Software
Q6 | CADEE | Micelle Maker | Q-RepEx | KIF
Crystal Structures
Crystal structures deposited with our work (73 total):
Serum paraoxonase 1, K192Q variant: 4Q1U, L69S/H115W/F222S variant: 6G82, L69G/H134R/F222S/T332S variant: 6GMU, L69G/H115W/H134R/F222S/T332S variant: 6H0A.
Potato epoxide hydrolase 1 variants: R-C1 4UHB, R-C1B1 4UFN, R-C1B1D33E6 4UFO, R-C1B1D33 4UFP, H300N 4Y9S.
Last common ancestors of Gram-negative bacteria beta-lactamase class A: GNCA W229D 4UHU, GNCA4 W229D/F290W 5FQI, GNCA W229D + TSA 5FQJ, GNCA4 W229D/F290W + TSA 5FQK, GNCA 5FQM, GNCA4 5FQQ, FuncLib Design GNCA4-2 6TY6, FuncLib Design GNCA4-12 6TXD, FuncLib Design GNCA4-19 6TWW.
Human Glycerol Dehydrogenase: Unliganded 6E8Y, binary complex with NAD 6E8Z, ternary complex 6E90.
Glucose oxidase mutant A2: 5NIT, 5NIW.
R. ruber ADH-A Y54G/L119Y variant: 5OD3, Y54G/F43T/L119Y/F282W variant: 6FG0.
Dihydrocoumarin hydrolase, AncDHCH1: 6C2C.
Crystal structures of chalcone isomerases engineered from ancestral inference: ancCC 5WKR, ancR1 5WKS, ancR2 5WL3, ancR3 5WL4, ancR5 5WL5, ancR7 5WL6, ancCHI* 5WL7, epR4 5WL8.
Crystal structure of Chalcone isomerase from Medicago Sativa with the G95T mutation: 6CJN and with the G95S mutation: 6CJO.
Crystal structure of Chalcone isomerase from Medicago truncatula complexes with (2S)-naringenin: 6MS8.
Pseudomonas aeruginosa arylsulfatase (PAS): G4 mutant 4CYR, G4 mutant in complex with phenylphosphonic acid 4CXS, G4 mutant in complex with 3-Br-phenylphosphonate 4CXU, G6 mutant 4CYS, G7 mutant 5AJ9, G9 mutant 4CXK
Pol2 Catalytic Domain of DNA Polymerase Epsilon: Pol2CORE-M644G in complex with DNA and an incoming nucleotide 6FWK, Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution 6G0A, Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution 6I8A.
VIM-2, Round 10 of a directed evolution trajectory: 6BM9.
Directed evolutionary changes in Kemp eliminase KE07: crystal 18 design Trp50Ala mutant 6C7H, crystal 19 round 5 6C7M, crystal 20 round 5 6C7T, crystal 21 round 5 6DKV, crystal 22 round 5 6C7V, crystal 23 round 6 6C8B, crystal 24 round 7 6CAI, crystal 25 round 7 6DC1, crystal 27 round 7-2 6CT3, and crystal 28 round 5 6DNJ.
EthR in complex with 2-(3-methylphenyl)-{N}-[[2-(oxan-4-yl)-7-oxidanyl-pyrazolo[1,5-a]pyrimidin-5-yl]methyl]ethanamide: 6R1S, in complex with 2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one: 6R1P.
Human glycerol-3-phosphate dehydrogenase, binary complex, R269A variant: 6PYP.
Protein tyrosine phosphatases: ligand-free PTP1B T177G variant 7L0C, vanadate-bound PTP1B T177G variant 7L0H, ligand-free YopH G352T variant 7L0I, vanadate-bound PTP1B G352T variant 7L0M, unliganded PTP1B/YopH WPD loop Chimera 3 6XE8, vanadate-bound PTP1B/YopH WPD loop Chimera 3 6XEA, tungstate-bound PTP1B/YopH WPD loop Chimera 3 6XED, unliganded PTP1B/YopH WPD loop Chimera 4 6XEE, vanadate-bound PTP1B/YopH WPD loop Chimera 4 6XEF, tungstate-bound PTP1B/YopH WPD loop Chimera 4 6XEG, hepes-bound PTP1B F182Q variant 7S4F.
