Publications

View all

Dana Matthews Dana Matthews

Exploring large protein sequence space through homology-and representation-based hierarchical clustering

John Z Chen, Barnabas Gall, Sacha B Pulsford, Nobuhiko Tokuriki, Colin J Jackson

Exploring large protein sequence space through homology-and representation-based hierarchical clustering

Molecular Biology and Evolution, 2025

Read More
fluorescent proteins, fret, nancanonical amino acids, cell microscopy, structural biology Dana Matthews fluorescent proteins, fret, nancanonical amino acids, cell microscopy, structural biology Dana Matthews

Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4‐Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites

Haocheng Qianzhu, Elwy H Abdelkader, Adarshi P Welegedara, Edan Habel, Nathan Paul, Rebecca L Frkic, Colin J Jackson, Thomas Huber, Gottfried Otting

Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4‐Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites

Angewandte Chemie, 2025

Read More
receptor proteins, fret, psychiatry Dana Matthews receptor proteins, fret, psychiatry Dana Matthews

An increased copy number of glycine decarboxylase (GLDC) associated with psychosis reduces extracellular glycine and impairs NMDA receptor function

Maltesh Kambali, Yan Li, Petr Unichenko, Jessica A Feria Pliego, Rachita Yadav, Jing Liu, Patrick McGuinness, Johanna G Cobb, Muxiao Wang, Rajasekar Nagarajan, Jinrui Lyu, Vanessa Vongsouthi, Colin J Jackson, Elif Engin, Joseph T Coyle, Jaeweon Shin, Nathaniel W Hodgson, Takao K Hensch, Michael E Talkowski, Gregg E Homanics, Vadim Y Bolshakov, Christian Henneberger, Uwe Rudolph

An increased copy number of glycine decarboxylase (GLDC) associated with psychosis reduces extracellular glycine and impairs NMDA receptor function

Molecular Psychiatry, 2025

Read More
plastic-degrading enzymes, ancestral sequence reconstruction, protein landscape analysis, biomathematics, protein characterization, protein engineering, protein evolution Dana Matthews plastic-degrading enzymes, ancestral sequence reconstruction, protein landscape analysis, biomathematics, protein characterization, protein engineering, protein evolution Dana Matthews

Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape

Vanessa Vongsouthi, Rosemary Georgelin, Dana S Matthews, Jake Saunders, Brendon M Lee, Jennifer Ton, Adam M Damry, Rebecca L Frkic, Matthew A Spence, Colin J Jackson

Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape

Science Advances, 2025

Read More
malaria, parasites, vaccine design, antigens Dana Matthews malaria, parasites, vaccine design, antigens Dana Matthews

Having your cake and eating it too–a new target for sporozoite-neutralising mAbs

Joe A Kaczmarski, Colin J Jackson, Ian A Cockburn

Having your cake and eating it too–a new target for sporozoite-neutralising mAbs

Trends in Parasitology, 2025

Read More
biomathematics, protein landscape analysis, protein evolution, machine learning Dana Matthews biomathematics, protein landscape analysis, protein evolution, machine learning Dana Matthews

Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains

Mahakaran Sandhu, John Z Chen, Dana S Matthews, Matthew A Spence, Sacha B Pulsford, Barnabas Gall, Joe A Kaczmarski, James Nichols, Nobuhiko Tokuriki, Colin J Jackson

Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains

Biochemistry, 2025

Read More
enzymatic chemical detoxification, protein characterization, structural biology Dana Matthews enzymatic chemical detoxification, protein characterization, structural biology Dana Matthews

Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC

Shanza Bibi, Callum W. Breeze, Vusqa Jadoon, Anum Fareed, Alina Syed, Rebecca L. Frkic, Habiba Zaffar, Muhammad Ali, Iftikhar Zeb, Colin J. Jackson, Tatheer Alam Naqvi

Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC

Scientific Reports, 2025

Read More
ancestral sequence reconstruction, machine learning, protein engineering, biomathematics Dana Matthews ancestral sequence reconstruction, machine learning, protein engineering, biomathematics Dana Matthews

