bda) water oxidation catalysts. Angew. Chem. Int. Ed. 2017, 56, 6962. Publisher’s Page


76. A. Barrozo, D. Blaha-Nelson, N. H. Williams and S. C. L. Kamerlin. The effect of magnesium ions on triphosphate hydrolysis. Pure Appl. Chem. 2017, 89, 715. Publisher’s PDF


75. D. Blaha-Nelson, D. M. Krüger, K. Szeler, M. Ben-David and S. C. L. Kamerlin. Active site hydrophobicity and the convergent evolution of paraoxonase activity in structurally divergent enzymes: The case of serum paraoxonase 1. J. Am. Chem. Soc. 2017, 139, 1155. Publisher’s PDF


74. Theory and Applications of the Empirical Valence Bond Approach: From Physical Chemistry to Chemical Biology. Editors: F. Duarte and  S. C. L. Kamerlin. Wiley 2017Purchase Online


73. B. Amrein, F. Steffen-Munsberg, I. Szeler, M. Purg, Y. Kulkarni and S. C. L. Kamerlin. CADEE: Computer Aided Directed Evolution of Enzymes. IUCrJ 2017, 4, 20160150. Publisher’s PDF

2016


72. M. Purg, A. Pabis, F. Baier, N. Tokuriki, C. Jackson and  S. C. L. Kamerlin. Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. Phil. Trans. R. Soc. A. 2016, 374, 20160150. Publisher’s PDF


71. Å. Janfalk Carlsson, P. Bauer, D. Dobritzsch, M. Nilsson, S. C. L. Kamerlin and M. Widersten. Laboratory evolved enzymes provide snapshots of the development of enantioconvergence in enzyme-catalyzed epoxide hydrolysis. ChemBioChem. 2016, 17, 1693. Publisher’s PDF


70. C. Wallin, Y. J. Kulkarni, A. Abelein, J. Jarvet, Q. Liao, B. Strodel, L. Olsson, J. Luo, J. P. Abrahams, S. B. Sholts, P. M. Roos, S. C. L. Kamerlin, A. Gräslund and S. K. T. S. Wärmlander. Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer’s disease. J. Trace Elem. Med. Biol. 2016, 38, 183. Publisher’s PDF


69. T. A. S. Brandao, A. C. Hengge, A. Barrozo and S. C. L. Kamerlin. Phosphoryl and sulfuryl transfer. Comprehensive Natural Products II 2010, 8, 315-348. ScienceDirect


68. F. Duarte, A. Barrozo, J. Åqvist, N. H. Williams and  S. C. L. Kamerlin. The competing mechanisms of phosphate monoester dianion hydrolysis. J. Am. Chem. Soc. 2016, 138, 10664. Publisher’s PDF


67. S. C. L. Kamerlin. Where are the female science professors? A personal perspective. F1000Research 2016, 5, 1224. Publisher’s PDF


66. S. C. L. Kamerlin. Hypercompetition in biomedical research evaluation and its impact o young scientist careers. Int. Microbiol. 18:4 Publisher’s PDF


65. P. Bauer, Å. J. Carlsson, B. A. Amrein, D. Dobritzsch, M. Widersten and S. C. L. Kamerlin. Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. Org. Biomol. Chem. 2016, 14, 5639. Publisher’s PDF


64. A. Pabis, F. Duarte and S. C. L. Kamerlin. Promiscuity in the enzymatic catalysis of phosphate and sulfate transfer. Biochemistry 201655, 3061. Publisher’s PDF


63. J. Åqvist and S. C. L. Kamerlin. Conserved motifs in different classes of GTPases dictate their specific modes of catalysis. ACS Catal. 2016, 6, 1737. Publisher’s PDF


62. A. Pabis and S. C. L. Kamerlin. Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily. Curr. Opin. Struct. Biol. 2016, 37, 14. Publisher’s PDF


61. H. Ma, K. Szeler, S. C. L. Kamerlin and M. Widersten. Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA). Chem. Sci. 2016, 7, 1415. Publisher’s PDF

2015


60. J. Aqvist and S. C. L. Kamerlin. Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome. Sci. Rep. 2015, 5, 15817. Publisher’s PDF


59. A. Barrozo, F. Duarte, P. Bauer, A. T. P. Carvalho and S. C. L. Kamerlin. Cooperative electrostatic interactions drive functional evolution in the alkaline phosphatase superfamily. J. Am. Chem. Soc. 2015, 137, 9061. Publisher’s PDF


58. P. Bauer, B. A. Amrein, F. Duarte, A. J. Carlsson, A. Naworyta, S. Mowbray, M. Widersten and S. C. L. Kamerlin. Expanding the catalytic triad in epoxide hydrolases and related enzymes. ACS Catal. 2015, 5, 5702. Publisher’s PDF


