Lynn Kamerlin
Visiting professor at Department of Chemistry - BMC; Biochemistry; Kamerlin group
- Telephone:
- +46 18 471 44 23, +46 70 425 01 81
- E-mail:
- lynn.kamerlin@kemi.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 576
75123 Uppsala
- ORCID:
- 0000-0002-3190-1173
More information is available to staff who log in.
Short presentation
Professor of Structural Biology at Uppsala University. Research interests range from fundamental theoretical organic chemistry to protein evolution and understanding DNA dynamics.
Keywords
- computational biochemistry
- enzyme catalysis
- phosphate hydrolysis
- protein evolution
- reaction mechanisms
Biography
I received my Master of Natural Sciences from the University of Birmingham (UK), in 2002, where I remained to complete a PhD in Theoretical Organic Chemistry under the supervision of Dr. John Wilkie (awarded 2005). Subsequently, I was a postdoctoral researcher in the labs of Stefan Boresch at the University of Vienna (2005-2007) and Arieh Warshel at the University of Southern California (2007-2009, Research Associate at the University of Southern California in 2010), as well as a Researcher with Fahmi Himo at Stockholm University (2010). I joined the faculty of Uppsala University in 2011, where I am currently a Full Professor of Biochemistry, a Fellow of the Royal Society of Chemistry, and a Wallenberg Academy Fellow. I was also the recipient of an ERC Starting Independent Researcher Grant (2012-2017) and the Chair of the Young Academy of Europe (YAE) in 2014-2015. My non-scientific interests include languages (fluent in 5), amateur photography and playing the piano.
Selected Distinctions and Professional Memberships
- The Svedberg Prize from SFBBM 2018
- Fellow of the Royal Society of Chemistry (FRSC) 2017
- Wallenberg Academy Fellowship 2014-2019
- MGMS Silver Jubilee Prize 2013
- Member, Young Academy of Europe (Chair 2014-2015)
- ERC Starting Independent Researcher 2012-2017
- Docent in Molecular Biotechnology, Uppsala University 2012
- Sven and Ebba-Christina Hagberg Prize in Biochemistry from the Swedish Royal Academy of Sciences 2011
- 4 year assistant professorship fellowship funded by the Swedish Research Council (VR) 2011-2015
- UK Royal Society of Chemistry Chartered Chemist (CChem) 2009
Research
The goal of my research team is to use advanced computational tools to understand the chemical basis for structure-function-dynamics relationships in (bio)molecular systems. Our ongoing projects include understanding ligand-gated conformational changes in enzyme catalysis, the physicochemical drivers for protein evolution, enzyme design, as well as GTPase regulation, protein-DNA recognition and the dynamical behavior and aggregation of short disordered peptides. For further information, please see our full publication list.
Publications
Selection of publications
- Force Field Independent Metal Parameters Using a Nonbonded Dummy Model (2014)
- The Alkaline Hydrolysis of Sulfonate Esters (2014)
- Concerted or Stepwise (2014)
- Modeling catalytic promiscuity in the alkaline phosphatase superfamily (2013)
- Why nature really chose phosphate (2013)
- Cellular Polyamines Promote Amyloid-Beta (A beta) Peptide Fibrillation and Modulate the Aggregation Pathways (2013)
- Cellular Polyamines Promote Amyloid-Beta Peptide Fibrillation and Modulate the Aggregation Pathways (2013)
- Energetics of activation of GTP hydrolysis on the ribosome (2013)
- Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution (2012)
- Computational Study of the pK(a) Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B (2012)
- Base-Catalyzed Dehydration of 3-Substituted Benzene cis-1,2-Dihydrodiols (2012)
- Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase (2012)
- Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution (2012)
- Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting (2012)
- Studying catalysis by QM/MM approaches should not be a black box process (2012)
- Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions (2011)
- Theoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution (2011)
Recent publications
- Key interaction networks (2024)
- Q-RepEx (2023)
- Loop dynamics and the evolution of enzyme activity (2023)
- KIF-Key Interactions Finder (2023)
- Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation (2023)
All publications
Articles
- Key interaction networks (2024)
- Q-RepEx (2023)
- Loop dynamics and the evolution of enzyme activity (2023)
- KIF-Key Interactions Finder (2023)
- Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation (2023)
- Representation matters (2023)
- The perceived decline of "disruptive" science and technology (2023)
- Science after Brexit (2023)
- A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides (2023)
- Computational Advances in Protein Engineering and Enzyme Design (2022)
- Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation (2022)
- Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021) (2022)
- Scholars in peril (2022)
- Late-termination of pregnancy for medical reasons (2022)
- 5 suggestions to increase grant application success rates (2022)
- From flying cats to dancing proteins (2022)
- A Structural View into the Complexity of Carbon Dioxide Fixation (2022)
- In Silico Ligand Docking Approaches to Characterise the Binding of Known Allosteric Modulators to the Glucagon-Like Peptide 1 Receptor and Prediction of ADME/Tox Properties (2022)
- Computational Investigation of Ligand Binding of Flavonoids in Cytochrome P450 Receptors (2022)
- Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase (2022)
- Exploiting enzyme evolution for computational protein design (2022)
- Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi (2022)
- Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases (2022)
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition (2021)
- Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases (2021)
- Dan Salah Tawfik (1955-2021) (2021)
- Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase (2021)
- Journal Open Access and Plan S (2021)
- Prenatal genetic screening and the evolving quest for "perfect babies" (2021)
- Academic motherhood - what happens when you can't make it happen? (2021)
- How to write a successful postdoc application (2021)
- Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases (2021)
- Enzyme Evolution An Epistatic Ratchet versus a Smooth Reversible Transition (2020)
- Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase (2020)
- Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation (2020)
- Harnessing Conformational Plasticity to Generate Designer Enzymes (2020)
- The Role of Substrate-Coenzyme Crosstalk in Determining Turnover Rates in Rhodococcus ruber Alcohol Dehydrogenase (2020)
- Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions (2020)
- Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures (2020)
- When we increase diversity in academia, we all win (2020)
