Publikationer i Lynn Kamerlins grupp

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.

Ingår i ACS ORGANIC & INORGANIC AU, s. 109-119, 2023.

DOI för Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation Ladda ner fulltext (pdf) av Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation

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

Ingår i Journal of Chemical Physics, 2023.

DOI för KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes Ladda ner fulltext (pdf) av KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

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.

Ingår i Journal of Molecular Graphics and Modelling, 2023.

DOI för Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations Ladda ner fulltext (pdf) av Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations

Science after Brexit: bright spots on the Horizon?

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

Ingår i EMBO Reports, 2023.

DOI för Science after Brexit: bright spots on the Horizon?

The perceived decline of "disruptive" science and technology

Kamerlin, Shina Caroline Lynn

Ingår i EMBO Reports, 2023.

DOI för The perceived decline of "disruptive" science and technology

5 suggestions to increase grant application success rates

Kamerlin, Shina C. Lynn

Ingår i EMBO Reports, 2022.

DOI för 5 suggestions to increase grant application success rates

A Structural View into the Complexity of Carbon Dioxide Fixation

Kourist, Robert; Kamerlin, Shina C. Lynn

Ingår i ACS CENTRAL SCIENCE, s. 1040-1042, 2022.

DOI för A Structural View into the Complexity of Carbon Dioxide Fixation Ladda ner fulltext (pdf) av A Structural View into the Complexity of Carbon Dioxide Fixation

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.

Ingår i Journal of Molecular Biology, 2022.

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

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.

Ingår i Nature Communications, 2022.

DOI för Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation Ladda ner fulltext (pdf) av Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

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.

Ingår i JACS Au, s. 943-960, 2022.

DOI för Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi Ladda ner fulltext (pdf) av Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi

Computational Advances in Protein Engineering and Enzyme Design

Derat, Etienne; Kamerlin, Shina C. Lynn

Ingår i Journal of Physical Chemistry B, s. 2449-2451, 2022.

DOI för Computational Advances in Protein Engineering and Enzyme Design

Computational Investigation of Ligand Binding of Flavonoids in Cytochrome P450 Receptors

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

Ingår i Current pharmaceutical design, s. 3637-3648, 2022.

DOI för 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.

Ingår i ACS Catalysis, s. 3357-3370, 2022.

DOI för Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase Ladda ner fulltext (pdf) av 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

Ingår i TIBS -Trends in Biochemical Sciences. Regular ed., s. 375-389, 2022.

DOI för Exploiting enzyme evolution for computational protein design Ladda ner fulltext (pdf) av Exploiting enzyme evolution for computational protein design

From flying cats to dancing proteins

Kamerlin, Shina C. Lynn

Ingår i Nature Reviews Chemistry, s. 85-85, 2022.

DOI för From flying cats to dancing proteins

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

Kamerlin, Shina C. Lynn

Ingår i Nature Reviews Chemistry, s. 85-85, 2022.

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

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.

Ingår i Applied Biosciences, s. 143-162, 2022.

DOI för 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 Ladda ner fulltext (pdf) av 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

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.

Ingår i Chemical Science, s. 13524-13540, 2022.

DOI för Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases Ladda ner fulltext (pdf) av 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

Ingår i EMBO Reports, 2022.

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

Scholars in peril: when being a scientist can land you in jail (or worse)

Kamerlin, Shina C. Lynn

Ingår i EMBO Reports, 2022.

DOI för Scholars in peril: when being a scientist can land you in jail (or worse)

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

Kamerlin, Shina Caroline Lynn

Ingår i EMBO Reports, 2021.

DOI för 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 för 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.

Ingår i Nature Communications, 2021.

DOI för Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase Ladda ner fulltext (pdf) av 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

Ingår i EMBO Reports, 2021.

DOI för 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.

Ingår i Development and Change, s. 627-650, 2021.

DOI för Journal Open Access and Plan S: Solving Problems or Shifting Burdens? Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the American Chemical Society, s. 3830-3845, 2021.

DOI för Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases Ladda ner fulltext (pdf) av 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

Ingår i EMBO Reports, 2021.

DOI för 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.

Ingår i JACS Au, s. 646-659, 2021.

DOI för Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases Ladda ner fulltext (pdf) av 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.

Ingår i Journal of Physical Chemistry B, s. 6791-6806, 2021.

DOI för The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition Ladda ner fulltext (pdf) av 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.

Ingår i Chemical Science, s. 6134-6148, 2020.

DOI för Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening Ladda ner fulltext (pdf) av 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.

Ingår i Molecular biology and evolution, s. 1133-1147, 2020.

DOI för 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

Ingår i Magnetic Resonance in Chemistry, s. 116-117, 2020.

DOI för 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

Ingår i Chemistry - A European Journal, s. 8319-8323, 2020.

DOI för 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.

Ingår i RSC Advances, s. 36337-36348, 2020.

DOI för G-Protein coupled receptors: structure and function in drug discovery Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the American Chemical Society, s. 20216-20231, 2020.

DOI för Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase Ladda ner fulltext (pdf) av 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

Ingår i Journal of the American Chemical Society, s. 11324-11342, 2020.

DOI för Harnessing Conformational Plasticity to Generate Designer Enzymes Ladda ner fulltext (pdf) av 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.

Ingår i Clinical Infectious Diseases, s. 3174-3181, 2020.

DOI för Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control Ladda ner fulltext (pdf) av 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.

Ingår i ACS Catalysis, s. 4863-4870, 2020.

DOI för Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions Ladda ner fulltext (pdf) av 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

Ingår i Journal of Organic Chemistry, s. 6489-6497, 2020.

DOI för Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study Ladda ner fulltext (pdf) av 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.

Ingår i ACS Catalysis, s. 11253-11267, 2020.

DOI för Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase Ladda ner fulltext (pdf) av 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

Ingår i EMBO Reports, 2020.

DOI för Open Access, Plan S, and researchers' needs Ladda ner fulltext (pdf) av 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

Ingår i ACS Omega, s. 4380-4385, 2020.

DOI för Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation Ladda ner fulltext (pdf) av 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 5310-5318, 2020.

DOI för 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

Ingår i ACS Catalysis, s. 9115-9128, 2020.

DOI för The Role of Substrate-Coenzyme Crosstalk in Determining Turnover Rates in Rhodococcus ruber Alcohol Dehydrogenase Ladda ner fulltext (pdf) av 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

Ingår i Journal of Chemical Information and Modeling, s. 3792-3803, 2020.

DOI för Toward a Computational Ecotoxicity Assay

Unravelling the mechanism of pH-regulation in dinoflagellate luciferase

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

Ingår i International Journal of Biological Macromolecules, s. 2671-2680, 2020.

DOI för Unravelling the mechanism of pH-regulation in dinoflagellate luciferase Ladda ner fulltext (pdf) av Unravelling the mechanism of pH-regulation in dinoflagellate luciferase

When we increase diversity in academia, we all win

Kamerlin, Shina C. Lynn

Ingår i EMBO Reports, 2020.

DOI för 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.

Ingår i ACS Catalysis, s. 8388-8396, 2019.

DOI för 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.

Ingår i Journal of Organic Chemistry, s. 6982-6991, 2019.

DOI för 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

Ingår i Advances in Physical Organic Chemistry, s. 69-104, 2019.

DOI för Computational physical organic chemistry using the empirical valence bond approach Ladda ner fulltext (pdf) av 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.

Ingår i eLIFE, 2019.

DOI för Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the American Chemical Society, s. 10684-10701, 2019.

DOI för 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.

Ingår i Nature Chemical Biology, s. 1120-1128, 2019.

DOI för 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.

Ingår i Biochemistry, s. 1061-1073, 2019.

DOI för 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.

Ingår i Journal of Physical Chemistry B, s. 3576-3590, 2019.

DOI för Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition Ladda ner fulltext (pdf) av 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

Ingår i Journal of Physical Chemistry Letters, s. 2244-2249, 2019.

DOI för Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2019.

DOI för Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon Ladda ner fulltext (pdf) av 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

Ingår i Biochemical Society Transactions, s. 1449-1460, 2019.

DOI för The role of ligand-gated conformational changes in enzyme catalysis Ladda ner fulltext (pdf) av 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

Ingår i Journal of the American Chemical Society, s. 16139-16150, 2019.

DOI för 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 Ladda ner fulltext (pdf) av 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.

Ingår i ACS Chemical Neuroscience, s. 1680-1692, 2018.

DOI för 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

Ingår i Chemical Communications, s. 3077-3089, 2018.

DOI för Challenges and advances in the computational modeling of biological phosphate hydrolysis Ladda ner fulltext (pdf) av 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.

Ingår i Organic and biomolecular chemistry, s. 2060-2073, 2018.

DOI för Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the Royal Society Interface, 2018.

DOI för Conformational dynamics and enzyme evolution

Cooperativity and flexibility in enzyme evolution

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

Ingår i Current opinion in structural biology, s. 83-92, 2018.

DOI för Cooperativity and flexibility in enzyme evolution Ladda ner fulltext (pdf) av Cooperativity and flexibility in enzyme evolution

Debate on academic freedom and open access is healthy

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

Ingår i Nature, s. 494-494, 2018.

DOI för 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

Ingår i 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

Ingår i PHOSPHATASES, s. 3-51, 2018.

DOI för 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.

Ingår i ACS Omega, s. 3665-3674, 2018.

DOI för Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase Ladda ner fulltext (pdf) av 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.

Ingår i ACS Catalysis, s. 8902-8914, 2018.

DOI för 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.

Ingår i IUCrJ, s. 269-282, 2018.