Scientific Articles, Books and Book Chapters
Preprints
148. S. Brickel, A. O. Demkiv, R. M. Crean, G. P. Pinto and S. C. L. Kamerlin. Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations. 2022. ChemRxiv preprint
147. J. M. Gardner, L. Willem, W. van der Wijngaart, S. C. L. Kamerlin, N. Brusselaers and P. M. Kasson. Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity. 2020. medRxiv preprint
2022
146. G. Fischer, M. Corbella, M. S. Alphey, J. Nicholson, B. J. Read, S. C. L. Kamerlin and R. G. da Silva. Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. 2022. Nat. Commun. 2022, 13, 7607. Publisher’s version ChemRxiv preprint
145. R. Shen, R. M. Crean, K. J. Olsen, T. Richan, T. A. S. Brandão, R. D. Berry, A. Tolman, J. P. Loria, S. J. Johnson, S. C. L. Kamerlin and A. C. Hengge. Insights into the importance of the WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Chem. Sci. 2022, 13, 13524. Publisher’s version ChemRxiv preprint
144. R. Kourist and S. C. L. Kamerlin. A structural view into the complexity of carbon dioxide fixation. ACS Cent. Sci. 2022, In Press. Publisher’s version
143. A. Romero-Rivera, M. Corbella, A. Parracino, W. M. Patrick and S. C. L. Kamerlin. Complex loop dynamics underpin activitiy, specificity and evolvability in the (βα)8 barrel enzymes of histidine and tryptophan biosynthesis. JACS Au 2022, 2, 943. ChemRxiv preprint Publisher’s version
142. E. Derat and S. C. L. Kamerlin. Computational advances in protein engineering and enzyme design. J. Phys. Chem. B 2022, 126, 2449. Publisher’s version
141. M. Pfeiffer, R. M. Crean, C. Moreira, A. Parracino, G. Oberdorfer, L. Brecker, F. Hammerschmidt, S. C. L. Kamerlin and B. Nidetzky. Essential functional interplay of the catalytic groups in acid phosphatase. ACS Catal. 2022, 12, 3357. ChemRxiv preprint Publisher’s version
140. Jackson, A. Toth-Petroczy, R. Kolodny, F. Hollfelder, M. Fuxreiter, S. C. L. Kamerlin and N. Tokuriki. Adventures on the routes of protein evolution – in memoriam Dan Salah Tawfik (1955-2021). J. Mol. Biol. 2022, 434, 167462. DOI: 10.1016/j.jmb.2022.167462. Publisher’s Version
139. S. C. L. Kamerlin. From flying cats to dancing proteins. Nat. Rev. Chem. 2022, DOI: 10.1038/s41570-021-00358-2 Publisher’s Version
138. G. P. Pinto, M. Corbella, A. O. Demkiv and S. C. L. Kamerlin. Exploiting enzyme evolution for computational protein design. Trends Biochem. Sci. 2022, 47, 375. DOI: 10.1016/j.tibs.2021.08.008 Publisher’s Version
2021
137. M. Corbella, Q. Liao, A. Parracino, P. M. Kasson and S. C. L. Kamerlin. The N-terminal helix-turn-helix motif of transcription factors MarA and Rob drives DNA recognition. J. Phys. Chem. B. 2021, 125, 6791, DOI: 10.1021/acs.jpcb/1c00771 Publisher’s Version ChemRxiv preprint
136. S. C. L. Kamerlin, D. J. Allen, B. de Bruin, E. Derat and H. Urdal. Journal Open Access and Plan S: Solving problems or shifting burdens? Dev. Change. 2021, 52, 627. DOI: 10.1111/dech.12635. Publisher’s Version
135. M. H. Elias, J. S. Fraser, S. C. L. Kamerlin, W. M. Patrick and C. J. Jackson. Dan Salah Tawfik (1955 – 2021) – A giant of protein evolution. EMBO Rep. 2021, e53256. Publisher’s Version
