Kamerlin Group

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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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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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 ε 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 ε discriminates ribonucleotides
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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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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

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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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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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

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

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
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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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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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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
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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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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

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
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