Kamerlin Group

Computational biochemistry

We develop and apply computational tools to solve important problems at the chemistry-biology interface. Using state-of-the-art computational techniques including quantum mechanical, classical mechanical, and hybrid methods, we explore the physical and chemical aspects that underlie enzyme catalysis. We are particularly interested in catalytic promiscuity and the evolution of protein function. Our aim is to develop new systems with greater catalytic proficiencies or altered functionalities. The lab takes an interdisciplinary approach, spanning physical organic chemistry, biochemistry, structural biology, and theory. At each stage, we work closely with leading experimental collaborators.

Group members

Research leader: Lynn Kamerlin

Group members: Andrei Demkiv, Antonietta Parracino, Michael Robinson

Publications

Targeting MarA N-terminal domain dynamics to prevent DNA binding

Corbella, Marina; Moreira, Catia; Bello-Madruga, Roberto; Torrent Burgas, Marc et al.

Part of Protein Science, 2025
- DOI for Targeting MarA N-terminal domain dynamics to prevent DNA binding
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Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families

Yehorova, Dariia; Crean, Rory M.; Kasson, Peter M.; Kamerlin, Shina C. L.

Part of Protein Science, 2024
- DOI for Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families
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Using residue interaction networks to understand protein function and evolution and to engineer new proteins

Yehorova, Dariia; Di Geronimo, Bruno; Robinson, Michael; Kasson, Peter M. et al.

Part of Current opinion in structural biology, 2024
- DOI for Using residue interaction networks to understand protein function and evolution and to engineer new proteins
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SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases

Shen, Ruidan; Brownless, Alfie-Louise R.; Alansson, Nikolas; Corbella, Marina et al.

Part of JACS Au, p. 2874-2885, 2024
- DOI for SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases
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Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation

Crnjar, Alessandro; Grinen, Aransa; Kamerlin, Shina C. Lynn; Ramirez-Sarmiento, Cesar A.

Part of ACS ORGANIC & INORGANIC AU, p. 109-119, 2023
- DOI for Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation
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KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

Crean, Rory M.; Slusky, Joanna S. G.; Kasson, Peter M.; Kamerlin, Shina C. Lynn

Part of Journal of Chemical Physics, 2023
- DOI for KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes
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The perceived decline of "disruptive" science and technology

Kamerlin, Shina Caroline Lynn

Part of EMBO Reports, 2023
- DOI for The perceived decline of "disruptive" science and technology
Science after Brexit: bright spots on the Horizon?

Mulholland, Adrian J.; Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2023
- DOI for Science after Brexit: bright spots on the Horizon?
Loop dynamics and the evolution of enzyme activity

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

Part of Nature Reviews Chemistry, p. 536-547, 2023
- DOI for Loop dynamics and the evolution of enzyme activity
Representation matters: responding to the current campaign against DEI efforts

Finn, M. G.; Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2023
- DOI for Representation matters: responding to the current campaign against DEI efforts
A sensor complements the steric gate when DNA polymerase Îµ discriminates ribonucleotides

Parkash, Vimal; Kulkarni, Yashraj; Bylund, Goran O.; Osterman, Pia et al.

Part of Nucleic Acids Research, p. 11225-11238, 2023
- DOI for A sensor complements the steric gate when DNA polymerase Îµ discriminates ribonucleotides
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Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations

Brickel, Sebastian; Demkiv, Andrey O.; Crean, Rory M.; Pinto, Gaspar P. et al.

Part of Journal of Molecular Graphics and Modelling, 2023
- DOI for Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations
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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
- DOI for A Structural View into the Complexity of Carbon Dioxide Fixation
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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
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Scholars in peril: when being a scientist can land you in jail (or worse)

Kamerlin, Shina C. Lynn

Part of EMBO Reports, 2022
- DOI for Scholars in peril: when being a scientist can land you in jail (or worse)
Computational Advances in Protein Engineering and Enzyme Design

Derat, Etienne; Kamerlin, Shina C. Lynn

Part of Journal of Physical Chemistry B, p. 2449-2451, 2022
- DOI for Computational Advances in Protein Engineering and Enzyme Design
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

Odoemelam, Chiemela S.; Hunter, Elena; Simms, John; Ahmad, Zeeshan et al.

Part of Applied Biosciences, p. 143-162, 2022
- DOI for 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
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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

Fisher, Gemma; Corbella, Marina; Alphey, Magnus S.; Nicholson, John et al.

Part of Nature Communications, 2022
- DOI for Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation
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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
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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
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
From flying cats to dancing proteins: Review of Arieh Warshel's 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 flying cats to dancing proteins: Review of Arieh Warshel's From Kibbutz Fishponds to the Nobel Prize: Taking Molecular Functions into Cyberspace
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
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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
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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
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?
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?
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
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
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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
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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
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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?
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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
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Dan Salah Tawfik (1955-2021): A giant of protein evolution

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

Part of EMBO Reports, 2021
- DOI for Dan Salah Tawfik (1955-2021): A giant of protein evolution
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
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
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
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
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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
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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
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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?
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
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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
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
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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
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
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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
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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
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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
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