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List of works by Shina Caroline Lynn Kamerlin

A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases

scientific article published on June 2009

A molecular dynamics study of WPD-loop flexibility in PTP1B.

scientific article published on 26 March 2007

A targeted molecular dynamics study of WPD loop movement in PTP1B.

scientific article published on 12 May 2006

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1.

scientific article published on 27 December 2016

Amyloid-β Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects

scientific article published on 04 May 2018

An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling

scientific article published on July 2010

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models

scientific article published in May 2009

Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies

scientific article published in August 2008

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

scientific article

Author Correction: Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme

scientific article published on 12 June 2020

Base-catalyzed dehydration of 3-substituted benzene cis-1,2-dihydrodiols: stabilization of a cyclohexadienide anion intermediate by negative aromatic hyperconjugation

scientific article published on 16 August 2012

CADEE: Computer-Aided Directed Evolution of Enzymes

scientific article

Capturing the Role of Explicit Solvent in the Dimerization of RuV (bda) Water Oxidation Catalysts

scientific article published on 11 May 2017

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

scientific article

Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry‐driven protein evolution ⬇️

scientific article published on April 25, 2012

Catalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1

scientific article

Cellular polyamines promote amyloid-beta (Aβ) peptide fibrillation and modulate the aggregation pathways

scientific article published on 16 January 2013

Challenges and advances in the computational modeling of biological phosphate hydrolysis

scientific article published on 7 February 2018

Challenges in computational studies of enzyme structure, function and dynamics

scientific article

Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease

scientific article

Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di- and Tri-Hydroxypentanones

scientific article published on 23 May 2019

Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones

Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems

scientific article published on January 2011

Computational Study of the pKa Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B.

scientific article published on 25 April 2012

Computational protein engineering: bridging the gap between rational design and laboratory evolution

scientific article

Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase.

scientific article

Concerted or stepwise: how much do free-energy landscapes tell us about the mechanisms of elimination reactions?

scientific article published on 24 January 2014

Conformational diversity and enantioconvergence in potato epoxide hydrolase 1

scientific article

Conformational dynamics and enzyme evolution.

scientific article published in July 2018

Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily

scientific article published on 10 July 2015

Cooperativity and flexibility in enzyme evolution

scientific article published on 12 November 2017

Correction to A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

scholarly article published in Biochemistry

Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

scientific article published on 05 February 2019

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.

scientific article published on 21 July 2017

De novo active sites for resurrected Precambrian enzymes

scientific article

Debate on academic freedom and open access is healthy

scientific article published in Nature

Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect

scientific article published on 18 June 2015

Dineopentyl phosphate hydrolysis: evidence for stepwise water attack

scientific article published on 27 August 2008

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

scientific article published on 13 August 2014

Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase.

scientific article published on 2 April 2018

Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice

scientific article published on 16 August 2018

Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine

scientific article published on 11 November 2014

Energetics of activation of GTP hydrolysis on the ribosome

scientific article published in January 2013

Enhancing a De Novo Enzyme Activity by Computationally-Focused, Ultra-Low-Throughput Sequence Screening

scientific article published on 29 January 2020

Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening

scientific article published on 19 May 2020

Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa

Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase

scientific article

Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition

scientific article published on 01 April 2020

Enzyme millisecond conformational dynamics do not catalyze the chemical step

scientific article

Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme.

scientific article published on 22 March 2018

Errors in DFT integration grids and their potential impact on chemical shift calculations

scientific article published on 01 January 2020

Europe's plan S could raise everyone else's publication paywall

scientific article published in Nature

Evolution of chalcone isomerase from a non-catalytic ancestor

Evolution of chalcone isomerase from a noncatalytic ancestor

scientific article published on 23 April 2018

Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset

article published in the Proceedings of the National Academy of Sciences of the United States of America

Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues

scientific article

Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: a comparison to analogous phosphatases.

scientific article

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

scientific article

Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes

scientific article published on 17 August 2015

Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions

scientific article published on 12 October 2017

Faculty of 1000 evaluation for A new family of iron-dependent halogenases acts on freestanding substrates

Faculty of 1000 evaluation for Comparative laboratory evolution of ordered and disordered enzymes

Faculty of 1000 evaluation for Connectivity between Catalytic Landscapes of the Metallo-β-Lactamase Superfamily

Faculty of 1000 evaluation for DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity

Faculty of 1000 evaluation for Direct evidence for a covalent ene adduct intermediate in NAD(P)H-dependent enzymes

article

Faculty of 1000 evaluation for Enzyme Architecture: Deconstruction of the Enzyme-Activating Phosphodianion Interactions of Orotidine 5'-Monophosphate Decarboxylase