57. A. Rushforth, S. de Rijcke, A. Beaulieu, P. Wouters, R. Muller, M. Burton, S. de Vries, M. Derksen, P. Faasen, M. Garfinkel, T. Holltrop, B. Hammarfelt, S. C. L. Kamerlin V. Lariviere, T. McPherson, F. Miedema, P. Mangeon, A. Paul-Hus, D. Pontille, E. Simons, S. van Weelden, J. van Zundert, D. Henriksen, W. Kaltenbrunner, M. Kieboom and L. van Kalshoven. The Author: Multiple reflections on a one-week Lorentz-workshop on authorship in transition. EASST Review 2015, 34. Publisher’s PDF


56. Q. Liao, S. C. L. Kamerlin and B. Strodel. Development and application of a non-bonded Cu2+ model that includes the Jahn-Teller effect. J. Phys. Chem. Lett. 2015, 6, 57. Publisher’s PDF


55. A. T. P. Carvalho, A. C. O’Donoghue, D. Hodgson and S. C. L. Kamerlin. Understanding thio-effects in simple phosphoryl systems: Role of solvent assistance and nucleophile charge. Org. Biomol. Chem. 2015, 13, 5391 (Cover Article). Publisher’s PDF


54. Johan Aqvist and S. C. L. Kamerlin. The conformation of a catalytic loop is essential to GTP hydrolysis on the ribosome. Biochemistry 2015, 54, 546. Publisher’s PDF


53. A. T. P. Carvalho, L. Gouveia, C. R. Kanna, S. K. T. S. Warmlander, J. Platts and S. C. L. Kamerlin. Theoretical modeling of epigenetically modified DNA sequences. F1000Research 2015, 4, 52. Publisher’s PDF


52. M. Ben-David, J. L. Sussman, C. I. Maxwell, K. Szeler, S. C. L. Kamerlin and D. S. Tawfik. Catalytic stimulation by restrained active-site floppiness – The case of high-density lipoprotein bound serum paraoxonase 1. J. Mol. Biol. 2015, 427, 1359. Publisher’s PDF


51. A. T. P. Carvalho, K. Szeler, K. Vavitsas, J. Aqvist and S. C. L. Kamerlin. Modelling the mechanisms of biological GTP hydrolysis. Arch. Biochem. Biophys. 2015, 582, 80. Publisher’s PDF


50. F. Duarte, B. A. Amrein, D. Blaha-Nelson and S. C. L. Kamerlin. Recent advances in QM/MM free energy calculations using reference potentials. BBA – General Subjects 2015, 1850, 9548. Publisher’s PDF


49. F. Duarte, J. Aqvist, N. H. Williams and S. C. L. Kamerlin. Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis. J. Am. Chem. Soc. 2015, 137, 1081 (Cover and Spotlight Article). Publisher’s PDF


48. A. Shurki, E. Derat, A. Barrozo and S. C. L. Kamerlin. How valence bond theory can help you understand your (bio)chemical reaction. Chem. Soc. Rev. 2015, 44, 1037-1052 (Cover Article). Publisher’s PDF

2014


47. M. Repic, R. Vianello, M. Purg, F. Duarte, R. Bauer, S. C. L. Kamerlin and J. Mavri. Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine. Proteins: Struct. Func. Bioinformat. 2014, 82, 3347. Publisher’s PDF


46. A. C. O’Donoghue and S. C. L. Kamerlin. Editorial overview: Mechanisms: Chemical and computational probes of biological mechanism. Curr. Opin. Chem. Biol. 2014, 21, vii. Publisher’s PDF


45. A. T. P. Carvalho, L. Gouveia, C. R. Kannu, S. K. T. S. Warmlander, J. Platts and S. C. L. Kamerlin. Understanding the structural and dynamical consequences of DNA epigenetic modifications: Computational insights and challenges. Epigenetics 2014, 9, 1604 (Cover Article). Publisher’s PDF


44. A. T. P. Carvalho, F. Duarte, K. Vavitsas and S. C. L. Kamerlin. Conformational and chemical landscapes of enzyme catalysis. In: Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods 2014 (Editor Monica Fuxreiter, Taylor and Francis Group, Boca Raton, Florida). Publisher’s PDF


43. A. T. P. Carvalho, A. Barrozo, D. Doron, A. Vardi Kilshtain, D. T. Major and S. C. L. Kamerlin. Challenges in computational studies of enzyme structure, function and dynamics. J. Mol. Graph. Mod. 2014, 54, 62 (Topical Perspective). Publisher’s PDF


42. F. Duarte, P. Bauer, A. Barrozo, B. A. Amrein, M. Purg, J. Aqvist and S. C. L. Kamerlin. Force field independent metal parameters using a nonbonded dummy model. J. Phys. Chem. B 2014, 118, 4351. Publisher’s PDF


