Lynn Kamerlin
Professor
Publications
Displaying of publications. Sorted by year, then title.
Engineering the substrate scope of the thermostable phenolic acid decarboxylase N31 towards sterically hindered phenolic acids
Kristin K.F. Bauer, Sonja Vaupel, Jacques Gay, Eva Vos, Aron Wanz, et al.
(2026) Protein Science, 35
ArticleMyosin Post-Translational Modifications Associated With Critical Illness Myopathy
Fernando Ribeiro, Bruno Di Geronimo, Nicola Cacciani, Anna Widgren, Yvette Hedström, et al.
(2026) Acta Physiologica, 242
ArticleThe borderlands of foldability : lessons from simplified proteins
Koh Seya, Alfie Louise R. Brownless, Shina C.L. Kamerlin, Liam M. Longo
(2026) Trends in Chemistry, 8 p.362-376
Review articleLoop dynamics, allostery, and function in protein tyrosine phosphatases : insights from molecular simulations
Colin L. Welsh, Shina Caroline Lynn Kamerlin
(2026) Biochemical Society Transactions, 54 p.1-12
Review articleConformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase
Dariia Yehorova, Nikolas Alansson, Ruidan Shen, Joshua M. Denson, Michael Robinson, et al.
(2026) JACS Au, 6 p.59-81
ArticleTargeting MarA N-terminal domain dynamics to prevent DNA binding
Marina Corbella, Cátia Moreira, Roberto Bello-Madruga, Marc Torrent Burgas, Shina C L Kamerlin, et al.
(2025) Protein Science, 34
ArticleThe need to implement FAIR principles in biomolecular simulations
R.E. Amaro, S.C.L. Kamerlin, M. Orozco
(2025) Nature Methods, 22 p.641-645
ArticleWatCon : A Python Tool for Analysis of Conserved Water Networks Across Protein Families
Alfie Louise R. Brownless, Travis Harrison-Rawn, Shina C.L. Kamerlin
(2025) JACS Au, 5 p.6379-6395
ArticleGenerative AI techniques for conformational diversity and evolutionary adaptation of proteins
Alfie Louise R. Brownless, Dariia Yehorova, Colin L. Welsh, Shina Caroline Lynn Kamerlin
(2025) Current Opinion in Structural Biology, 94
Review articleMechanistic Elucidation and Stereochemical Consequences of Alternative Binding of Alkenyl Substrates by Engineered Arylmalonate Decarboxylase
Elske van der Pol, Thomas Schlatzer, Gyula Hoffka, Bruno Di Geronimo, Johannes Eder, et al.
(2025) Journal of the American Chemical Society, 147 p.39271-39283
ArticleComplete computational design of high-efficiency Kemp elimination enzymes
Dina Listov, Eva Vos, Gyula Hoffka, Shlomo Yakir Hoch, Andrej Berg, et al.
(2025) Nature, 643 p.1421-1427
ArticleEnzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic Hotspots
Luis I. Gutierrez-Rus, Eva Vos, David Pantoja-Uceda, Gyula Hoffka, Jose Gutierrez-Cardenas, et al.
(2025) Journal of the American Chemical Society, 147 p.14978-14996
ArticleRedefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases
Andrey O. Demkiv, Saacnicteh Toledo-Patiño, Encarnación Medina-Carmona, Andrej Berg, Gaspar P. Pinto, et al.
(2025) Molecular biology and evolution, 42
ArticleThe winter holidays are glorious-except when they're not
Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.5223-5224
Debate/Note/EditorialCatalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases
Marina Corbella, Joe Bravo, Andrey O Demkiv, Ana Rita Calixto, Kitty Sompiyachoke, et al.
(2024) JACS Au, 4 p.3519-3536
ArticleConformational Modulation of a Mobile Loop Controls Catalysis in the (βα)8-Barrel Enzyme of Histidine Biosynthesis HisF
Enrico Hupfeld, Sandra Schlee, Jan Philip Wurm, Chitra Rajendran, Dariia Yehorova, et al.
(2024) JACS Au, 4 p.3258-3276
ArticleSHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases
Ruidan Shen, Alfie-Louise R Brownless, Nikolas Alansson, Marina Corbella, Shina C L Kamerlin, et al.
(2024) JACS Au, 4 p.2874-2885
ArticleArtificial, biomimetic and hybrid enzymes : general discussion
Carlos Acevedo-Rocha, Amulyasai Bakshi, Uwe T Bornscheuer, Dominic J Campopiano, Janko Čivić, et al.
