Lynn Kamerlin

Targeting 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
Journal article

The winter holidays are glorious-except when they're not

Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.5223-5224
Journal article (comment)

Catalytic 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
Journal article

Artificial, 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
Journal article (comment)

Mandatory national language requirements in higher education

Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.3739-3740
Journal article (comment)

Conformational 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
Journal article

SHP-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
Journal article

In vitro fertilization and the ethics of frozen embryos

Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.2817-2818
Journal article (comment)

Key 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
Journal article

The 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
Journal article (comment)

How to write a successful graduate school application

Shina Caroline Lynn Kamerlin
(2024) EMBO Reports, 25 p.1-2
Journal article (comment)

Sequence - 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
Journal article

A 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
Journal article

Progress in using deep learning to treat cancer

Shina Caroline Lynn Kamerlin
(2023) Nature computational science, 3 p.739-740
Journal article

Loop dynamics and the evolution of enzyme activity

Marina Corbella, Gaspar P Pinto, Shina C L Kamerlin
(2023) Nature reviews. Chemistry, 7 p.536-547
Journal article review

Science after Brexit : bright spots on the Horizon?

Adrian J Mulholland, Shina Caroline Lynn Kamerlin
(2023) EMBO Reports, 24
Journal article (comment)

KIF-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
Journal article

Conformational 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
Journal article

The perceived decline of "disruptive" science and technology

Shina Caroline Lynn Kamerlin
(2023) EMBO Reports, 24
Journal article (comment)

Q-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
Journal article

Allosteric 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
Journal article

Scholars in peril : when being a scientist can land you in jail (or worse)

Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Journal article (comment)

Insights 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
Journal article

A Structural View into the Complexity of Carbon Dioxide Fixation

Robert Kourist, Shina Caroline Lynn Kamerlin
(2022) ACS Central Science, 8 p.1040-1042
Journal article

Late-termination of pregnancy for medical reasons : when abortion isn't really by choice

Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Journal article (comment)

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
Journal article review

Complex 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
Journal article

Adventures 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
Journal article review

Computational 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
Journal article

5 suggestions to increase grant application success rates

Shina Caroline Lynn Kamerlin
(2022) EMBO Reports, 23
Journal article (comment)

Essential 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
Journal article

From flying cats to dancing proteins

Shina Caroline Lynn Kamerlin
(2022) Nature reviews. Chemistry, 6
Review

How to write a successful postdoc application - the PI perspective

Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Journal article (comment)

Prenatal genetic screening and the evolving quest for "perfect babies" : at what cost for genetic diversity?

Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Journal article (comment)

The 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
Journal article

Academic motherhood - what happens when you can't make it happen?

Shina Caroline Lynn Kamerlin
(2021) EMBO Reports, 22
Journal article (comment)

Single 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
Journal article

Heme-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
Journal article

Loop 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
Journal article

Managing 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
Journal article

When we increase diversity in academia, we all win

Shina Caroline Lynn Kamerlin
(2020) EMBO Reports, 21
Journal article (comment)

Ground-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
Journal article

Open Access, Plan S, and researchers' needs

Shina Caroline Lynn Kamerlin
(2020) EMBO Reports, 21
Journal article (comment)

Modeling 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
Journal article

Female Faculty : Why So Few and Why Care?

Shina Caroline Lynn Kamerlin, Pernilla Wittung-Stafshede
(2020) Chemistry: A European Journal, 26 p.8319-8323
Journal article

Harnessing 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
Journal article review

Enhancing 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
Journal article

Modeling 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
Journal article

Enzyme 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
Journal article

Short 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
Journal article

Recent 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
Journal article review

Errors 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
Journal article

Higher-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
Journal article

The 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
Journal article review

Uncovering 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
Journal article

GTP 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
Journal article

Relative 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
Journal article

Human 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
Journal article

Cryptic 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
Journal article

Structural 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
Journal article

In 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
Journal article

Loop 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
Journal article

Debate on academic freedom and open access is healthy

J Britt Holbrook, Stephen Curry, Shina C L Kamerlin
(2018) Nature, 562
Journal article (comment)

The 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
Journal article

Evolutionary 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.7293-7302
Journal article

Amyloid-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
Journal article

Conformational 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
Journal article review

Evolution 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
Journal article

Epoxide 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
Journal article review

Empirical 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
Journal article

Computer 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
Journal article

Challenges 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
Journal article review

Role 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
Journal article

Cooperativity 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
Journal article review

Empirical Valence Bond Simulations of Organophosphate Hydrolysis : Theory and Practice

Miha Purg, Shina Caroline Lynn Kamerlin
(2018) Methods in Enzymology, 607 p.3-51
Book chapter