134. R. Shen, R. M. Crean, S. J. Johnson, S. C. L. Kamerlin and A. C. Hengge. A single residue on the WPD-loop affects the pH dependency of catalysis in protein tyrosine phosphatases. JACS Au 2021, 5, 646. Publisher’s Version ChemRxiv preprint
133. R. M. Crean, M. Biler, M. van der Kamp, A. C. Hengge and S. C. L. Kamerlin. Loop dynamics and enzyme catalysis in protein tyrosine phosphatases. J. Am. Chem. Soc. 2021, 143, 3820. Publisher’s Version ChemRxiv preprint
132. G. Gamiz-Arco, L. Gutiérrez-Rus, V. A. Risso, B. Ibarra-Molero, Y. Hoshino, D. Petrovic, J. Justicia, J. M. Cuerva, A. Romero-Rivera, B. Seelig, J. A. Gavira, S. C. L. Kamerlin, E. A. Gaucher and J. M. Sanchéz-Ruiz. Novel heme binding enables allosteric modulation in an ancient enzyme. Nat. Commun. 2021, 12, 380. Publisher’s Version bioRxiv preprint
2020
131. S. C. L. Kamerlin and P. Wittung-Stafshede. Female faculty: why so few, and why care? Chem. Eur. J. 26 (2020), 8319 (invited contribution to the “Science Voices” series). Publisher’s Version
130. S. C. L. Kamerlin and P. M. Kasson. Managing COVID-19 spread with voluntary public health measures: Sweden as a case study for pandemic control. Clin. Infect. Dis. 2020, 71, 3174. Publisher’s Version
129. M. Biler, A. K. Schweiger, R. Kourist and S. C. L. Kamerlin. Ground-state destabilization controls the selectivity of a cofactor-free decarboxylase. J. Am. Chem. Soc. 2020, 142, 20216. Publisher’s Version ChemRxiv preprint
128. A. R. Mhashal, R. Romero-Rivera, L. S. Mydy, J. R. Cristobal, A. M. Gulick, J. P. Richard and S. C. L. Kamerlin. Modeling the role of a flexible loop and active site side chains in hydride transfer catalyzed by glycerol-3-phosphate dehydrogenase. ACS Catal. 2020, 10, 11253. Publisher’s Version ChemRxiv preprint
127. S. Odoemelam, B. Percival, H. Wallis, M.-W. Chang, Z. Ahmad, D. Scholey, E. Burton, I. H. Williams, S. C. L. Kamerlin and P. B. Wilson. G-Protein coupled receptors: Structure and function in drug discovery. RSC Adv. 2020, 10, 36337. Publisher’s Version
126. T. Reddy Enugula, M. Corbella Mórato, S. C. L. Kamerlin and M. Widersten. The role of substrate-coenzyme crosstalk in determining turnover rates in Rhodococcus ruber alcohol dehydrogenase. ACS Catal. 2020, 10, 9115. Publisher’s Version
125. R. Crean, J. M. Gardner and S. C. L. Kamerlin. Harnessing conformational plasticity to generate designer enzymes. J. Am. Chem. Soc. 2020, 142, 11324. Publisher’s Version
124. V. A. Risso, A. Romero-Rivera, L. I. Gutiérrez-Ruiz, M. Ortega-Muñoz, F. Santoyo-Gonzalez, J. A. Gavri, J. M. Sanchéz-Ruiz and S. C. L. Kamerlin. Enhancing a de novo enzyme activity by computationally-focused, ultra-low-throughput sequence screening. Chem. Sci. 2020, 11, 6134 (“Pick of the Week”, Cover and “HOT” article), DOI: 10.1039/D0SC01935F. Publisher’s Version | ChemRxiv preprint
123. K. Szeler, N. H. Williams, A. Hengge and S. C. L. Kamerlin. Modeling the alkaline hydrolysis of diaryl sulfate diesteras: a mechanistic study. J. Org. Chem. 2020, 85, 6489. Publisher’s Version | ChemRxiv preprint