41. F. Duarte, T. Geng, G. Marloie, A. O. Al Hussain, N. H. Williams and S. C. L. Kamerlin. The alkaline hydrolysis of sulfonate esters: Challenges in interpreting experimental and theoretical data. J. Org. Chem. 2014, 79, 2816 (Cover and Feature article). Publisher’s PDF


40. F. Duarte, S. Gronert and S. C. L. Kamerlin. Concerted or stepwise: How much do free energy landscapes tell us about the mechanisms of elimination reactions? J. Org. Chem. 2014, 79, 1280. Publisher’s PDF

2013


39. S. C. L. Kamerlin. Catalytic promiscuity in the alkaline phosphatase superfamily as an example of chemistry-driven protein evolution. AE Lett. 2013 (Contribution to the AE Letters session of the annual meeting of the Academia Europaea, Wroclaw 2013)


38. F. Duarte, B. A. Amrein and  S. C. L. Kamerlin. Modelling catalytic promiscuity in the alkaline phosphatase superfamily. Phys. Chem. Chem. Phys. 2013, 15, 11160 (Cover and HOT article). Publisher’s PDF


37. G. Wallin, S. C. L. Kamerlin and Johan Aqvist. Energetics of GTP hydrolysis on the ribosome. Nat. Commun. 2013, 4, 1733. Publisher’s PDF


36. J. Luo, C.-H. Yu, H. Yu, R. Borstnar, S. C. L. Kamerlin, A. Gräslund, J. P. Abrahams and S. K. T. S. Wärmländer. Cellular polyamines promote amyloid beta (Aβ) fibrillation and modulate the aggregation pathways. ACS Chem. Neurosci. 2013, 4, 3. Publisher’s PDF


35. S. C. L. Kamerlin, P. K. Sharma, R. B. Prasad and A. Warshel. Why Nature really chose phosphate. Q. Rev. Biophys. 2013, 15, 1. Publisher’s PDF

2012


34. B. R. Prasad, S. C. L. Kamerlin, J. Florin and A. Warshel. Prechemistry barriers and checkpoints do not contribute to catalysis as long as they are not rate limiting. Theor. Chem. Acc. 2012, 131, 1288. Publisher’s PDF


33. R. Borstnar, M. Repic, S. C. L. Kamerlin, R. Vianello and J. Mavri. Computational study of the pKa values of potential catalytic residues in the active site of monoamine oxidase B. J. Chem. Theory Comput. 2012, 8, 3864. Publisher’s PDF


32. B. R. Prasad, S. C. L. Kamerlin, N. V. Plotnikov and A. Warshel. Studying catalysis by QM/MM approaches should not be a black box process. J. Thermodynam. Cat. 2012, 3, 4. Publisher’s PDF


31. A. Barrozo, R. Borstnar, G. Marloie and S. C. L. Kamerlin. Computational protein engineering: Bridging the gap between rational design and laboratory evolution. Int. J. Mol. Sci. 2012, 13, 12428 (Invited Review). Publisher’s PDF


30. J. S. Kudavalli, S. N. Rao, D. E. Bean, N. D. Sharma, D. R. Boyd, P. W. Fowler, S. Gronert, S. C. L. Kamerlin, J. R. Keefe and R. More-O’Ferrall. Base-catalyzed dehydration of 3-substituted benzene cis-1,2-dihydrodiols: Stabilization of a cyclohexadienide anion intermediate. J. Am. Chem Soc. 2012, 134, 14056. Publisher’s PDF


29. J. Luo, B. van Loo and S. C. L. Kamerlin. Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution. FEBS Lett. 2012, 586, 1622. Publisher’s PDF


28. J. Luo, B. van Loo and S. C. L. Kamerlin. Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: A comparison to analogous phosphatases. Proteins: Struct. Funct. Bioinformat. 2012, 80, 1211 (Cover Article). Publisher’s PDF

2011


27. S. C. L. Kamerlin. Theoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution: Implications for enzyme-catalyzed sulfuryl transfer. J. Org. Chem. 2011, 76, 9228. Publisher’s PDF


26. A. Adamczyk, J. Cao, S. C. L. Kamerlin and A. Warshel. Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc. Natl. Acad. Sci. USA 2011, 108, 14115. Publisher’s PDF


25. S. C. L. Kamerlin and A. Warshel. Multiscale modeling of biological functions.
PhysChemChemPhys 2011, 13, 10401. Publisher’s PDF


24.N. Plotnikov, S. C. L. Kamerlin and A. Warshel. Paradynamics: An effective and reliable model for ab initio QM/MM free-energy calculations and related tasks. J. Phys. Chem. B. 2011, 115, 7950. Publisher’s PDF


23. S. C. L. Kamerlin and J. Wilkie. The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis. Org. Biomol. Chem. 2011, 9, 5394. Publisher’s PDF