Leveraging ancestral sequence reconstruction for protein representation learning

Dana S. Matthews, Matthew A. Spence, Adam C. Mater, James Nichols, Sacha B. Pulsford, Mahakaran Sandhu, Joe A. Kaczmarski, Charlotte M. Miton, Nobuhiko Tokuriki, Colin J. Jackson

Leveraging ancestral sequence reconstruction for protein representation learning

Nature Machine Intelligence, 2024

Read More
protein characterization, solute-binding proteins, structural biology Dana Matthews protein characterization, solute-binding proteins, structural biology Dana Matthews

The ultra-high affinity transport proteins of ubiquitous marine bacteria

Ben E. Clifton, Uria Alcolombri, Gen-Ichiro Uechi, Colin J. Jackson and Paola Laurino

The ultra-high affinity transport proteins of ubiquitous marine bacteria

Nature, 2024

Read More
non-canonical amino acids, structural biology Dana Matthews non-canonical amino acids, structural biology Dana Matthews

1.3Å Crystal Structure of E.coli Peptidyl–Prolyl Isomerase B with Uniform Substitution of Valine by (2S,3S)-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered Rotamers of CH2F Groups

Rebecca L. Frkic, Yi Jiun Tan, Ansis Maleckis, Nicholas F. Chilton, Gottfried Otting* and Colin J. Jackson*

1.3 Å Crystal Structure of E. coli Peptidyl–Prolyl Isomerase B with Uniform Substitution of Valine by (2S,3S)-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered Rotamers of CH2F Groups

Biochemistry, 2024

Read More
pesticide-degrading enzymes, nanomaterials, molecular dynamics Dana Matthews pesticide-degrading enzymes, nanomaterials, molecular dynamics Dana Matthews

Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates

Benjamin M. Carter, Graham J. Day, William H. Zhang, Richard B. Sessions, Colin J. Jackson, and Adam W. Perriman*

Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates

Small, 2024

Read More
receptor proteins, gmo, receptor regulation Dana Matthews receptor proteins, gmo, receptor regulation Dana Matthews

An increased copy number of glycine decarboxylase (GLDC) associated with psychosis reduces extracellular glycine and impairs NMDA receptor function

Maltesh Kambali, Yan Li, Petr Unichenko, Jessica A. Feria Pliego, Rachita Yadav, Jing Liu, Patrick McGuinness, Johanna G. Cobb, Muxiao Wang, Rajasekar Nagarajan, Jinrui Lyu, Vanessa Vongsouthi, Colin J. Jackson, Elif Engin, Joseph T. Coyle, Jaeweon Shin, Nathaniel W. Hodgson, Takao K. Hensch, Michael E. Talkowski, Gregg E. Homanics, Vadim Y. Bolshakov, Christian Henneberger and Uwe Rudolph*

An increased copy number of glycine decarboxylase (GLDC) associated with psychosis reduces extracellular glycine and impairs NMDA receptor function

Molecular Psychiatry, 2024

Read More
pesticide-degrading enzymes, molecular dynamics, structural biology, nanomaterials Dana Matthews pesticide-degrading enzymes, molecular dynamics, structural biology, nanomaterials Dana Matthews

Partitioning of an Enzyme‐Polymer Surfactant Nanocomplex into Lipid‐Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates

Benjamin M Carter, Graham J Day, William H Zhang, Richard B Sessions, Colin J. Jackson, Adam W Perriman

Partitioning of an Enzyme‐Polymer Surfactant Nanocomplex into Lipid‐Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates

Small, 2024

Read More
consensus design, molecular dynamics, structural biology, protein engineering Dana Matthews consensus design, molecular dynamics, structural biology, protein engineering Dana Matthews

Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design

Jake W Saunders, Adam M Damry, Vanessa Vongsouthi, Matthew A Spence, Rebecca L Frkic, Chloe Gomez, Patrick A Yates, Dana S Matthews, Nobuhiko Tokuriki, Malcolm D McLeod and Colin J Jackson*

Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design

Biochemistry, 2024

Read More
peptide inhibitor design, SARS-CoV-2, cyclic peptides, molecular dynamics Dana Matthews peptide inhibitor design, SARS-CoV-2, cyclic peptides, molecular dynamics Dana Matthews

Exploiting Hydrophobic Amino Acid Scanning to Develop Cyclic Peptide Inhibitors of the SARS-CoV-2 Main Protease with Antiviral Activity

Katriona Harrison, Patrick W. Carlos, Sven Ullrich, Anupriya Aggarwal, Jason Johansen‐Leete, Vishnu Mini Sasi, Isabel Barter, Joshua WC. Maxwell, Max J. Bedding, Mark Larance, Stuart Turville, Alexander Norman, Colin J. Jackson, Christoph Nitsche, and Richard J. Payne*

Exploiting Hydrophobic Amino Acid Scanning to Develop Cyclic Peptide Inhibitors of the SARS-CoV-2 Main Protease with Antiviral Activity

Chemistry – A European Journal, 2024

Read More
structural biology, protein conformation, non-canonical amino acids Dana Matthews structural biology, protein conformation, non-canonical amino acids Dana Matthews

Conformational Preferences of the Non-Canonical Amino Acids (2S,4S)-5-Fluoroleucine, (2S,4R)-5-Fluoroleucine, and 5,5'-Difluoroleucine in a Protein

Rebecca L Frkic, Yi Jiun Tan, Elwy H Abdelkader, Ansis Maleckis, Eliza Tarcoveanu, Christoph Nitsche, Gottfried Otting*, Colin J Jackson*

Conformational Preferences of the Non-Canonical Amino Acids (2S,4S)-5-Fluoroleucine, (2S,4R)-5-Fluoroleucine, and 5,5'-Difluoroleucine in a Protein

Biochemistry, 2024

Read More
directed evolution, plastic-degrading enzymes, enzyme screening, protein engineering Dana Matthews directed evolution, plastic-degrading enzymes, enzyme screening, protein engineering Dana Matthews

Improving plastic degrading enzymes via directed evolution

Yvonne Joho, Vanessa Vongsouthi, Chloe Gomez, Joachim S Larsen, Albert Ardevol and Colin J Jackson*

Improving plastic degrading enzymes via directed evolution

Protein Engineering, Design, & Selection, 2024

Read More
sequence similarity network, structural biology, molecular dynamics, protein characterization Dana Matthews sequence similarity network, structural biology, molecular dynamics, protein characterization Dana Matthews

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides

Oliver B Smith, Rebecca L Frkic, Marina G Rahman, Colin J Jackson* and Joe A Kaczmarski*

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides

Biochemistry, 2024

Read More
ancestral sequence reconstruction, deep mutational scanning, protein evolution, epistasis analysis Dana Matthews ancestral sequence reconstruction, deep mutational scanning, protein evolution, epistasis analysis Dana Matthews

Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors

Anthony T Meger, Matthew A Spence, Mahakaran Sandhu, Dana S Matthews, Jackie Chen, Colin J Jackson and Srivatsan Raman

Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors

Cell Systems, 2024

Read More
lanthanide catalysts, structural biology, protein characterization Dana Matthews lanthanide catalysts, structural biology, protein characterization Dana Matthews

Mononuclear binding and catalytic activity of europium (III) and gadolinium (III) at the active site of the model metalloenzyme phosphotriesterase

Callum W Breeze, Yuji Nakano, Eleanor C Campbell, Rebecca L Frkic, David W Lupton and Colin J Jackson

Mononuclear binding and catalytic activity of europium (III) and gadolinium (III) at the active site of the model metalloenzyme phosphotriesterase

Acta Crystallographica Section D: Structural Biology, 2024

Read More

A full list of publications can be found on Google Scholar: