Publications in Lynn Kamerlin Group

5 suggestions to increase grant application success rates

Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2022.

DOI for 5 suggestions to increase grant application success rates

A Structural View into the Complexity of Carbon Dioxide Fixation

Kourist, Robert; Kamerlin, Shina C. Lynn

Part of ACS CENTRAL SCIENCE, p. 1040-1042, 2022.

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Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021)

Jackson, Colin; Toth-Petroczy, Agnes; Kolodny, Rachel; Hollfelder, Florian et al.

Part of Journal of Molecular Biology, 2022.

DOI for Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021)

Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi

Romero-Rivera, Adrian; Corbella Morató, Marina; Parracino, Antonietta; Patrick, Wayne M. et al.

Part of JACS Au, p. 943-960, 2022.

DOI for Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi Download full text (pdf) of Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi

Computational Investigation of Ligand Binding of Flavonoids in Cytochrome P450 Receptors

Odoemelam, Chiemela S. S.; Hunter, Elena; Ahmad, Zeeshan; Kamerlin, Caroline Lynn et al.

Part of Current pharmaceutical design, p. 3637-3648, 2022.

DOI for Computational Investigation of Ligand Binding of Flavonoids in Cytochrome P450 Receptors

Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

Pfeiffer, Martin; Crean, Rory M.; Moreira, Catia; Parracino, Antonietta et al.

Part of ACS Catalysis, p. 3357-3370, 2022.

DOI for Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase Download full text (pdf) of Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

Exploiting enzyme evolution for computational protein design

Pinto, Gaspar P.; Corbella Morató, Marina; Demkiv, Andrey O.; Kamerlin, Shina C. Lynn

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 375-389, 2022.

DOI for Exploiting enzyme evolution for computational protein design Download full text (pdf) of Exploiting enzyme evolution for computational protein design

From Kibbutz Fishponds to the Nobel Prize: Taking Molecular Functions into Cyberspace

Kamerlin, Shina C. Lynn

Part of Nature Reviews Chemistry, p. 85-85, 2022.

DOI for From Kibbutz Fishponds to the Nobel Prize: Taking Molecular Functions into Cyberspace

Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases

Shen, Ruidan; Crean, Rory M.; Olsen, Keith J.; Corbella Morató, Marina et al.

Part of Chemical Science, p. 13524-13540, 2022.

DOI for Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases Download full text (pdf) of Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases

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

Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2022.

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

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

Kamerlin, Shina Caroline Lynn

Part of EMBO Reports, 2021.

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

Biographical item: Dan Salah Tawfik (1955-2021): A giant of protein evolution. In: EMBO Reports, Volume 22, Issue 7, Article Number e53256, 2021

Elias, Mikael H.; Fraser, James S.; Kamerlin, Shina C. Lynn; Patrick, Wayne M. et al.

2021.

DOI for Biographical item: Dan Salah Tawfik (1955-2021): A giant of protein evolution. In: EMBO Reports, Volume 22, Issue 7, Article Number e53256, 2021

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

Gamiz-Arco, Gloria; Gutierrez-Rus, Luis I.; Risso, Valeria A.; Ibarra-Molero, Beatriz et al.

Part of Nature Communications, 2021.

DOI for Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase Download full text (pdf) of Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

How to write a successful postdoc application: the PI perspective

Kamerlin, Shina Caroline Lynn

Part of EMBO Reports, 2021.

DOI for How to write a successful postdoc application: the PI perspective

Journal Open Access and Plan S: Solving Problems or Shifting Burdens?

Kamerlin, Shina C. Lynn; Allen, David J.; de Bruin, Bas; Derat, Etienne et al.

Part of Development and Change, p. 627-650, 2021.

DOI for Journal Open Access and Plan S: Solving Problems or Shifting Burdens? Download full text (pdf) of Journal Open Access and Plan S: Solving Problems or Shifting Burdens?

Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases

Crean, Rory M.; Biler, Michal; van der Kamp, Marc W.; Hengge, Alvan C. et al.

Part of Journal of the American Chemical Society, p. 3830-3845, 2021.

DOI for Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases Download full text (pdf) of Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases

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

Kamerlin, Shina Caroline Lynn

Part of EMBO Reports, 2021.