122. J. M. Gardner, M. Biler, V. A. Risso, J. M. Sanchéz Ruiz and S. C. L. Kamerlin. Manipulating conformational dynamics to repurpose ancient proteins for modern catalytic functions. ACS Catal. 2020, 10, 4863. Publisher’s Version
121. A. R. Calixto, C. Moreira, and S. C. L. Kamerlin. Recent advances in understanding biological phosphate hydrolysis. ACS Omega 2020, 5, 4380. Publisher’s PDF
120. L. Longo, D. Petrovic, S. C. L. Kamerlin and D. S. Tawfik. Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proc. Natl. Acad. Sci. USA 2020, 117, 5310. Publisher’s Version
119. M. Ben-David, M. Soskine, A. Dubotevsky, K.-P. Cherukuri, O. Dym, J. L. Sussman, Q. Liao, K. Szeler, S. C. L. Kamerlin and D. S. Tawfik. Enzyme evolution: an epistatic rachet versus a smooth reversible trajectory. Mol. Biol. Evol. 2020, 37, 1133. Publisher’s PDF
118. P. B. Wilson, M. Grootveld and S. C. L. Kamerlin. Errors in DFT integration grids and their potential impact on chemical shift calculations. Magn. Reson. Chem. 2020, 58, 116. Publisher’s Version
2019
117. C. Moreira, A. R. Caixto, J. Richard and S. C. L. Kamerlin. The role of ligand-gated conformational changes in enzyme catalysis. Trends Biochem. Sci. 2019, 47, 1449. Manuscript PDF
116. Y. Kulkarni and S. C. L. Kamerlin. Computational physical organic chemistry using the empirical valence bond approach. Adv. Phys. Org. Chem. 2019, 53, 69. Publisher’s Version
115. G. Yang, D. W. Anderson, F. Baier, E. Dohmen, N. Hong, P. D. Carr, S. C. L. Kamerlin, C. Jackson, E. Bornberg-Bauer and N. Tokuriki. Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme. Nat. Chem Biol. 2019, 15, 1220. Publisher’s Version
114. Y. S. Kulkarni, T. L. Amyes, J. P. Richard and S. C. L. Kamerlin. Uncovering the role of key active site side chains in catalysis: An extended Brønsted relationship for substrate deprotonation catalysed by wild-type and variants of triosephosphate isomerase. J. Am. Chem. Soc. 2019, 141, 16139. Publisher’s Version | chemRxiv Preprint
113. J. Burke, J. La Clair, R. Philippe, A. Pabis, M. Corbella, J. M. Jez, G. Cortina, M. Kaltenbach, M. E. Bowman, G. Louie, K. Woods, A. T. Nelson, D. S. Tawfik, S. C. L. Kamerlin and J. P. Noel. Bifunctional substrate activation via an arginine residue drives catalysis in chalcone isomerases. ACS Catal. 2019, 9, 8388. (Cover Article) Publisher’s Version
112. A. R. Calixto, C. Moreira, A. Pabis, C. Kötting, K. Gerwert, T. Rudack and S. C. L. Kamerlin. GTP hydrolysis without an active site base: A unifying mechanism for Ras and related GTPases. J. Am. Chem. Soc. 2019, 141, 10684. Publisher’s Version
111. D. Al-Smadi, T. R. Enugala, V. Kessler, A. R. Mhashal, S. C. L. Kamerlin, J. Kihlberg, T. Norberg and M. Widersten. Chemical and biochemical approaches for the synthesis of substituted dihydroxybutanones and di- and tri-hydroxypentanones. J. Org. Chem. 2019, 84, 6982. Publisher’s Version
110. N. Tatum, F. Duarte, S. C. L. Kamerlin and E. Pohl. Relative binding energies predict crystallographic binding modes of ethionamide booster lead compounds. J. Phys. Chem. Lett. 2019, 10, 2244. DOI: 10.1021/acs.jpclett.9b00741 Publisher’s Version
