Dr Marc Van der Kamp
M.Sc.(Wageningen), PhD(Bristol)
Expertise
Current positions
Associate Professor in Computational Biochemistry
School of Biochemistry
Contact
Press and media
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Research interests
Research in my group involves the use of biomolecular simulation to investigate and predict the behaviour of biomolecules. Of particular interest are enzymes and their specificity, catalysis and dynamics. The main techniques used are combined quantum mechanical / molecular mechanical modelling (QM/MM) and molecular dynamics simulation. The current primary area of interest is the use and development of biomolecular simulation protocols to aid development of biocatalysts.
Starting as a BBSRC David Phillips Fellow (2015-2021) I investigated biosynthetic enzymes that are responsible for a wide range of natural products, such as terpene and polyketide synthases. To efficiently tackle the chemical and structural complexity involved in the catalytic cycles of these enzymes, new simulation protocols and methods are developed and applied. By modifying enzymes according to predictions from simulation, in collaboration with experimentalists, the aim is to develop new biocatalysts for the sustainable production of high-value chemicals.
Similar methods are also used to gain insights for tackling the important problem of antibiotic resistance. We study a range of beta-lactamase enzymes, in particular focusing on how these can change (evolve) to efficiently breakdown even so-called 'last resort' antiobiotic treatments.
Our overall research interests are: enzymes involved in antibiotic resistance, computational simulation methods to aid enzyme engineering and (biologic) drug design, and understanding the fundamental principles of enzyme catalysis.
Projects and supervisions
Research projects
Multiscale simulation with Machine-Learned potentials for better G-quadruplex ligand design
Principal Investigator
Managing organisational unit
School of BiochemistryDates
01/03/2024 to 21/05/2024
Resistance to β-lactam antibiotics: Exploring the mechanism and inhibition of Class C β-lactamases
Principal Investigator
Managing organisational unit
School of BiochemistryDates
01/02/2023 to 31/01/2025
Simulating catalysis: Multiscale embedding of machine learning potentials
Principal Investigator
Managing organisational unit
School of BiochemistryDates
01/05/2021 to 30/04/2024
Simulating Catalysis: Multiscale Embedding Of Machine Learning Potentials
Principal Investigator
Managing organisational unit
School of BiochemistryDates
01/05/2021 to 30/04/2024
8043 BBSRC FTMA - Testing Fukui function-based activity descriptors for efficient in silico biocatalyst screening
Principal Investigator
Managing organisational unit
School of BiochemistryDates
01/06/2020 to 31/03/2022
Thesis supervisions
Publications
Recent publications
23/01/20244-Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude
Protein science : a publication of the Protein Society
Antibiotic Origami
Chemical Science
Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis
ACS Catalysis
Delineation of the Complete Reaction Cycle of a Natural Diels-Alderase
Chemical Science
Electric Fields Are a Key Determinant of Carbapenemase Activity in Class A β-Lactamases
ACS Catalysis