Kamerlins grupp

Beräkningsbiokemi
Vi utvecklar och tillämpar en rad beräkningsverktyg för att lösa viktiga problem i gränslandet mellan kemi och biologi. Med toppmoderna beräkningstekniker som bygger på kvantmekanik, klassisk mekanik och hybridmetoder utforskar vi de fysikaliska och kemiska aspekterna som ligger till grund för enzymkatalys. Vi är särskilt intresserade av katalytisk promiskuitet och utvecklingen av proteiners funktion. Vårt mål är att utveckla nya enzymer med större katalytiska förmågor och förändrad funktionalitet. Gruppen är tvärvetenskaplig och använder tekniker som spänner över fysikalisk organisk kemi, biokemi, strukturbiologi och teori. I varje steg har vi nära samarbeten med ledande experimentella grupper.
Gruppmedlemmar
Publikationer
Targeting MarA N-terminal domain dynamics to prevent DNA binding
Ingår i Protein Science, 2025
- DOI för Targeting MarA N-terminal domain dynamics to prevent DNA binding
- Ladda ner fulltext (pdf) av Targeting MarA N-terminal domain dynamics to prevent DNA binding
Ingår i Protein Science, 2024
- DOI för Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families
- Ladda ner fulltext (pdf) av Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families
Ingår i Current opinion in structural biology, 2024
- DOI för Using residue interaction networks to understand protein function and evolution and to engineer new proteins
- Ladda ner fulltext (pdf) av Using residue interaction networks to understand protein function and evolution and to engineer new proteins
SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases
Ingår i JACS Au, s. 2874-2885, 2024
- DOI för SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases
- Ladda ner fulltext (pdf) av SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases
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
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
The perceived decline of "disruptive" science and technology
Ingår i EMBO Reports, 2023
Science after Brexit: bright spots on the Horizon?
Ingår i EMBO Reports, 2023
Loop dynamics and the evolution of enzyme activity
Ingår i Nature Reviews Chemistry, s. 536-547, 2023
Representation matters: responding to the current campaign against DEI efforts
Ingår i EMBO Reports, 2023
A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
Ingår i Nucleic Acids Research, s. 11225-11238, 2023
- DOI för A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
- Ladda ner fulltext (pdf) av A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations
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
A Structural View into the Complexity of Carbon Dioxide Fixation
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
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
Scholars in peril: when being a scientist can land you in jail (or worse)
Ingår i EMBO Reports, 2022
Computational Advances in Protein Engineering and Enzyme Design
Ingår i Journal of Physical Chemistry B, s. 2449-2451, 2022
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
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
Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021)
Ingår i Journal of Molecular Biology, 2022
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
Late-termination of pregnancy for medical reasons: when abortion isn't really by choice
Ingår i EMBO Reports, 2022
5 suggestions to increase grant application success rates
Ingår i EMBO Reports, 2022
Ingår i Nature Reviews Chemistry, s. 85-85, 2022
Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase
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
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
Computational Investigation of Ligand Binding of Flavonoids in Cytochrome P450 Receptors
Ingår i Current pharmaceutical design, s. 3637-3648, 2022
Academic motherhood - what happens when you can't make it happen?
Ingår i EMBO Reports, 2021
How to write a successful postdoc application: the PI perspective
Ingår i EMBO Reports, 2021
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
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
Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases
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
Journal Open Access and Plan S: Solving Problems or Shifting Burdens?
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?
Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
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
Dan Salah Tawfik (1955-2021): A giant of protein evolution
Ingår i EMBO Reports, 2021
Ingår i EMBO Reports, 2021
Errors in DFT integration grids and their potential impact on chemical shift calculations
Ingår i Magnetic Resonance in Chemistry, s. 116-117, 2020
Enzyme Evolution An Epistatic Ratchet versus a Smooth Reversible Transition
Ingår i Molecular biology and evolution, s. 1133-1147, 2020
Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 5310-5318, 2020
Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study
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
Harnessing Conformational Plasticity to Generate Designer Enzymes
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
Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening
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
Female Faculty: Why So Few and Why Care?
Ingår i Chemistry - A European Journal, s. 8319-8323, 2020
Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation
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
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
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
When we increase diversity in academia, we all win
Ingår i EMBO Reports, 2020
Open Access, Plan S, and researchers' needs
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
G-Protein coupled receptors: structure and function in drug discovery
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
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
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