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

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

Shen, Ruidan; Crean, Rory M.; Johnson, Sean J.; Kamerlin, Shina C. L. et al.

Part of JACS Au, p. 646-659, 2021.

DOI for Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases Download full text (pdf) of Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases

The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

Corbella Morató, Marina; Liao, Qinghua; Moreira, Catia; Parracino, Antonietta et al.

Part of Journal of Physical Chemistry B, p. 6791-6806, 2021.

DOI for The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition Download full text (pdf) of The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

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

Risso, Valeria A.; Romero-Rivera, Adrian; Gutierrez-Rus, Luis I.; Ortega-Muñoz, Mariano et al.

Part of Chemical Science, p. 6134-6148, 2020.

DOI for Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening Download full text (pdf) of Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening

Enzyme Evolution An Epistatic Ratchet versus a Smooth Reversible Transition

Ben-David, Moshe; Soskine, Misha; Dubovetskyi, Artem; Cherukuri, Kesava-Phaneendra et al.

Part of Molecular biology and evolution, p. 1133-1147, 2020.

DOI for Enzyme Evolution An Epistatic Ratchet versus a Smooth Reversible Transition

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

Wilson, Philippe B.; Grootveld, Martin; Kamerlin, Shina C. Lynn

Part of Magnetic Resonance in Chemistry, p. 116-117, 2020.

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

Female Faculty: Why So Few and Why Care?

Kamerlin, Shina Caroline Lynn; Wittung-Stafshede, Pernilla

Part of Chemistry - A European Journal, p. 8319-8323, 2020.

DOI for Female Faculty: Why So Few and Why Care?

G-Protein coupled receptors: structure and function in drug discovery

Odoemelam, Chiemela S.; Percival, Benita; Wallis, Helen; Chang, Ming-Wei et al.

Part of RSC Advances, p. 36337-36348, 2020.

DOI for G-Protein coupled receptors: structure and function in drug discovery Download full text (pdf) of G-Protein coupled receptors: structure and function in drug discovery

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

Biler, Michal; Crean, Rory M.; Schweiger, Anna K.; Kourist, Robert et al.

Part of Journal of the American Chemical Society, p. 20216-20231, 2020.

DOI for Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase Download full text (pdf) of Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase

Harnessing Conformational Plasticity to Generate Designer Enzymes

Crean, Rory M.; Gardner, Jasmine M.; Kamerlin, Shina C. Lynn

Part of Journal of the American Chemical Society, p. 11324-11342, 2020.

DOI for Harnessing Conformational Plasticity to Generate Designer Enzymes Download full text (pdf) of Harnessing Conformational Plasticity to Generate Designer Enzymes

Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control

Kamerlin, Shina C. L.; Kasson, Peter M.

Part of Clinical Infectious Diseases, p. 3174-3181, 2020.

DOI for Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control Download full text (pdf) of Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control

Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions

Gardner, Jasmine M.; Biler, Michal; Risso, Valeria A.; Sanchez-Ruiz, Jose M. et al.

Part of ACS Catalysis, p. 4863-4870, 2020.

DOI for Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions Download full text (pdf) of Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions

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

Szeler, Klaudia; Williams, Nicholas H.; Hengge, Alvan C.; Kamerlin, Shina C. Lynn

Part of Journal of Organic Chemistry, p. 6489-6497, 2020.

DOI for Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study Download full text (pdf) of Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

Mhasal, Anil Rhanu; Romero-Rivera, Adrian; Mydy, Lisa S.; Cristobal, Judith R. et al.

Part of ACS Catalysis, p. 11253-11267, 2020.

DOI for Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase Download full text (pdf) of Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

Open Access, Plan S, and researchers' needs

Kamerlin, Shina Caroline Lynn

Part of EMBO Reports, 2020.

DOI for Open Access, Plan S, and researchers' needs Download full text (pdf) of Open Access, Plan S, and researchers' needs

Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation

Calixto, Ana Rita; Moreira, Catia; Kamerlin, Shina Caroline Lynn

Part of ACS Omega, p. 4380-4385, 2020.

DOI for Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation Download full text (pdf) of Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation

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

Longo, Liam M.; Petrovic, Dusan; Kamerlin, Shina C. Lynn; Tawfik, Dan S.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 5310-5318, 2020.