(2024) Faraday Discussions, 252 p.354-386
Debate/Note/EditorialMandatory national language requirements in higher education
Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.3739-3740
Debate/Note/EditorialIn vitro fertilization and the ethics of frozen embryos
Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.2817-2818
Debate/Note/EditorialSequence - dynamics - function relationships in protein tyrosine phosphatases
Rory M Crean, Marina Corbella, Ana R Calixto, Alvan C Hengge, Shina C L Kamerlin
(2024) QRB Discovery, 5
ArticleKey interaction networks : Identifying evolutionarily conserved non-covalent interaction networks across protein families
Dariia Yehorova, Rory M Crean, Peter M Kasson, Shina C L Kamerlin
(2024) Protein Science, 33
ArticleThe ineligibility barrier for international researchers in US academia
Mikael H Elias, Kitty Sompiyachoke, Facundo M Fernández, Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.457-458
Debate/Note/EditorialHow to write a successful graduate school application
Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.1-2
Debate/Note/EditorialLoop dynamics and the evolution of enzyme activity
Marina Corbella, Gaspar P Pinto, Shina C L Kamerlin
(2023) Nature reviews. Chemistry, 7 p.536-547
Review articleProgress in using deep learning to treat cancer
Shina Caroline Lynn Kamerlin
(2023) Nature computational science, 3 p.739-740
ArticleA sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides
Vimal Parkash, Yashraj Kulkarni, Göran O. Bylund, Pia Osterman, Shina Caroline Lynn Kamerlin, et al.
(2023) Nucleic Acids Research, 51 p.11225-11238
ArticleScience after Brexit : bright spots on the Horizon?
Adrian J Mulholland, Shina Caroline Lynn Kamerlin
(2023) EMBO Reports, 24
Debate/Note/EditorialKIF-Key Interactions Finder : A program to identify the key molecular interactions that regulate protein conformational changes
Rory M Crean, Joanna S G Slusky, Peter M Kasson, Shina Caroline Lynn Kamerlin
(2023) The Journal of chemical physics, 158
ArticleConformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation
Alessandro Crnjar, Aransa Griñen, Shina C L Kamerlin, César A Ramírez-Sarmiento
(2023) ACS organic & inorganic Au, 3 p.109-119
ArticleThe perceived decline of "disruptive" science and technology
Shina Caroline Lynn Kamerlin
(2023) EMBO Reports, 24
Debate/Note/EditorialQ-RepEx : A Python pipeline to increase the sampling of empirical valence bond simulations
Sebastian Brickel, Andrey O Demkiv, Rory M Crean, Gaspar P Pinto, Shina Caroline Lynn Kamerlin
(2023) Journal of Molecular Graphics and Modelling, 119
Article5 suggestions to increase grant application success rates
Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Debate/Note/EditorialInsights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases
Ruidan Shen, Rory M Crean, Keith J Olsen, Marina Corbella, Ana R Calixto, et al.
(2022) Chemical Science, 13 p.13524-13540
ArticleAllosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation
Gemma Fisher, Marina Corbella, Magnus S Alphey, John Nicholson, Benjamin J Read, et al.
(2022) Nature Communications, 13
ArticleScholars in peril : when being a scientist can land you in jail (or worse)
Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Debate/Note/EditorialA Structural View into the Complexity of Carbon Dioxide Fixation
Robert Kourist, Shina Caroline Lynn Kamerlin
(2022) ACS Central Science, 8 p.1040-1042
ArticleLate-termination of pregnancy for medical reasons : when abortion isn't really by choice
Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Debate/Note/EditorialComplex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis
Adrian Romero-Rivera, Marina Corbella, Antonietta Parracino, Wayne M Patrick, Shina Caroline Lynn Kamerlin
(2022) JACS Au, 2 p.943-960
ArticleComputational Advances in Protein Engineering and Enzyme Design
Etienne Derat, Shina Caroline Lynn Kamerlin
(2022) The Journal of Physical Chemistry Part B, 126 p.2449-2451
ArticleEssential Functional Interplay of the Catalytic Groups in Acid Phosphatase
Martin Pfeiffer, Rory M Crean, Catia Moreira, Antonietta Parracino, Gustav Oberdorfer, et al.
(2022) ACS Catalysis, 12 p.3357-3370
ArticleAdventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021)
Colin Jackson, Agnes Toth-Petroczy, Rachel Kolodny, Florian Hollfelder, Monika Fuxreiter, et al.
(2022) Journal of Molecular Biology, 434
Review articleFrom flying cats to dancing proteins
Shina Caroline Lynn Kamerlin
(2022) Nature reviews. Chemistry, 6
Review (Book/Film/Exhibition/etc.)Exploiting enzyme evolution for computational protein design
Gaspar P Pinto, Marina Corbella, Andrey O Demkiv, Shina Caroline Lynn Kamerlin
(2022) Trends in Biochemical Sciences, 47 p.375-389
Review articleHow to write a successful postdoc application - the PI perspective
Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Debate/Note/EditorialPrenatal genetic screening and the evolving quest for "perfect babies" : at what cost for genetic diversity?
Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Debate/Note/EditorialSingle Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases
Ruidan Shen, Rory M Crean, Sean J Johnson, Shina C L Kamerlin, Alvan C Hengge
(2021) JACS Au, 1 p.646-659
ArticleThe N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition
Marina Corbella, Qinghua Liao, Cátia Moreira, Antonietta Parracino, Peter M Kasson, et al.
(2021) The Journal of Physical Chemistry Part B, 125 p.6791-6806
ArticleAcademic motherhood - what happens when you can't make it happen?
Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Debate/Note/EditorialHeme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
Gloria Gamiz-Arco, Luis I Gutierrez-Rus, Valeria A Risso, Beatriz Ibarra-Molero, Yosuke Hoshino, et al.
(2021) Nature Communications, 12
ArticleLoop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases
Rory M. Crean, Michal Biler, Marc W. Van Der Kamp, Alvan C. Hengge, Shina C.L. Kamerlin
(2021) Journal of the American Chemical Society, 143 p.3830-3845
ArticleOpen Access, Plan S, and researchers' needs
Shina Caroline Lynn Kamerlin
(2020) EMBO Reports, 21
Debate/Note/EditorialWhen we increase diversity in academia, we all win
Shina Caroline Lynn Kamerlin
(2020) EMBO Reports, 21
Debate/Note/EditorialGround-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase
Michal Biler, Rory M Crean, Anna K Schweiger, Robert Kourist, Shina Caroline Lynn Kamerlin
(2020) Journal of the American Chemical Society, 142 p.20216-20231
ArticleModeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase
Anil R Mhashal, Adrian Romero-Rivera, Lisa S Mydy, Judith R Cristobal, Andrew M Gulick, et al.
(2020) ACS Catalysis, 10 p.11253-11267
ArticleEnhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening
Valeria A Risso, Adrian Romero-Rivera, Luis I Gutierrez-Rus, Mariano Ortega-Muñoz, Francisco Santoyo-Gonzalez, et al.
(2020) Chemical Science, 11 p.6134-6148
ArticleManaging Coronavirus Disease 2019 Spread With Voluntary Public Health Measures : Sweden as a Case Study for Pandemic Control
Shina C L Kamerlin, Peter M Kasson
(2020) Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 71 p.3174-3181
ArticleFemale Faculty : Why So Few and Why Care?
Shina Caroline Lynn Kamerlin, Pernilla Wittung-Stafshede
(2020) Chemistry: A European Journal, 26 p.8319-8323
ArticleHarnessing Conformational Plasticity to Generate Designer Enzymes
Rory M Crean, Jasmine M Gardner, Shina C L Kamerlin
(2020) Journal of the American Chemical Society, 142 p.11324-11342
Review articleModeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters : A Mechanistic Study
Klaudia Szeler, Nicholas H Williams, Alvan C Hengge, Shina C L Kamerlin
(2020) The Journal of Organic Chemistry, 85 p.6489-6497
ArticleRecent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation
Ana Rita Calixto, Cátia Moreira, Shina Caroline Lynn Kamerlin
(2020) ACS Omega, 5 p.4380-4385
Review articleShort and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes
Liam M Longo, Dušan Petrović, Shina Caroline Lynn Kamerlin, Dan S Tawfik
(2020) Proceedings of the National Academy of Sciences of the United States of America, 117 p.5310-5318
ArticleEnzyme Evolution : An Epistatic Ratchet versus a Smooth Reversible Transition
Moshe Ben-David, Misha Soskine, Artem Dubovetskyi, Kesava-Phaneendra Cherukuri, Orly Dym, et al.
(2020) Molecular biology and evolution, 37 p.1133-1147
ArticleErrors in DFT integration grids and their potential impact on chemical shift calculations
Philippe B Wilson, Martin Grootveld, Shina Caroline Lynn Kamerlin
(2020) Magnetic Resonance in Chemistry, 58 p.116-117
ArticleCryptic genetic variation shapes the adaptive evolutionary potential of enzymes
Florian Baier, Nansook Hong, Gloria Yang, Anna Pabis, Charlotte M Miton, et al.