- Open Access, Plan S, and researchers' needs (2020)
- Female Faculty (2020)
- Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes (2020)
- Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase (2020)
- G-Protein coupled receptors (2020)
- Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening (2020)
- Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters (2020)
- Errors in DFT integration grids and their potential impact on chemical shift calculations (2020)
- Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones (2019)
- Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes (2019)
- Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases (2019)
- GTP Hydrolysis Without an Active Site Base (2019)
- Uncovering the Role of Key Active-Site Side Chains in Catalysis (2019)
- Computational physical organic chemistry using the empirical valence bond approach (2019)
- Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition (2019)
- The role of ligand-gated conformational changes in enzyme catalysis (2019)
- Human Glycerol 3-Phosphate Dehydrogenase (2019)
- Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon (2019)
- Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds (2019)
- Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme (2019)
- Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase (2018)
- Q6 (2018)
- Debate on academic freedom and open access is healthy (2018)
- The evolution of multiple active site configurations in a designed enzyme (2018)
- Epoxide Hydrolysis as a Model System for Understanding Flux Through a Branched Reaction Scheme (2018)
- Evolution of chalcone isomerase from a noncatalytic ancestor (2018)
- Role of Ligand-Driven Conformational Changes in Enzyme Catalysis (2018)
- Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case (2018)
- Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase (2018)
- 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 (2018)
- Evolutionary repurposing of a sulfatase (2018)
- Amyloid-beta Peptide Interactions with Amphiphilic Surfactants (2018)
- Cooperativity and flexibility in enzyme evolution (2018)
- Molecular modeling of conformational dynamics and its role in enzyme evolution (2018)
- Effects of conformational dynamics on enzyme evolution in TIM-barrel-fold proteins (2018)
- Legend of a perfect enzyme (2018)
- Conformational dynamics and enzyme evolution (2018)
- Challenges and advances in the computational modeling of biological phosphate hydrolysis (2018)
- Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa (2018)
- CADEE (2017)
- The effect of magnesium ions on triphosphate hydrolysis (2017)
- Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes (2017)
- Preface (2017)
- Micelle Maker (2017)
- Enzyme Architecture (2017)
- Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions (2017)
- Computational study of relative thermodynamic stability of mutant base pairs between keto, enol and deprotonated forms of guanine and thymine at DNA polymerase lambda active site (2017)
- DNA Polymerase lambda Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template (2017)
- Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer (2017)
- Shuffling Active Site Substate Populations Affects Catalytic Activity (2017)
- Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis (2017)
- De novo active sites for resurrected Precambrian enzymes (2017)
- Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts (2017)
- Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis (2016)
- Phosphoryl and Sulfuryl Transfer (2016)
- Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1 (2016)
- The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis (2016)
- Laboratory evolved enzymes provide snapshots of the development of enantioconvergence in enzyme-catalyzed epoxide hydrolysis (2016)
- Where are the female science professors? A personal perspective (2016)
- Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA) (2016)
- Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer (2016)
- Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily (2016)
- Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. (2016)
- Characterization of Mn(II) ion binding to the amyloid-beta peptide in Alzheimer's disease (2016)
- Expanding the catalytic triad in epoxide hydrolases and related enzymes (2015)
- Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome (2015)
- Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily (2015)
- Catalytic Stimulation by Restrained Active-Site Floppiness-The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1 (2015)
- Understanding thio-effects in simple phosphoryl systems (2015)
- Modeling the mechanisms of biological GTP hydrolysis (2015)
- Recent advances in QM/MM free energy calculations using reference potentials (2015)
- Understanding phosphoryl/sulfuryl transfer reactions (2015)
- Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis. (2015)
- Hypercompetition in biomedical research evaluation and its impact on young scientist careers (2015)
- Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn-Teller Effect (2015)
- How valence bond theory can help you understand your (bio)chemical reaction (2015)
- The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome (2015)
- Challenges in computational studies of enzyme structure, function and dynamics (2014)
- Understanding the structural and dynamic consequences of DNA epigenetic modifications (2014)
- Force Field Independent Metal Parameters Using a Nonbonded Dummy Model (2014)
- The Alkaline Hydrolysis of Sulfonate Esters (2014)
- Concerted or Stepwise (2014)
- Mechanisms (2014)
- Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine (2014)
- Modeling catalytic promiscuity in the alkaline phosphatase superfamily (2013)
- Rationalizing the Catalytic Activity of an Unusual Oxidoreductase (FucO) (2013)
- Why nature really chose phosphate (2013)
- Cellular Polyamines Promote Amyloid-Beta (A beta) Peptide Fibrillation and Modulate the Aggregation Pathways (2013)
- Cellular Polyamines Promote Amyloid-Beta Peptide Fibrillation and Modulate the Aggregation Pathways (2013)
- Energetics of activation of GTP hydrolysis on the ribosome (2013)
- Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution (2012)
- Computational Study of the pK(a) Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B (2012)
- Base-Catalyzed Dehydration of 3-Substituted Benzene cis-1,2-Dihydrodiols (2012)
- Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase (2012)
- Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution (2012)
- Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting (2012)
- Studying catalysis by QM/MM approaches should not be a black box process (2012)
- Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions (2011)
- Theoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution (2011)
- Stereoselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases
Chapters