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

The Role of Substrate-Coenzyme Crosstalk in Determining Turnover Rates in Rhodococcus ruber Alcohol Dehydrogenase

Enugala, Thilak Reddy; Corbella Morató, Marina; Kamerlin, Shina C. L.; Widersten, Mikael

Part of ACS Catalysis, p. 9115-9128, 2020.

DOI for The Role of Substrate-Coenzyme Crosstalk in Determining Turnover Rates in Rhodococcus ruber Alcohol Dehydrogenase Download full text (pdf) of The Role of Substrate-Coenzyme Crosstalk in Determining Turnover Rates in Rhodococcus ruber Alcohol Dehydrogenase

Toward a Computational Ecotoxicity Assay

Kamerlin, Natasha; Delcey, Mickaël G; Manzetti, Sergio; Van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 3792-3803, 2020.

DOI for Toward a Computational Ecotoxicity Assay

Unravelling the mechanism of pH-regulation in dinoflagellate luciferase

Kamerlin, Natasha; Delcey, Mickael G; Lindh, Roland

Part of International Journal of Biological Macromolecules, p. 2671-2680, 2020.

DOI for Unravelling the mechanism of pH-regulation in dinoflagellate luciferase Download full text (pdf) of Unravelling the mechanism of pH-regulation in dinoflagellate luciferase

When we increase diversity in academia, we all win

Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2020.

DOI for When we increase diversity in academia, we all win

Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases

Burke, Jason R.; La Clair, James J.; Philippe, Ryan N.; Pabis, Anna et al.

Part of ACS Catalysis, p. 8388-8396, 2019.

DOI for Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases

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

Al-Smadi, Derar; Enugala, Thilak Reddy; Kessler, Vadim; Mhasal, Anil Rhanu et al.

Part of Journal of Organic Chemistry, p. 6982-6991, 2019.

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

Computational physical organic chemistry using the empirical valence bond approach

Kulkarni, Yashraj; Kamerlin, Shina C. Lynn

Part of Advances in Physical Organic Chemistry, p. 69-104, 2019.

DOI for Computational physical organic chemistry using the empirical valence bond approach Download full text (pdf) of Computational physical organic chemistry using the empirical valence bond approach

Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

Baier, Florian; Hong, Nansook; Yang, Gloria; Pabis, Anna et al.

Part of eLIFE, 2019.

DOI for Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes Download full text (pdf) of Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

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

Calixto, Ana R.; Moreira, Catia; Pabis, Anna; Kötting, Carsten et al.

Part of Journal of the American Chemical Society, p. 10684-10701, 2019.

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

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

Yang, Gloria; Anderson, Dave W.; Baier, Florian; Dohmen, Elias et al.

Part of Nature Chemical Biology, p. 1120-1128, 2019.

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

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

Mydy, Lisa S.; Cristobal, Judith R.; Katigbak, Roberto D.; Bauer, Paul et al.

Part of Biochemistry, p. 1061-1073, 2019.

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

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

Liao, Qinghua; Lüking, Malin; Krueger, Dennis M.; Deindl, Sebastian et al.

Part of Journal of Physical Chemistry B, p. 3576-3590, 2019.

DOI for Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition Download full text (pdf) of Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

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

Tatum, Natalie J.; Duarte, Fernanda; Kamerlin, Shina C. Lynn; Pohl, Ehmke

Part of Journal of Physical Chemistry Letters, p. 2244-2249, 2019.

DOI for Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds Download full text (pdf) of Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds

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

Parkash, Vimal; Kulkarni, Yashraj; ter Beek, Josy; Shcherbakova, Polina V. et al.

Part of Nature Communications, 2019.

DOI for Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon Download full text (pdf) of Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon

The role of ligand-gated conformational changes in enzyme catalysis

Moreira, Catia; Calixto, Ana R.; Richard, John P.; Kamerlin, Shina Caroline Lynn

Part of Biochemical Society Transactions, p. 1449-1460, 2019.

DOI for The role of ligand-gated conformational changes in enzyme catalysis Download full text (pdf) of The role of ligand-gated conformational changes in enzyme catalysis

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

Kulkarni, Yashraj; Amyes, Tina L.; Richard, John P.; Kamerlin, Shina C. Lynn

Part of Journal of the American Chemical Society, p. 16139-16150, 2019.