109. Q. Liao, M. Lüking, D. M. Krüger, S. Deindl, J. Elf, P. M. Kasson and S. C. L. Kamerlin. Long time-scale atomistic simulations of the structure and dynamics of transcription factor-DNA recognition. J. Phys. Chem. B 2019, 123, 3576. Manuscript PDF
108. V. Prakash, Y. Kulkarni, J. ter Beek, P. V. Scherbakova, S. C. L. Kamerlin and E. Johansson. Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε. Nature Commun. 2019, 10, 373. Manuscript PDF
107. L. Mydy, J. Cristobal, R. Katigbak, P. Bauer, A. C. Reyes, S. C. L. Kamerlin, J. Richard and A. M. Gulick. Human glycerol 3-phosphate dehydrogenase: X-ray crystal structures that guide the interpretation of mutagenesis studies. Biochemistry 2019, 58, 1061. Publisher’s Version
106. F. Baier, N. Hong, G. Yang, A. Pabis, C. M. Miton, A. Barrozo, P. D. Carr, S. C. L. Kamerlin, C. J. Jackson and N. Tokuriki. Cryptic genetic variation defines the adaptive evolutionary potential of enzymes. eLife 2019, 8:e40789. DOI: 10.7554/eLife.40789 Accepted Version | bioRxiv Preprint
2018
105. J. R. Burke, J. J. LaClair, R. N. Philippe, A. Pabis, J. M. Jez, G. A. Cortina, M. Kaltenbach, M. E. Bowman, G. V. Louie, K. B. Woods, A. T. Nelson, D. S. Tawfik, S. C. L. Kamerlin and J. P. Noel. Bifunctional substrate activation via an arginine residue drives catalysis in chalcone isomerases. bioRxiv 2018, Pre-print. DOI: 10.1101/457440 Manuscript PDF
104. P. Bauer, A. Barrozo, M. Purg, B. Amrein, M. Esguerra, P. B. Wilson, D. T. Major, J. Åqvist and S. C. L. Kamerlin. Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations. SoftwareX 2018, 7, 388. Manuscript PDF
103. C. M. Miton, S. Jonas, G. Fischer, F. Duarte, M. F. Mohamed, B. van Loo, B. Kintses, S. C. L. Kamerlin, N. Tokuriki, M. Hyvönen and F. Hollfelder. Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Proc. Natl. Acad. Sci. USA 2018, 115, E7293-E7302. Manuscript PDF
102. Q. Liao, Y. Kulkarni, U. Sengupta, D. Petrovic, A. J. Mulholland, M. W. van der Kamp, B. Strodel and S. C. L. Kamerlin. Loop motion in triosephosphate isomerase is not a simple open and shut case. J. Am. Chem. Soc. 2018, 140, 15889-15903. Manuscript PDF
101. N.-S. Hong, D. Petrović, R. Lee, G. Gryn’ova, M. Purg, J. Saunders, P. Bauer, P. Carr, C.-Y. Lin, P. Mabbitt, W. Zhang, T. Altamore, C. Easton, M. Coote, S. C. L. Kamerlin and C. Jackson. The evolution of multiple active site configurations in a designed enzyme. Nature Commun. 2018, 9, 3900 Manuscript PDF
100. M. Purg and S. C. L. Kamerlin. Empirical valence bond simulations of the evolution of enzyme function. Methods Enz. 2018, in Phosphatases. Ed. K. Allen. Manuscript PDF
99. B. Amrein, A. Runthala and S. C. L. Kamerlin. In silico directed evolution using CADEE. Methods Mol. Biol. 2018, in Computational Methods in Protein Evolution. Ed. T. T. Sikosek. Purchase Volume
98. D. R. Uduwela, A. Pabis, B. J. Stevenson, S. C. L. Kamerlin and M. Mcleod. Enhancing the steroid sulfatase activity of the arylsulfatase from Pseudomonas aeruginosa. ACS Catal. 2018, 8, 8902. Manuscript PDF Dryad Data Package
97. D. Petrović and S. C. L. Kamerlin. Molecular modeling of conformational dynamics and its role in enzyme evolution. Curr. Opin. Struct. Biol. 2018, 52, 50. Manuscript PDF
96. D. Maurer, T. R. Enugala, E. Hamnevik, P. Bauer, M. Lüking, H. Hiller, S. C. L. Kamerlin, D. Dobritzsch and M. Widersten. Stereo- and regioselectivity in catalyzed transformation of a 1,2-disubstituted vicinal diol and the corresponding diketone by wild type and laboratory evolved alcohol dehydrogenases. ACS Catal. 2018, 8, 7526. Manuscript PDF
95. D. Petrović, V. A. Risso, S. C. L. Kamerlin and J. M. Sanchéz-Ruiz. Conformational dynamics and enzyme evolution. J. R. Soc. Interface 2018, 15, 20180330. Manuscript PDF
94. N. Österlund, Y. Kulkarni, A. Misiaszek, C. Wallin, D. M. Krüger, Q. Liao, F. Mashayekhy Rad, J. Jarvet, B. Strodel, S. K. T. S. Wärmländer, L. Ilag, S. C. L. Kamerlin and A. Gräslund. Amyloid β-peptide interactions with amphiphilic surfactants: Electrostatic and hydrophobic effects. ACS Chem. Neurosci. 2018, 9, 1680. Manuscript PDF
93. M. Kaltenbach, J. Burke, M. Dindo, A. Pabis, F. Steffen-Munsberg, A. Rabin, S. C. L. Kamerlin, J. Noel and D. Tawfik. Evolution of chalcone isomerase from a non-catalytic ancestor. Nat. Chem. Biol. 2018, 14, 548. Manuscript PDF bioRxiv Preprint
92. A. Maršavelski, D. Petrović, P. Bauer, R. Vianello and S. C. L. Kamerlin. Empirical valence bond simulations suggest a direct hydride transfer mechanism for human diamine oxidase. ACS Omega 2018, 3, 3665. Manuscript PDF
91. A. Barrozo, Q. Liao, M. Esguerra, G. Marloie, J. Florián, N. H. Williams and S. C. L. Kamerlin. Computer simulations of the catalytic mechanisms of wild-type and mutant β-phosphoglucomutase. Org. Biomol. Chem. 2018, 16, 2060. Manuscript PDF
90. Y. Kulkarni, Q. Liao, F. Byléhn, T. Amyes, J. Richard and S. C. L. Kamerlin. The role of ligand- driven conformational changes in enzyme catalysis: Modeling the reactivity of the catalytic cage of triosephosphate isomerase. J. Am. Chem. Soc. 2018, 140, 3854. Manuscript PDF
89. Å. Janfalk-Carlsson, P. Bauer, D. Dobritzsch, S. C. L. Kamerlin and M. Widersten. Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme. IUCrJ 2018, 5. Manuscript PDF
88. D. Petrović, K. Szeler and S. C. L. Kamerlin. Challenges and advances in the computational modeling of biological phosphate hydrolysis. ChemComm 2018, 54, 377 (Cover, Feature and HOT Article). Manuscript PDF
87. A. Pabis, V. Risso, J. M. Sanchéz-Ruiz and S. C. L. Kamerlin. Cooperativity and flexibility in enzyme evolution. Curr. Opin. Struct. Biol. 2018, 48, 83. Manuscript PDF
2017
86. 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. 2017, 139, 17533. 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 Dryad Data Package
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. Sanchéz-Ruiz. De novo active sites for resurrected Precambrian enzymes. Nat. Commun. 2017, 8, 16113. Publisher’s PDF Dryad Data Package
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 2017. Purchase 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, 50. 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. Biochemistry2016, 55, 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
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