DOI för Epoxide Hydrolysis as a Model System for Understanding Flux Through a Branched Reaction Scheme Ladda ner fulltext (pdf) av 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.

Ingår i Nature Chemical Biology, s. 548-555, 2018.

DOI för Evolution of chalcone isomerase from a noncatalytic ancestor Ladda ner fulltext (pdf) av 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. E7293-E7302, 2018.

DOI för 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

Ingår i Computational Methods in Protein Evolution, s. 381-415, 2018.

DOI för 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

Ingår i 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.

Ingår i Journal of the American Chemical Society, s. 15889-15903, 2018.

DOI för Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case Ladda ner fulltext (pdf) av 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

Ingår i Current opinion in structural biology, s. 50-57, 2018.

DOI för Molecular modeling of conformational dynamics and its role in enzyme evolution Ladda ner fulltext (pdf) av 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.

Ingår i SoftwareX, s. 388-395, 2018.

DOI för Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the American Chemical Society, s. 3854-3857, 2018.

DOI för Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase Ladda ner fulltext (pdf) av 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.

Ingår i ACS Catalysis, s. 7526-7538, 2018.

DOI för 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 Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2018.

DOI för The evolution of multiple active site configurations in a designed enzyme Ladda ner fulltext (pdf) av 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.

Ingår i Journal of the American Chemical Society, s. 1155-1167, 2017.

DOI för Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1 Ladda ner fulltext (pdf) av 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.

Ingår i IUCrJ, s. 50-64, 2017.

DOI för CADEE: Computer-Aided Directed Evolution of Enzymes Ladda ner fulltext (pdf) av 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.

Ingår i Angewandte Chemie International Edition, s. 6962-6965, 2017.

DOI för Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts Ladda ner fulltext (pdf) av 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

Ingår i Abstracts of Papers of the American Chemical Society, 2017.

Kamerlin, Natasha

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

2017.

Ladda ner fulltext (pdf) av Kamerlin, Natasha

De novo active sites for resurrected Precambrian enzymes

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

Ingår i Nature Communications, 2017.

DOI för De novo active sites for resurrected Precambrian enzymes Ladda ner fulltext (pdf) av De novo active sites for resurrected Precambrian enzymes

Deformation Behavior and Failure of Bimodal Networks

Kamerlin, Natasha; Elvingson, Christer

Ingår i Macromolecules, s. 7628-7635, 2017.

DOI för Deformation Behavior and Failure of Bimodal Networks

Deformation Behavior of Homogeneous and Heterogeneous Bimodal Networks

Kamerlin, Natasha; Elvingson, Christer

Ingår i Macromolecules, s. 9353-9359, 2017.

DOI för Deformation Behavior of Homogeneous and Heterogeneous Bimodal Networks

Deformation behaviour of homogeneous and heterogeneous bimodal networks

Kamerlin, Natasha; Elvingson, Christer

Ingår i 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

Ingår i Journal of Physical Chemistry B, s. 7813-7822, 2017.

DOI för 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.

Ingår i Journal of the American Chemical Society, s. 10514-10525, 2017.

DOI för Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase Ladda ner fulltext (pdf) av 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

Ingår i Journal of Physical Chemistry Letters, s. 5408-5414, 2017.

DOI för Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions Ladda ner fulltext (pdf) av Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions

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

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

Ingår i ACS Omega, s. 4524-4530, 2017.

DOI för Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations Ladda ner fulltext (pdf) av Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations

Preface

Braida, Benoit; Kamerlin, Shina C. Lynn

Ingår i Computational and Theoretical Chemistry, s. 1-1, 2017.

DOI för Preface Ladda ner fulltext (pdf) av Preface

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.

Ingår i ACS Catalysis, s. 6188-6197, 2017.

DOI för Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase Ladda ner fulltext (pdf) av Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase

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

Ingår i Journal of the American Chemical Society, s. 17533-17546, 2017.

DOI för Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering Ladda ner fulltext (pdf) av 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.

Ingår i Organic and biomolecular chemistry, s. 7308-7316, 2017.

DOI för Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer Ladda ner fulltext (pdf) av 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

Ingår i Pure and Applied Chemistry, s. 715-727, 2017.

DOI för The effect of magnesium ions on triphosphate hydrolysis Ladda ner fulltext (pdf) av The effect of magnesium ions on triphosphate hydrolysis

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.

Ingår i Journal of Trace Elements in Medicine and Biology, s. 183-193, 2016.

DOI för Characterization of Mn(II) ion binding to the amyloid-beta peptide in Alzheimer's disease Ladda ner fulltext (pdf) av Characterization of Mn(II) ion binding to the amyloid-beta peptide in Alzheimer's disease

Collapse Dynamics of Core-Shell Nanogels

Kamerlin, Natasha; Elvingson, Christer

Ingår i Macromolecules, s. 5740-5749, 2016.

DOI för Collapse Dynamics of Core-Shell Nanogels