Similar 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
Journal article

Extending 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
Journal article

Simulating 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
Journal article

Shuffling 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
Journal article

Micelle 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
Journal article

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

Sergey N Maximoff, Shina Caroline Lynn Kamerlin, Jan Florián
(2017) The Journal of Physical Chemistry Part B, 121 p.7813-7822
Journal article

Enzyme 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
Journal article

De 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
Journal article

Capturing the Role of Explicit Solvent in the Dimerization of Ru^V(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
Journal article

Active 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
Journal article

CADEE : 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
Journal article

Characterization 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
Journal article

Probing 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
Journal article

Laboratory-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.7-1693
Journal article

The 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.73-10664
Journal article

Conformational 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.51-5639
Journal article

Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer

Anna Pabis, Fernanda Duarte, Shina C L Kamerlin
(2016) Biochemistry, 55 p.81-3061
Journal article review

Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily

Anna Pabis, Shina Caroline Lynn Kamerlin
(2016) Current Opinion in Structural Biology, 37 p.14-21
Journal article review

Linking 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
Journal article

Where are the female science professors? : A personal perspective

Shina Caroline Lynn Kamerlin
(2016) F1000Research, 5
Journal article

Hypercompetition 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.61-253
Journal article

Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome

Johan Åqvist, Shina C L Kamerlin
(2015) Scientific Reports, 5
Journal article

Expanding 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
Journal article

Modeling 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
Journal article review

Cooperative 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.76-9061
Journal article

Development 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.62-2657
Journal article

Understanding 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.8-5391
Journal article

Recent 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
Journal article review

Catalytic 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
Journal article

How 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.52-1037
Journal article review

Resolving 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.93-1081
Journal article

The conformation of a catalytic loop is central to GTPase activity on the ribosome

Johan Åqvist, Shina C L Kamerlin
(2015) Biochemistry, 54 p.56-546
Journal article

Understanding 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.12-1604
Journal article

Empirical 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.55-3347
Journal article

Challenges 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
Journal article

Editorial overview : Mechanisms: Chemical and computational probes of biological mechanism

AnnMarie C O'Donoghue, Shina C L Kamerlin
(2014) Current Opinion in Chemical Biology, 21
Journal article (comment)

Force 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.62-4351
Journal article

The 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.28-2816
Journal article

Concerted 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.8-1280
Journal article

Modeling catalytic promiscuity in the alkaline phosphatase superfamily

Fernanda Duarte, Beat Anton Amrein, Shina Caroline Lynn Kamerlin
(2013) Physical chemistry chemical physics : PCCP, 15 p.77-11160
Journal article

Cellular 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.62-454
Journal article

Why 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
Journal article review

Energetics of activation of GTP hydrolysis on the ribosome

Göran Wallin, Shina C L Kamerlin, Johan Åqvist
(2013) Nature Communications, 4
Journal article

Computational Study of the pK_a 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.70-3864
Journal article

Computational 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.60-12428
Journal article review

Base-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.69-14056
Journal article

Catalytic 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.30-1622
Journal article

Examining 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.26-1211
Journal article

Theoretical 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.38-9228
Journal article

Catalysis 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.20-14115
Journal article

The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis

Shina C L Kamerlin, John Wilkie
(2011) Organic and Biomolecular Chemistry, 9 p.406-5394
Journal article

Paradynamics : 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.62-7950
Journal article

Multiscale modeling of biological functions

Shina Caroline Lynn Kamerlin, Arieh Warshel
(2011) Physical chemistry chemical physics : PCCP, 13 p.11-10401
Journal article review

Coarse-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
Journal article review

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

Shina C L Kamerlin, Zhen T Chu, A Warshel
(2010) The Journal of Organic Chemistry, 75 p.401-6391
Journal article

Examining 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.66-2759
Journal article review

An 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
Journal article

At 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.75-1339
Journal article review

Ketosteroid 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.80-4075
Journal article

The 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
Journal article

On the energetics of ATP hydrolysis in solution

Shina C L Kamerlin, Arieh Warshel
(2009) The Journal of Physical Chemistry Part B, 113 p.8-15692
Journal article

Enzyme 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.64-17359
Journal article

On 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.15-10905
Journal article

A 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.71-5963
Journal article

Are 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.34-1125
Journal article

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins : accelerated QM/MM studies of pK_a, redox reactions and solvation free energies

Shina C L Kamerlin, Maciej Haranczyk, Arieh Warshel
(2009) The Journal of Physical Chemistry Part B, 113 p.72-1253
Journal article review

Dineopentyl phosphate hydrolysis : evidence for stepwise water attack

Shina C L Kamerlin, Nicholas H Williams, Arieh Warshel
(2008) The Journal of Organic Chemistry, 73 p.9-6960
Journal article

Associative 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.73-1767
Journal article

On 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.35-3725
Journal article

Lynn Kamerlin

Publications

Research group member