DOI for 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 Download full text (pdf) of 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

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

Osterlund, Nicklas; Kulkarni, Yashraj S.; Misiaszek, Agata D.; Wallin, Cecilia et al.

Part of ACS Chemical Neuroscience, p. 1680-1692, 2018.

DOI for Amyloid-beta Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects

Challenges and advances in the computational modeling of biological phosphate hydrolysis

Petrovic, Dusan; Szeler, Klaudia; Kamerlin, Shina C. Lynn

Part of Chemical Communications, p. 3077-3089, 2018.

DOI for Challenges and advances in the computational modeling of biological phosphate hydrolysis Download full text (pdf) of Challenges and advances in the computational modeling of biological phosphate hydrolysis

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

Barrozo, Alexandre; Liao, Qinghua; Esguerra, Mauricio; Marloie, Gael et al.

Part of Organic and biomolecular chemistry, p. 2060-2073, 2018.

DOI for Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase Download full text (pdf) of Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase

Conformational dynamics and enzyme evolution

Petrovic, Dusan; Risso, Valeria A.; Kamerlin, Shina Caroline Lynn; Sanchez-Ruiz, Jose M.

Part of Journal of the Royal Society Interface, 2018.

DOI for Conformational dynamics and enzyme evolution

Cooperativity and flexibility in enzyme evolution

Pabis, Anna; Risso, Valeria A.; Sanchez-Ruiz, Jose M.; Kamerlin, Shina C. Lynn

Part of Current opinion in structural biology, p. 83-92, 2018.

DOI for Cooperativity and flexibility in enzyme evolution Download full text (pdf) of Cooperativity and flexibility in enzyme evolution

Debate on academic freedom and open access is healthy

Holbrook, J. Britt; Curry, Stephen; Kamerlin, Shina C. L.

Part of Nature, p. 494-494, 2018.

DOI for Debate on academic freedom and open access is healthy

Effects of conformational dynamics on enzyme evolution in TIM-barrel-fold proteins

Petrovic, Dusan; Kamerlin, Shina C. Lynn

Part of Abstracts of Papers of the American Chemical Society, 2018.

Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice

Purg, Miha; Kamerlin, Shina C. Lynn

Part of PHOSPHATASES, p. 3-51, 2018.

DOI for Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice

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

Marsavelski, Aleksandra; Petrovic, Dusan; Bauer, Paul; Vianello, Robert et al.

Part of ACS Omega, p. 3665-3674, 2018.

DOI for Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase Download full text (pdf) of Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase

Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa

Uduwela, Dimanthi R.; Pabis, Anna; Stevenson, Bradley J.; Kamerlin, Shina C. Lynn et al.

Part of ACS Catalysis, p. 8902-8914, 2018.

DOI for Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa

Epoxide Hydrolysis as a Model System for Understanding Flux Through a Branched Reaction Scheme

Janfalk Carlsson, Åsa; Bauer, Paul; Dobritzsch, Doreen; Kamerlin, Shina C Lynn et al.

Part of IUCrJ, p. 269-282, 2018.

DOI for Epoxide Hydrolysis as a Model System for Understanding Flux Through a Branched Reaction Scheme Download full text (pdf) of Epoxide Hydrolysis as a Model System for Understanding Flux Through a Branched Reaction Scheme

Evolution of chalcone isomerase from a noncatalytic ancestor

Kaltenbach, Miriam; Burke, Jason R.; Dindo, Mirco; Pabis, Anna et al.

Part of Nature Chemical Biology, p. 548-555, 2018.

DOI for Evolution of chalcone isomerase from a noncatalytic ancestor Download full text (pdf) of Evolution of chalcone isomerase from a noncatalytic ancestor

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

Miton, Charlotte M.; Jonas, Stefanie; Fischer, Gerhard; Duarte, Fernanda et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. E7293-E7302, 2018.

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

In Silico-Directed Evolution Using CADEE

Amrein, Beat Anton; Runthala, Ashish; Kamerlin, Shina C. Lynn

Part of Computational Methods in Protein Evolution, p. 381-415, 2018.