22. S. C. L. Kamerlin and A. Warshel. The empirical valence bond model: Theory and applications. Wiley Interdisciplinary Reviews, 2011, 1, 30. Publisher’s PDF


21. S. C. L. Kamerlin, S. Vicatos, A. Dryga and A. Warshel. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu. Rev. Phys. Chem. 2011, 62, 41. Publisher’s PDF

2010


20. S. C. L. Kamerlin, Z. T. Chu and A. Warshel. On catalytic preorganization in oxyanion holes: Highlighting the problems with the gas phase modeling of oxyanion holes and illustrating the need for complete enzyme models. J. Org. Chem. 2010, 75, 6391. Publisher’s PDF


19. S. C. L. Kamerlin, J. Mavri and A. Warshel. Examining the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. FEBS Lett. 2010, 584, 2759 (Cover Article). Publisher’s PDF


18. S. C. L. Kamerlin and A. Warshel. An analysis of all the relevant facts indicates that enzyme catalysis does not involve large contributions from nuclear tunnelling. J. Phys. Org. Chem. 2010, 23, 677 (Special Issue Review Commentary). Publisher’s PDF


17. S. C. L. Kamerlin and A. Warshel. Reply to Karplus: Conformational dynamics have no role in the chemical step. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, E72. Publisher’s PDF


16. S. C. L. Kamerlin and A. Warshel. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins: Struct. Func. Bioinformat. 2010, 78, 1339 (Cover Article). Publisher’s PDF


15. S. C. L. Kamerlin, P. K. Sharma, Z. T. Chu and A. Warshel. Ketosteroid isomerase provides further support to the idea that enzymes work by electrostatic preorganisation. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 4075. Publisher’s PDF


14. A. Alkherraz, S. C. L. Kamerlin, G. Feng, I. Sheik, A. Warshel and N. H. Williams. Phosphate ester analogues as probes for understanding enzyme catalyzed phosphoryl transfer. Faraday Discuss. 2010, 145, 281. Publisher’s PDF


13. S. C. L. Kamerlin and A. Warshel. The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions. Faraday Discuss. 2010, 145, 71. Publisher’s PDF

2009


12. S. C. L. Kamerlin and A. Warshel. On the energetics of ATP hydrolysis in solution. J. Phys. Chem. B. 2009, 113, 15692. Publisher’s PDF


11. A. V. Pisliakov, J. Cao, S. C. L. Kamerlin and A. Warshel. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 17359. Publisher’s PDF


10. S. C. L. Kamerlin, J. Cao, E. Rosta and A. Warshel. On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. J. Phys. Chem. B. 2009, 113, 10905. Publisher’s PDF


9. S. C. L. Kamerlin, C. McKenna, M. Goodman and A. Warshel. A computational study of the hydrolysis of dGTP analogues in solution: Implications for the mechanism of DNA polymerases. Biochemistry 2009, 48, 5963. Publisher’s PDF


8. S. C. L. Kamerlin, M. Haranczyk and A. Warshel. Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvati on models. ChemPhysChem 2009, 10, 1125. Publisher’s PDF


7. S. C. L. Kamerlin, M. Haranczyk and A. Warshel. Progress in ab initio QM/MM free energy simulations of electrostatic energies in proteins: Accelerated QM/MM studies of pKa, redox reactions and solv ation free energies. J. Phys. Chem. B. 2009, 113, 1253 (Centennial Feature Article and Cover Article). Publisher’s PDF

2008


6. S. C. L. Kamerlin, N. H. Williams and A. Warshel. Dineopentyl phosphate hydrolysis: Evidence for stepwise water attack. J. Org. Chem. 2008, 73, 6960 (Feature Article). Publisher’s PDF


5. S. C. L. Kamerlin, J. Florin and A. Warshel. Associative versus dissociative mechanisms of phosphate monoester hydrolysis: On the interpretation of activation entropies. ChemPhysChem 2008, 9, 1767. Publisher’s PDF


4. E. Rosta, S. C. L. Kamerlin and A. Warshel. On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: A thorough computational study of phosphate diester hydrolysis. Biochemistry 2008, 47, 3725. Publisher’s PDF

2007


3. S. C. L. Kamerlin, R. Rucker and S. Boresch. A molecular dynamics study of WPD-loop flexibility in PTP1B. Biochem. Biophys. Res. Commun. 2007, 356, 1011. Publisher’s PDF


2. S. C. L. Kamerlin and J. Wilkie. The role of metal ions in phosphate ester hydrolysis. Org. Biomol. Chem. 2007, 5, 2098. Publisher’s PDF

2006


1. S. C. L. Kamerlin, R. Rucker and S. Boresch. A targeted molecular dynamics study of WPD-loop movement in PTP1B. Biochem. Biophys. Res. Commun. 2006, 345, 1161. Publisher’s PDF