Faculty of 1000 evaluation for Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+

Faculty of 1000 evaluation for New reactions and products resulting from alternative interactions between the P450 enzyme and redox partners

Faculty of 1000 evaluation for Physics-based method to validate and repair flaws in protein structures

Faculty of 1000 evaluation for Site-Specific Protonation Kinetics of Acidic Side Chains in Proteins Determined by pH-Dependent Carboxyl (13)C NMR Relaxation

Faculty of 1000 evaluation for Structure of the key species in the enzymatic oxidation of methane to methanol

Female Faculty: Why So Few and Why Care?

scientific article published on 25 June 2020

Force field independent metal parameters using a nonbonded dummy model

scientific article

GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases

scientific article published on 26 June 2019

Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase

scientific article published on 12 November 2020

Harnessing Conformational Plasticity to Generate Designer Enzymes

scientific article published on 04 June 2020

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

scientific article published on 15 January 2021

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme

scientific article published on 21 October 2019

Higher-order epistatic networks underlie the evolutionary fitness landscape of a xenobiotic- degrading enzyme: Supplementary information

How valence bond theory can help you understand your (bio)chemical reaction

scientific article

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

scientific article published on 31 January 2019

Hypercompetition in biomedical research evaluation and its impact on young scientist careers

scientific article published in December 2015

In Silico-Directed Evolution Using CADEE

scientific article published on 01 January 2019

Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity

scientific article published on 15 April 2020

Introduction to the Empirical Valence Bond Approach

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

scientific article

Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)† †Electronic supplementary information (ESI) available: Further experimental and computational data. See DOI: 10.1039/c5sc03666f.

scientific article

Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

scientific article published on 18 April 2019

Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

scientific article published on 26 December 2018

Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case

scholarly article by Qinghua Liao et al published 8 November 2018 in Journal of the American Chemical Society

Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations

scientific article published on 15 August 2017

Modeling catalytic promiscuity in the alkaline phosphatase superfamily

scientific article published on 3 June 2013

Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

scientific article published on 20 April 2020

Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

Modeling the mechanisms of biological GTP hydrolysis

scientific article published on 27 February 2015

Multiscale modeling of biological functions

scientific article

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

scientific article

On the energetics of ATP hydrolysis in solution

scientific article published in November 2009

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

scientific article published on 29 February 2008

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

scientific article published on August 2009

Open Access, Plan S, and researchers' needs

scientific article published on 07 September 2020

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

scientific article published on 27 May 2011

Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer

Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase

scientific article

Progress 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

scientific article published on February 2009

Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily

scientific article

Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer

scientific article

Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor

scientific article published on 01 October 2018

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation

scientific article published on 28 February 2020

Recent advances in QM/MM free energy calculations using reference potentials

scientific article

Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds

Reply to Karplus: Conformational dynamics have no role in the chemical step

article published in the Proceedings of the National Academy of Sciences of the United States of America

Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis

scientific article

Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase

scientific article published on 8 March 2018

Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes

scientific article published on 20 February 2020

Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase

scientific article published in August 2017

Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering.

scientific article published on 7 November 2017

Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer

scientific article published on 18 August 2017

Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases

scientific article published on 23 April 2021

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

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε

scientific article published in Nature Communications

The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

scientific article

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

scientific article published on January 2010

The alkaline hydrolysis of sulfonate esters: challenges in interpreting experimental and theoretical data

scientific article

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

scientific article published on 30 December 2014

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

scientific article published on 7 June 2011

The effect of magnesium ions on triphosphate hydrolysis

scholarly article by Alexandre Barrozo et al published 27 June 2017 in Pure and Applied Chemistry

The empirical valence bond model: theory and applications

article

The evolution of multiple active site configurations in a designed enzyme

scientific article published in Nature Communications

The role of ligand-gated conformational changes in enzyme catalysis

scientific article published on 01 October 2019

The role of metal ions in phosphate ester hydrolysis

scientific article published on 30 May 2007

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer ⬇️

scientific article published on October 19, 2011

Theoretical modelling of epigenetically modified DNA sequences

scientific article published on 24 February 2015

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

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

scientific article published on 25 September 2019

Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation

scientific article

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge

scientific article published on May 2015

When we increase diversity in academia, we all win

scientific article published on 20 November 2020

Where are the female science professors? A personal perspective

scientific article published on 06 June 2016

Why nature really chose phosphate

scientific article published on 15 January 2013

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