DOI for In Silico-Directed Evolution Using CADEE

Legend of a perfect enzyme: Active site architecture and loop dynamics in triosephosphate isomerase

Petrovic, Dusan; Kamerlin, Shina C. Lynn

Part of Abstracts of Papers of the American Chemical Society, 2018.

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

Liao, Qinghua; Kulkarni, Yashraj; Sengupta, Ushnish; Petrovic, Dusan et al.

Part of Journal of the American Chemical Society, p. 15889-15903, 2018.

DOI for Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case Download full text (pdf) of Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case

Molecular modeling of conformational dynamics and its role in enzyme evolution

Petrovic, Dusan; Kamerlin, Shina C. Lynn

Part of Current opinion in structural biology, p. 50-57, 2018.

DOI for Molecular modeling of conformational dynamics and its role in enzyme evolution Download full text (pdf) of Molecular modeling of conformational dynamics and its role in enzyme evolution

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

Bauer, Paul; Barrozo, Alexandre; Purg, Miha; Amrein, Beat Anton et al.

Part of SoftwareX, p. 388-395, 2018.

DOI for Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations Download full text (pdf) of Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

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

Kulkarni, Yashraj S.; Liao, Qinghua; Bylehn, Fabian; Amyes, Tina L. et al.

Part of Journal of the American Chemical Society, p. 3854-3857, 2018.

DOI for Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase Download full text (pdf) of Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase

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

Maurer, Dirk; Enugala, Thilak Reddy; Hamnevik, Emil; Bauer, Paul et al.

Part of ACS Catalysis, p. 7526-7538, 2018.

DOI for 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 Download full text (pdf) of 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

The evolution of multiple active site configurations in a designed enzyme

Hong, Nan-Sook; Petrovic, Dusan; Lee, Richmond; Gryn'ova, Ganna et al.

Part of Nature Communications, 2018.

DOI for The evolution of multiple active site configurations in a designed enzyme Download full text (pdf) of The evolution of multiple active site configurations in a designed enzyme

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

Blaha-Nelson, David; Krüger, Dennis M.; Szeler, Klaudia; Ben-David, Moshe et al.

Part of Journal of the American Chemical Society, p. 1155-1167, 2017.

DOI for Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1 Download full text (pdf) of Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

CADEE: Computer-Aided Directed Evolution of Enzymes

Amrein, Beat Anton; Steffen-Munsberg, Fabian; Szeler, Ireneusz; Purg, Miha et al.

Part of IUCrJ, p. 50-64, 2017.

DOI for CADEE: Computer-Aided Directed Evolution of Enzymes Download full text (pdf) of CADEE: Computer-Aided Directed Evolution of Enzymes

Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts

Zhan, Shaoqi; Martensson, Daniel; Purg, Miha; Kamerlin, Shina C. Lynn et al.

Part of Angewandte Chemie International Edition, p. 6962-6965, 2017.

DOI for Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts Download full text (pdf) of Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts

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

Maximoff, Sergey; Eloge, Josh; Kamerlin, Shina C. Lynn; Florian, Jan

Part of Abstracts of Papers of the American Chemical Society, 2017.

Kamerlin, Natasha

Computer Simulations of Polymer Gels: Structure, Dynamics, and Deformation

2017.

Download full text (pdf) of Kamerlin, Natasha

De novo active sites for resurrected Precambrian enzymes

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M. et al.

Part of Nature Communications, 2017.

DOI for De novo active sites for resurrected Precambrian enzymes Download full text (pdf) of De novo active sites for resurrected Precambrian enzymes

Deformation Behavior and Failure of Bimodal Networks

Kamerlin, Natasha; Elvingson, Christer

Part of Macromolecules, p. 7628-7635, 2017.

DOI for Deformation Behavior and Failure of Bimodal Networks

Deformation Behavior of Homogeneous and Heterogeneous Bimodal Networks

Kamerlin, Natasha; Elvingson, Christer

Part of Macromolecules, p. 9353-9359, 2017.

DOI for Deformation Behavior of Homogeneous and Heterogeneous Bimodal Networks

Deformation behaviour of homogeneous and heterogeneous bimodal networks

Kamerlin, Natasha; Elvingson, Christer

Part of Macromolecules, 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: A Free Energy Perturbation Study

Maximoff, Sergey N.; Kamerlin, Shina Caroline Lynn; Florian, Jan

Part of Journal of Physical Chemistry B, p. 7813-7822, 2017.