(2019) eLife, 8
ArticleThe role of ligand-gated conformational changes in enzyme catalysis
Cátia Moreira, Ana Rita Calixto, John P Richard, Shina Caroline Lynn Kamerlin
(2019) Biochemical Society Transactions, 47 p.1449-1460
Review articleUncovering the Role of Key Active-Site Side Chains in Catalysis : An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase
Yashraj S Kulkarni, Tina L Amyes, John P Richard, Shina C L Kamerlin
(2019) Journal of the American Chemical Society, 141 p.16139-16150
ArticleGTP Hydrolysis Without an Active Site Base : A Unifying Mechanism for Ras and Related GTPases
Ana R Calixto, Cátia Moreira, Anna Pabis, Carsten Kötting, Klaus Gerwert, et al.
(2019) Journal of the American Chemical Society, 141 p.10684-10701
ArticleRelative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds
Natalie J Tatum, Fernanda Duarte, Shina C L Kamerlin, Ehmke Pohl
(2019) The Journal of Physical Chemistry Letters, 10 p.2244-2249
ArticleStructural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε
Vimal Parkash, Yashraj Kulkarni, Josy Ter Beek, Polina V Shcherbakova, Shina Caroline Lynn Kamerlin, et al.
(2019) Nature Communications, 10
ArticleHuman Glycerol 3-Phosphate Dehydrogenase : X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies
Lisa S Mydy, Judith R Cristobal, Roberto D Katigbak, Paul Bauer, Archie C Reyes, et al.
(2019) Biochemistry, 58 p.1061-1073
ArticleIn Silico-Directed Evolution Using CADEE
Beat Anton Amrein, Ashish Runthala, Shina Caroline Lynn Kamerlin
(2019) Methods in molecular biology (Clifton, N.J.), 1851 p.381-415
ArticleHigher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme
Gloria Yang, Dave W Anderson, Florian Baier, Elias Dohmen, Nansook Hong, et al.
(2019) Nature Chemical Biology, 15 p.1120-1128
ArticleRole of Ligand-Driven Conformational Changes in Enzyme Catalysis : Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase
Yashraj S Kulkarni, Qinghua Liao, Fabian Byléhn, Tina L Amyes, John P Richard, et al.
(2018) Journal of the American Chemical Society, 140 p.3854-3857
ArticleLoop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case
Qinghua Liao, Yashraj Kulkarni, Ushnish Sengupta, Dušan Petrović, Adrian J Mulholland, et al.
(2018) Journal of the American Chemical Society, 140 p.15889-15903
ArticleDebate on academic freedom and open access is healthy
J Britt Holbrook, Stephen Curry, Shina C L Kamerlin
(2018) Nature, 562
Debate/Note/EditorialThe evolution of multiple active site configurations in a designed enzyme
Nan-Sook Hong, Dušan Petrović, Richmond Lee, Ganna Gryn'ova, Miha Purg, et al.
(2018) Nature Communications, 9
ArticleEmpirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase
Aleksandra Maršavelski, Dušan Petrović, Paul Bauer, Robert Vianello, Shina Caroline Lynn Kamerlin
(2018) ACS Omega, 3 p.3665-3674
ArticleConformational dynamics and enzyme evolution
Dušan Petrović, Valeria A Risso, Shina Caroline Lynn Kamerlin, Jose M Sanchez-Ruiz
(2018) Journal of the Royal Society, Interface, 15
Review articleEvolutionary repurposing of a sulfatase : A new Michaelis complex leads to efficient transition state charge offset
Charlotte M Miton, Stefanie Jonas, Gerhard Fischer, Fernanda Duarte, Mark F Mohamed, et al.
(2018) Proceedings of the National Academy of Sciences of the United States of America, 115 p.E7293-E7302
ArticleEpoxide hydrolysis as a model system for understanding flux through a branched reaction scheme
Åsa Janfalk Carlsson, Paul Bauer, Doreen Dobritzsch, Shina C L Kamerlin, Mikael Widersten
(2018) IUCrJ, 5 p.269-282
Review articleEvolution of chalcone isomerase from a noncatalytic ancestor
Miriam Kaltenbach, Jason R Burke, Mirco Dindo, Anna Pabis, Fabian S Munsberg, et al.
(2018) Nature Chemical Biology, 14 p.548-555
ArticleEmpirical Valence Bond Simulations of Organophosphate Hydrolysis : Theory and Practice
Miha Purg, Shina Caroline Lynn Kamerlin
(2018) Methods in Enzymology , p.3-51
Book chapterAmyloid-β Peptide Interactions with Amphiphilic Surfactants : Electrostatic and Hydrophobic Effects
Nicklas Österlund, Yashraj S Kulkarni, Agata D Misiaszek, Cecilia Wallin, Dennis M Krüger, et al.
(2018) ACS Chemical Neuroscience, 9 p.1680-1692
ArticleComputer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase
Alexandre Barrozo, Qinghua Liao, Mauricio Esguerra, Gaël Marloie, Jan Florián, et al.
(2018) Organic and Biomolecular Chemistry, 16 p.2060-2073
ArticleChallenges and advances in the computational modeling of biological phosphate hydrolysis
Dušan Petrović, Klaudia Szeler, Shina Caroline Lynn Kamerlin
(2018) Chemical Communications, 54 p.3077-3089
Review articleCooperativity and flexibility in enzyme evolution
Anna Pabis, Valeria A Risso, Jose M Sanchez-Ruiz, Shina Cl Kamerlin
(2018) Current Opinion in Structural Biology, 48 p.83-92
Review articleCADEE : Computer-Aided Directed Evolution of Enzymes
Beat Anton Amrein, Fabian Steffen-Munsberg, Ireneusz Szeler, Miha Purg, Yashraj Kulkarni, et al.
(2017) IUCrJ, 4 p.50-64
ArticleShuffling Active Site Substate Populations Affects Catalytic Activity : The Case of Glucose Oxidase
Dušan Petrović, David Frank, Shina Caroline Lynn Kamerlin, Kurt Hoffmann, Birgit Strodel
(2017) ACS Catalysis, 7 p.6188-6197
ArticleSimilar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis : Implications for Biotherapeutic Engineering
Miha Purg, Mikael Elias, Shina Caroline Lynn Kamerlin
(2017) Journal of the American Chemical Society, 139 p.17533-17546
ArticleExtending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions
Qinghua Liao, Anna Pabis, Birgit Strodel, Shina Caroline Lynn Kamerlin
(2017) The Journal of Physical Chemistry Letters, 8 p.5408-5414
ArticleMicelle Maker : An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations
Dennis M Krüger, Shina C L Kamerlin
(2017) ACS Omega, 2 p.4524-4530
ArticleSimulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer
Anna Pabis, Nicholas H Williams, Shina C L Kamerlin
(2017) Organic and Biomolecular Chemistry, 15 p.7308-7316
ArticleDNA 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
Sergey N Maximoff, Shina Caroline Lynn Kamerlin, Jan Florián
(2017) The Journal of Physical Chemistry Part B, 121 p.7813-7822
ArticleDe novo active sites for resurrected Precambrian enzymes
Valeria A Risso, Sergio Martinez-Rodriguez, Adela M Candel, Dennis M Krüger, David Pantoja-Uceda, et al.
(2017) Nature Communications, 8
ArticleEnzyme Architecture : Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
Yashraj S Kulkarni, Qinghua Liao, Dušan Petrović, Dennis M Krüger, Birgit Strodel, et al.
(2017) Journal of the American Chemical Society, 139 p.10514-10525
ArticleCapturing the Role of Explicit Solvent in the Dimerization of RuV(bda) Water Oxidation Catalysts
Shaoqi Zhan, Daniel Mårtensson, Miha Purg, Shina C L Kamerlin, Mårten S G Ahlquist
(2017) Angewandte Chemie (International edition), 56 p.6962-6965
ArticleActive Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes : The Case of Serum Paraoxonase 1
David Blaha-Nelson, Dennis M Krüger, Klaudia Szeler, Moshe Ben-David, Shina Caroline Lynn Kamerlin
(2017) Journal of the American Chemical Society, 139 p.1155-1167
ArticleProbing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase
Miha Purg, Anna Pabis, Florian Baier, Nobuhiko Tokuriki, Colin Jackson, et al.
(2016) Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Science, 374
ArticleThe Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis
Fernanda Duarte, Alexandre Barrozo, Johan Åqvist, Nicholas H Williams, Shina C L Kamerlin
(2016) Journal of the American Chemical Society, 138 p.10664-73
ArticleLaboratory-Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis
Åsa Janfalk Carlsson, Paul Bauer, Doreen Dobritzsch, Mikael Nilsson, S C Lynn Kamerlin, et al.
(2016) ChemBioChem, 17 p.1693-7
ArticleCharacterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease
Cecilia Wallin, Yashraj S Kulkarni, Axel Abelein, Jüri Jarvet, Qinghua Liao, et al.
(2016) Journal of Trace Elements in Medicine and Biology, 38 p.183-193
ArticleWhere are the female science professors? : A personal perspective
Shina Caroline Lynn Kamerlin
(2016) F1000Research, 5
ArticlePromiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer
Anna Pabis, Fernanda Duarte, Shina C L Kamerlin
(2016) Biochemistry, 55 p.3061-81
Review articleConformational diversity and enantioconvergence in potato epoxide hydrolase 1
P Bauer, Å Janfalk Carlsson, B A Amrein, D Dobritzsch, M Widersten, et al.
(2016) Organic and Biomolecular Chemistry, 14 p.5639-51
ArticleLinking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)
Huan Ma, Klaudia Szeler, Shina C L Kamerlin, Mikael Widersten
(2016) Chemical Science, 7 p.1415-1421
ArticlePromiscuity and electrostatic flexibility in the alkaline phosphatase superfamily
Anna Pabis, Shina Caroline Lynn Kamerlin
(2016) Current Opinion in Structural Biology, 37 p.14-21
Review articleCatalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1
Moshe Ben-David, Joel L Sussman, Christopher I Maxwell, Klaudia Szeler, Shina C L Kamerlin, et al.
(2015) Journal of Molecular Biology, 427 p.1359-1374
ArticleHypercompetition in biomedical research evaluation and its impact on young scientist careers
Shina Caroline Lynn Kamerlin
(2015) International microbiology : the official journal of the Spanish Society for Microbiology, 18 p.253-61
ArticleExpanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes
Beat A Amrein, Paul Bauer, Fernanda Duarte, Åsa Janfalk Carlsson, Agata Naworyta, et al.
(2015) ACS Catalysis, 5 p.5702-5713
ArticleExceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome
Johan Åqvist, Shina C L Kamerlin
(2015) Scientific Reports, 5
ArticleDevelopment and Application of a Nonbonded Cu2+ Model That Includes the Jahn-Teller Effect
Qinghua Liao, Shina Caroline Lynn Kamerlin, Birgit Strodel
(2015) The Journal of Physical Chemistry Letters, 6 p.2657-62
ArticleCooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily
Alexandre Barrozo, Fernanda Duarte, Paul Bauer, Alexandra T P Carvalho, Shina C L Kamerlin
(2015) Journal of the American Chemical Society, 137 p.9061-76
ArticleUnderstanding thio-effects in simple phosphoryl systems : role of solvent effects and nucleophile charge
Alexandra T P Carvalho, AnnMarie C O'Donoghue, David R W Hodgson, Shina C L Kamerlin
(2015) Organic and Biomolecular Chemistry, 13 p.5391-8
ArticleModeling the mechanisms of biological GTP hydrolysis
Alexandra T P Carvalho, Klaudia Szeler, Konstantinos Vavitsas, Johan Åqvist, Shina C L Kamerlin
(2015) Archives of Biochemistry and Biophysics, 582 p.80-90
Review articleThe conformation of a catalytic loop is central to GTPase activity on the ribosome
Johan Åqvist, Shina C L Kamerlin
(2015) Biochemistry, 54 p.546-56
ArticleResolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis
Fernanda Duarte, Johan Åqvist, Nicholas H Williams, Shina C L Kamerlin
(2015) Journal of the American Chemical Society, 137 p.1081-93
ArticleHow valence bond theory can help you understand your (bio)chemical reaction
Avital Shurki, Etienne Derat, Alexandre Barrozo, Shina Caroline Lynn Kamerlin
(2015) Chemical Society Reviews, 44 p.1037-52
Review articleRecent advances in QM/MM free energy calculations using reference potentials
Fernanda Duarte, Beat A Amrein, David Blaha-Nelson, Shina C L Kamerlin
(2015) Biochimica et Biophysica Acta, 1850 p.954-965
Review articleUnderstanding the structural and dynamic consequences of DNA epigenetic modifications : Computational insights into cytosine methylation and hydroxymethylation
Alexandra T P Carvalho, Leonor Gouveia, Charan Raju Kanna, Sebastian K T S Wärmländer, Jamie A Platts, et al.
(2014) Epigenetics, 9 p.1604-12
ArticleChallenges in computational studies of enzyme structure, function and dynamics
Alexandra T P Carvalho, Alexandre Barrozo, Dvir Doron, Alexandra Vardi Kilshtain, Dan Thomas Major, et al.
(2014) Journal of Molecular Graphics and Modelling, 54 p.62-79
ArticleEmpirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine
Matej Repič, Robert Vianello, Miha Purg, Fernanda Duarte, Paul Bauer, et al.
(2014) Proteins, 82 p.3347-55
ArticleEditorial overview : Mechanisms: Chemical and computational probes of biological mechanism
AnnMarie C O'Donoghue, Shina C L Kamerlin
(2014) Current Opinion in Chemical Biology, 21 p.viii-x
Debate/Note/EditorialForce field independent metal parameters using a nonbonded dummy model
Fernanda Duarte, Paul Bauer, Alexandre Barrozo, Beat Anton Amrein, Miha Purg, et al.
(2014) The Journal of Physical Chemistry Part B, 118 p.4351-62
ArticleConcerted or stepwise : how much do free-energy landscapes tell us about the mechanisms of elimination reactions?
Fernanda Duarte, Scott Gronert, Shina Caroline Lynn Kamerlin
(2014) The Journal of Organic Chemistry, 79 p.1280-8
ArticleThe alkaline hydrolysis of sulfonate esters : challenges in interpreting experimental and theoretical data
Fernanda Duarte, Ting Geng, Gaël Marloie, Adel O Al Hussain, Nicholas H Williams, et al.
(2014) The Journal of Organic Chemistry, 79 p.2816-28
ArticleWhy nature really chose phosphate
Shina C L Kamerlin, Pankaz K Sharma, Ram B Prasad, Arieh Warshel
(2013) Quarterly Reviews of Biophysics, 46 p.1-132
Review articleModeling catalytic promiscuity in the alkaline phosphatase superfamily
Fernanda Duarte, Beat Anton Amrein, Shina Caroline Lynn Kamerlin
(2013) Physical chemistry chemical physics : PCCP, 15 p.11160-77
ArticleEnergetics of activation of GTP hydrolysis on the ribosome
Göran Wallin, Shina C L Kamerlin, Johan Åqvist
(2013) Nature Communications, 4
ArticleCellular polyamines promote amyloid-beta (Aβ) peptide fibrillation and modulate the aggregation pathways
Jinghui Luo, Chien-Hung Yu, Huixin Yu, Rok Borstnar, Shina C L Kamerlin, et al.
(2013) ACS Chemical Neuroscience, 4 p.454-62
ArticleComputational protein engineering : bridging the gap between rational design and laboratory evolution
Alexandre Barrozo, Rok Borstnar, Gaël Marloie, Shina Caroline Lynn Kamerlin
(2012) International Journal of Molecular Sciences, 13 p.12428-60
Review articleBase-catalyzed dehydration of 3-substituted benzene cis-1,2-dihydrodiols : stabilization of a cyclohexadienide anion intermediate by negative aromatic hyperconjugation
Jaya Satyanarayana Kudavalli, S Nagaraja Rao, David E Bean, Narain D Sharma, Derek R Boyd, et al.
(2012) Journal of the American Chemical Society, 134 p.14056-69
ArticleComputational Study of the pKa Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B
Rok Borštnar, Matej Repič, Shina Caroline Lynn Kamerlin, Robert Vianello, Janez Mavri
(2012) Journal of Chemical Theory and Computation, 8 p.3864-70
ArticleCatalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution
Jinghui Luo, Bert van Loo, Shina C L Kamerlin
(2012) FEBS Letters, 586 p.1622-30
ArticleExamining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase : a comparison to analogous phosphatases
Jinghui Luo, Bert van Loo, S C L Kamerlin
(2012) Proteins, 80 p.1211-26
ArticleCoarse-grained (multiscale) simulations in studies of biophysical and chemical systems
Shina C L Kamerlin, Spyridon Vicatos, Anatoly Dryga, Arieh Warshel
(2011) Annual Review of Physical Chemistry, 62 p.41-64
Review articleMultiscale modeling of biological functions
Shina Caroline Lynn Kamerlin, Arieh Warshel
(2011) Physical chemistry chemical physics : PCCP, 13 p.10401-11
Review articleTheoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution : implications for enzyme-catalyzed sulfuryl transfer
Shina Caroline Lynn Kamerlin
(2011) The Journal of Organic Chemistry, 76 p.9228-38
ArticleCatalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
Andrew J Adamczyk, Jie Cao, Shina C L Kamerlin, Arieh Warshel
(2011) Proceedings of the National Academy of Sciences of the United States of America, 108 p.14115-20
ArticleParadynamics : an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks
Nikolay V Plotnikov, Shina C L Kamerlin, Arieh Warshel
(2011) The Journal of Physical Chemistry Part B, 115 p.7950-62
ArticleThe effect of leaving group on mechanistic preference in phosphate monoester hydrolysis
Shina C L Kamerlin, John Wilkie
(2011) Organic and Biomolecular Chemistry, 9 p.5394-406
ArticleKetosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization
Shina C L Kamerlin, Pankaz K Sharma, Zhen T Chu, Arieh Warshel
(2010) Proceedings of the National Academy of Sciences of the United States of America, 107 p.4075-80
ArticleExamining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues
Shina Caroline Lynn Kamerlin, Janez Mavri, A Warshel
(2010) FEBS Letters, 584 p.2759-66
Review articleAn Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling
Shina C L Kamerlin, Arieh Warshel
(2010) Journal of Physical Organic Chemistry, 23 p.677-684
ArticleAt the dawn of the 21st century : Is dynamics the missing link for understanding enzyme catalysis?
Shina C L Kamerlin, Arieh Warshel
(2010) Proteins, 78 p.1339-75
Review articleOn catalytic preorganization in oxyanion holes : highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models
Shina C L Kamerlin, Zhen T Chu, A Warshel
(2010) The Journal of Organic Chemistry, 75 p.6391-401
ArticleThe EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions
Shina C L Kamerlin, Arieh Warshel
(2010) Faraday Discussions, 145 p.71-106
ArticleOn the energetics of ATP hydrolysis in solution
Shina C L Kamerlin, Arieh Warshel
(2009) The Journal of Physical Chemistry Part B, 113 p.15692-8
ArticleProgress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins : accelerated QM/MM studies of pKa, redox reactions and solvation free energies
Shina C L Kamerlin, Maciej Haranczyk, Arieh Warshel
(2009) The Journal of Physical Chemistry Part B, 113 p.1253-72
Review articleA computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution : implications for the mechanism of DNA polymerases
Shina C L Kamerlin, Charles E McKenna, Myron F Goodman, A Warshel
(2009) Biochemistry, 48 p.5963-71
ArticleEnzyme millisecond conformational dynamics do not catalyze the chemical step
Andrei V Pisliakov, Jie Cao, Shina C L Kamerlin, Arieh Warshel
(2009) Proceedings of the National Academy of Sciences of the United States of America, 106 p.17359-64
ArticleAre mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? : A comparative study of continuum, explicit and mixed solvation models
Shina C L Kamerlin, Maciej Haranczyk, Arieh Warshel
(2009) ChemPhysChem, 10 p.1125-34
ArticleOn unjustifiably misrepresenting the EVB approach while simultaneously adopting it
Shina C L Kamerlin, Jie Cao, Edina Rosta, Arieh Warshel
(2009) The Journal of Physical Chemistry Part B, 113 p.10905-15
ArticleDineopentyl phosphate hydrolysis : evidence for stepwise water attack
Shina C L Kamerlin, Nicholas H Williams, Arieh Warshel
(2008) The Journal of Organic Chemistry, 73 p.6960-9
ArticleOn the interpretation of the observed linear free energy relationship in phosphate hydrolysis : a thorough computational study of phosphate diester hydrolysis in solution
Edina Rosta, Shina C L Kamerlin, Arieh Warshel
(2008) Biochemistry, 47 p.3725-35
ArticleAssociative versus dissociative mechanisms of phosphate monoester hydrolysis : on the interpretation of activation entropies
Shina C L Kamerlin, Jan Florián, Arieh Warshel
(2008) ChemPhysChem, 9 p.1767-73
ArticleA molecular dynamics study of WPD-loop flexibility in PTP1B
Shina Caroline Lynn Kamerlin, Robert Rucker, Stefan Boresch
(2007) Biochemical and Biophysical Research Communications, 356 p.1011-6
ArticleThe role of metal ions in phosphate ester hydrolysis
Shina C L Kamerlin, John Wilkie
(2007) Organic and Biomolecular Chemistry, 5 p.2098-108
ArticleA targeted molecular dynamics study of WPD loop movement in PTP1B
Shina Caroline Lynn Kamerlin, Robert Rucker, Stefan Boresch
(2006) Biochemical and Biophysical Research Communications, 345 p.1161-6
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