All Stories

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

    Article • IUCrJ, March 2018, International Union of Crystallography

    Dr Shina Caroline Lynn Kamerlin, Professor Mikael Widersten, Shina Caroline Lynn Kamerlin

  2. The effect of magnesium ions on triphosphate hydrolysis

    Article • Pure and Applied Chemistry, June 2017, De Gruyter

    Professor Nicholas H Williams, Dr Shina Caroline Lynn Kamerlin

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

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, October 2016, Royal Society Publishing

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  4. Where are the female science professors? A personal perspective

    Article • F1000Research, June 2016, Faculty of 1000, Ltd.

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  5. Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)

    Article • Chemical Science, January 2016, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Professor Mikael Widersten, Shina Caroline Lynn Kamerlin

  6. Modeling the mechanisms of biological GTP hydrolysis

    Article • Archives of Biochemistry and Biophysics, September 2015, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Biochimica et Biophysica Acta (BBA) - General Subjects, May 2015, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  8. Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

    Article • Journal of Molecular Biology, March 2015, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  9. Theoretical modelling of epigenetically modified DNA sequences

    Article • F1000Research, February 2015, Faculty of 1000, Ltd.

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  10. Faculty Opinions recommendation of Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

    Article • February 2015, F1000Research

    Dr Shina Caroline Lynn Kamerlin

  11. Resolving Apparent Conflicts between Theoretical and Experimental Models of Phosphate Monoester Hydrolysis

    Article • Journal of the American Chemical Society, January 2015, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  12. The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

    Article • Biochemistry, January 2015, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Chemical Society Reviews, January 2015, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Organic & Biomolecular Chemistry, January 2015, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  15. Faculty Opinions recommendation of New reactions and products resulting from alternative interactions between the P450 enzyme and redox partners.

    Article • December 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Epigenetics, December 2014, Taylor & Francis

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proteins Structure Function and Bioinformatics, November 2014, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  18. Faculty Opinions recommendation of A new family of iron-dependent halogenases acts on freestanding substrates.

    Article • November 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  19. Challenges in computational studies of enzyme structure, function and dynamics

    Article • Journal of Molecular Graphics and Modelling, November 2014, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  20. Faculty Opinions recommendation of Direct evidence for a covalent ene adduct intermediate in NAD(P)H-dependent enzymes.

    Article • October 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  21. Faculty Opinions recommendation of Physics-based method to validate and repair flaws in protein structures.

    Article • September 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Current Opinion in Chemical Biology, August 2014, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  23. Faculty Opinions recommendation of Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+.

    Article • July 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  24. Faculty Opinions recommendation of DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity.

    Article • July 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  25. Faculty Opinions recommendation of Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily.

    Article • July 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  26. Faculty Opinions recommendation of Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase.

    Article • July 2014, F1000Research

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  27. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

    Article • The Journal of Physical Chemistry, April 2014, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  28. The Alkaline Hydrolysis of Sulfonate Esters: Challenges in Interpreting Experimental and Theoretical Data

    Article • The Journal of Organic Chemistry, April 2014, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  29. Concerted or Stepwise: How Much Do Free-Energy Landscapes Tell Us about the Mechanisms of Elimination Reactions?

    Article • The Journal of Organic Chemistry, February 2014, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  30. Energetics of activation of GTP hydrolysis on the ribosome

    Article • Nature Communications, April 2013, Springer Science + Business Media

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  31. Cellular Polyamines Promote Amyloid-Beta (Aβ) Peptide Fibrillation and Modulate the Aggregation Pathways

    Article • ACS Chemical Neuroscience, March 2013, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  32. Why nature really chose phosphate

    Article • Quarterly Reviews of Biophysics, January 2013, Cambridge University Press

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  33. Modeling catalytic promiscuity in the alkaline phosphatase superfamily

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  34. Rationalizing the Catalytic Activity of an Unusual Oxidoreductase (FucO)

    Article • Biophysical Journal, January 2013, Elsevier

    Dr Shina Caroline Lynn Kamerlin

  35. Cellular Polyamines Promote Amyloid-Beta Peptide Fibrillation and Modulate the Aggregation Pathways

    Article • Biophysical Journal, January 2013, Elsevier

    Dr Shina Caroline Lynn Kamerlin

  36. Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

    Article • Theoretical Chemistry Accounts, November 2012, Springer Science + Business Media

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  37. Computational Study of the p K a Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B

    Article • Journal of Chemical Theory and Computation, October 2012, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  38. Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

    Article • International Journal of Molecular Sciences, September 2012, MDPI AG

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  39. Base-Catalyzed Dehydration of 3-Substituted Benzene cis -1,2-Dihydrodiols: Stabilization of a Cyclohexadienide Anion Intermediate by Negative Aromatic Hyperconjugation

    Article • Journal of the American Chemical Society, August 2012, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  40. Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution

    Article • FEBS Letters, April 2012, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proteins Structure Function and Bioinformatics, January 2012, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  42. Theoretical Comparison of p -Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

    Article • The Journal of Organic Chemistry, November 2011, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proceedings of the National Academy of Sciences, August 2011, Proceedings of the National Academy of Sciences

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  44. Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

    Article • The Journal of Physical Chemistry, June 2011, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  45. Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

    Article • Annual Review of Physical Chemistry, May 2011, Annual Reviews

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  46. Multiscale modeling of biological functions

    Article • Physical Chemistry Chemical Physics, January 2011, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Organic & Biomolecular Chemistry, January 2011, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  48. The empirical valence bond model: theory and applications

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, January 2011, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  49. 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

    Article • The Journal of Organic Chemistry, October 2010, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • FEBS Letters, April 2010, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proceedings of the National Academy of Sciences, April 2010, Proceedings of the National Academy of Sciences

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proceedings of the National Academy of Sciences, February 2010, Proceedings of the National Academy of Sciences

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  53. An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling

    Article • Journal of Physical Organic Chemistry, January 2010, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  54. Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer

    Article • Faraday Discussions, January 2010, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Faraday Discussions, January 2010, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  56. Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step

    Article • Biophysical Journal, January 2010, Elsevier

    Dr Shina Caroline Lynn Kamerlin

  57. On the Energetics of ATP Hydrolysis in Solution

    Article • The Journal of Physical Chemistry, November 2009, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Proteins Structure Function and Bioinformatics, November 2009, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  59. Enzyme millisecond conformational dynamics do not catalyze the chemical step

    Article • Proceedings of the National Academy of Sciences, October 2009, Proceedings of the National Academy of Sciences

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  60. 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

    Article • Biochemistry, August 2009, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  61. On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It

    Article • The Journal of Physical Chemistry, August 2009, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Biochemistry, June 2009, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  63. Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models

    Article • ChemPhysChem, May 2009, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  64. Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of p K a , Redox Reactions and Solvation Free Energies †

    Article • The Journal of Physical Chemistry, February 2009, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  65. Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack

    Article • The Journal of Organic Chemistry, September 2008, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  66. Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

    Article • ChemPhysChem, August 2008, Wiley

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  67. On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution †

    Article • Biochemistry, March 2008, American Chemical Society (ACS)

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Biochemical and Biophysical Research Communications, May 2007, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

  69. The role of metal ions in phosphate ester hydrolysis

    Article • Organic & Biomolecular Chemistry, January 2007, Royal Society of Chemistry

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin

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

    Article • Biochemical and Biophysical Research Communications, July 2006, Elsevier

    Dr Shina Caroline Lynn Kamerlin, Shina Caroline Lynn Kamerlin