DOI for DNA Polymerase lambda 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

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

Kulkarni, Yashraj S.; Liao, Qinghua; Petrovic, Dusan; Krüger, Dennis M. et al.

Part of Journal of the American Chemical Society, p. 10514-10525, 2017.

DOI for Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase Download full text (pdf) of Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase

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

Liao, Qinghua; Pabis, Anna; Strodel, Birgit; Kamerlin, Shina Caroline Lynn

Part of Journal of Physical Chemistry Letters, p. 5408-5414, 2017.

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

Krüger, Dennis M.; Kamerlin, Shina C. Lynn

Part of ACS Omega, p. 4524-4530, 2017.

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Preface

Braida, Benoit; Kamerlin, Shina C. Lynn

Part of Computational and Theoretical Chemistry, p. 1-1, 2017.

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

Petrovic, Dusan; Frank, David; Kamerlin, Shina C. Lynn; Hoffmann, Kurt et al.

Part of ACS Catalysis, p. 6188-6197, 2017.

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

Purg, Miha; Elias, Mikael; Kamerlin, Shina C. Lynn

Part of Journal of the American Chemical Society, p. 17533-17546, 2017.

DOI for Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering Download full text (pdf) of Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering

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

Pabis, Anna; Williams, Nicholas H.; Kamerlin, Shina C. L.

Part of Organic and biomolecular chemistry, p. 7308-7316, 2017.

DOI for Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer Download full text (pdf) of Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer

The effect of magnesium ions on triphosphate hydrolysis

Barrozo, Alexandre; Blaha-Nelson, David; Williams, Nicholas H.; Kamerlin, Shina C. Lynn

Part of Pure and Applied Chemistry, p. 715-727, 2017.

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

Wallin, Cecilia; Kulkarni, Yashraj S.; Abelein, Axel; Jarvet, Jüri et al.

Part of Journal of Trace Elements in Medicine and Biology, p. 183-193, 2016.

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Collapse Dynamics of Core-Shell Nanogels

Kamerlin, Natasha; Elvingson, Christer

Part of Macromolecules, p. 5740-5749, 2016.

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Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1

Bauer, Paul; Janfalk Carlsson, Åsa; Amrein, Beat A.; Dobritzsch, Doreen et al.

Part of Organic and biomolecular chemistry, p. 5639-5651, 2016.

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

Aqvist, Johan; Kamerlin, Shina C. L.

Part of ACS Catalysis, p. 1737-1743, 2016.

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Laboratory evolved enzymes provide snapshots of the development of enantioconvergence in enzyme-catalyzed epoxide hydrolysis

Janfalk Carlsson, Åsa; Bauer, Paul; Dobritzsch, Doreeen; Nilsson, Mikael et al.

Part of ChemBioChem (Print), p. 1693-1697, 2016.

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

Ma, Huan; Szeler, Klaudia; Kamerlin, Shina Caroline Lynn; Widersten, Mikael

Part of Chemical Science, p. 1415-1421, 2016.

DOI for Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA) Download full text (pdf) of Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)

Phosphoryl and Sulfuryl Transfer

Barrozo, Alexandre; Kamerlin, Shina Caroline Lynn; Brandao, Tiago; Hengge, Alvan

Part of Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, 2016.

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

Purg, Miha; Pabis, Anna; Baier, Florian; Tokuriki, Nobuhiki et al.

Part of Philosophical Transactions of the Royal Society of London A, Mathematical, Physical and Engineering Sciences, p. 20160150-, 2016.

DOI for Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. Download full text (pdf) of Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase.

Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily

Pabis, Anna; Kamerlin, Shina Caroline Lynn

Part of Current opinion in structural biology, p. 14-21, 2016.

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Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer

Pabis, Anna; Duarte, Fernanda; Kamerlin, Shina C. L.

Part of Biochemistry, p. 3061-3081, 2016.

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The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

Duarte, Fernanda; Barrozo, Alexandre; Åqvist, Johan; Williams, Nicholas H. et al.

Part of Journal of the American Chemical Society, p. 10664-10673, 2016.

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Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions

Kamerlin, Natasha; Elvingson, Christer

Part of Journal of Physics, 2016.

DOI for Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions