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Abstract
We describe a protocol to perform empirical valence bond (EVB) simulations using GROMACS software. EVB is a fast and reliable method that allows one to determine the reaction free-energy profiles in complex systems, such as enzymes, by employing classical force fields to represent a chemical reaction. Therefore, running EVB simulations is basically as fast as any classical molecular dynamics simulation, and the method uses standard free-energy calculations to map the free-energy change along a given reaction path. To exemplify and validate our EVB implementation, we replicated two cases of our earlier enzyme simulations. One of these addresses the decomposition of the activation free energy into its enthalpic and entropic components, and the other is focused on calculating the overall catalytic effect of the enzyme compared to the same reaction in water. These two examples give virtually identical results to those obtained with programs that were specifically designed for EVB simulations and show that the GROMACS implementation is robust and can be used for very large systems.
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Affiliation(s)
- Gabriel Oanca
- Department of Cell and Molecular Biology,
Biomedical Center, Uppsala University, Uppsala SE-751 24, Sweden
| | - Florian van der Ent
- Department of Cell and Molecular Biology,
Biomedical Center, Uppsala University, Uppsala SE-751 24, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology,
Biomedical Center, Uppsala University, Uppsala SE-751 24, Sweden
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van der Ent F, Skagseth S, Lund BA, Sǒan J, Griese JJ, Brandsdal BO, Åqvist J. Computational design of the temperature optimum of an enzyme reaction. Sci Adv 2023; 9:eadi0963. [PMID: 37379391 DOI: 10.1126/sciadv.adi0963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic α-amylase from an Antarctic bacterium, the inactivation is thought to originate from a specific enzyme-substrate interaction that breaks around room temperature. Here, we report a computational redesign of this enzyme aimed at shifting its temperature optimum upward. A set of mutations designed to stabilize the enzyme-substrate interaction were predicted by computer simulations of the catalytic reaction at different temperatures. The predictions were verified by kinetic experiments and crystal structures of the redesigned α-amylase, showing that the temperature optimum is indeed markedly shifted upward and that the critical surface loop controlling the temperature dependence approaches the target conformation observed in a mesophilic ortholog.
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Affiliation(s)
- Florian van der Ent
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Susann Skagseth
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjarte A Lund
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Jaka Sǒan
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
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3
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Åqvist J, van der Ent F. Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding. J Chem Theory Comput 2022; 18:6345-6353. [PMID: 36094903 PMCID: PMC9558309 DOI: 10.1021/acs.jctc.2c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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It has been suggested that heat capacity changes in enzyme
catalysis
may be the underlying reason for temperature optima that are not related
to unfolding of the enzyme. If this were to be a common phenomenon,
it would have major implications for our interpretation of enzyme
kinetics. In most cases, the support for the possible existence of
a nonzero (negative) activation heat capacity, however, only relies
on fitting such a kinetic model to experimental data. It is therefore
of fundamental interest to try to use computer simulations to address
this issue. One way is simply to calculate the temperature dependence
of the activation free energy and determine whether the relationship
is linear or not. An alternative approach is to calculate the absolute
heat capacities of the reactant and transition states from plain molecular
dynamics simulations using either the temperature derivative or fluctuation
formula for the enthalpy. Here, we examine these different approaches
for a designer enzyme with a temperature optimum that is not caused
by unfolding. Benchmark calculations for the heat capacity of liquid
water are first carried out using different thermostats. It is shown
that the derivative formula for the heat capacity is generally the
most robust and insensitive to the thermostat used and its parameters.
The enzyme calculations using this method give results in agreement
with direct calculations of activation free energies and show no sign
of a negative activation heat capacity. We also provide a simple scheme
for the calculation of binding heat capacity changes, which is of
clear interest in ligand design, and demonstrate it for substrate
binding to the designer enzyme. Neither in that case do the simulations
predict any negative heat capacity change.
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Affiliation(s)
- Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Florian van der Ent
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
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van der Ent F, Lund BA, Svalberg L, Purg M, Chukwu G, Widersten M, Isaksen GV, Brandsdal BO, Åqvist J. Structure and Mechanism of a Cold-Adapted Bacterial Lipase. Biochemistry 2022; 61:933-942. [PMID: 35503728 PMCID: PMC9118546 DOI: 10.1021/acs.biochem.2c00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural origin of enzyme cold-adaptation has been the subject of considerable research efforts in recent years. Comparative studies of orthologous mesophilic-psychrophilic enzyme pairs found in nature are an obvious strategy for solving this problem, but they often suffer from relatively low sequence identity of the enzyme pairs. Small bacterial lipases adapted to distinctly different temperatures appear to provide an excellent model system for these types of studies, as they may show a very high degree of sequence conservation. Here, we report the first crystal structures of lipase A from the psychrophilic bacterium Bacillus pumilus, which confirm the high structural similarity to the mesophilic Bacillus subtilis enzyme, as indicated by their 81% sequence identity. We further employ extensive QM/MM calculations to delineate the catalytic reaction path and its energetics. The computational prediction of a rate-limiting deacylation step of the enzymatic ester hydrolysis reaction is verified by stopped-flow experiments, and steady-state kinetics confirms the psychrophilic nature of the B. pumilus enzyme. These results provide a useful benchmark for examining the structural basis of cold-adaptation and should now make it possible to disentangle the effects of the 34 mutations between the two enzymes on catalytic properties and thermal stability.
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Affiliation(s)
- Florian van der Ent
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Bjarte A Lund
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Linn Svalberg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Miha Purg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Ghislean Chukwu
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Geir V Isaksen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
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