Publications List

2015

59.
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
58.
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
57.
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
56.
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
55.
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
54.
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)
53.
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
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
52.
M. Ben-David, J. L. Sussman, C. I. Maxwell, K. Szeler, S. C. L. Kamerlin and D. Tawfik
Catalytic stimulation by restrained active-site floppiness - The case of high-density lipoprotein bound serum paraoxonase 1.
J. Mol. Biol. 2015, 427, 1359
51.
A. T. P. Carvalho, K. Szeler, K. Vavitsas, J. Aqvist and S. C. L. Kamerlin
Modeling the mechanisms of biological GTP hydrolysis.
Arch. Biochem. Biophys. 2015, 582, 80
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
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)
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)

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
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
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)
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)
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)
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
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)
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

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
Modeling catalytic promiscuity in the alkaline phosphatase superfamily.
Phys. Chem. Chem. Phys. 2013, 15, 11160 (Cover and HOT article)
37.
G. Wallin, S. C. L. Kamerlin and Johan Aqvist
Energetics of GTP hydrolysis on the ribosome.
Nat. Commun. 2013, 4, 1733
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
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

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
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
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
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)
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
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
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)

2011

27.
S. C. L. Kamerlin
Theoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution: Implications for enzyme-catalyzed sulfuryl tranf ser.
J. Org. Chem. 2011, 76, 9228
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
25.
S. C. L. Kamerlin and A. Warshel
Multiscale modeling of biological functions.
PhysChemChemPhys 2011, 13, 10401
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
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
22.
S. C. L. Kamerlin and A. Warshel
The empirical valence bond model: Theory and applications.
Wiley Interdisciplinary Reviews, 2011, 1, 30
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

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
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)
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 tunneling.
J. Phys. Org. Chem. 2010, 23, 677 (Special Issue Review Commentary)
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
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)
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 preorganization.
Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 4075
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
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

2009

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

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)
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
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 hy drolysis.
Biochemistry 2008, 47, 3725

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

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