Award details

Computational tools for enzyme engineering: bridging the gap between enzymologists and expert simulation

Reference	BB/L018756/1
Principal Investigator / Supervisor	Professor Adrian Mulholland
Co-Investigators / Co-Supervisors	Dr Marc van der Kamp
Institution	University of Bristol
Department	Chemistry
Funding type	Research
Value (£)	146,027
Status	Completed
Type	Research Grant
Start date	15/07/2014
End date	14/06/2016
Duration	23 months

Abstract

To obtain efficient biocatalysts, re-design or 'de novo' design of enzymes is often needed. Computational methods are increasingly employed for this purpose, but general and efficient workflows to assess how mutations affect enzymes are not yet available and accessible to experimentalists. The aim of this project is therefore to provide computational tools to a) run state-of-the-art simulation to assess the influence of mutations by non-experts on standard computers and b) perform computational high-throughput screening of enzyme variants on HPC facilities. The tools will be geared towards enzyme (re)design, but will also be useful more generally for structural and synthetic biology, drug design and health research. The protocols will go significantly beyond what is currently accessible to experimentalists, by assessing effects on the structure, dynamics, electronic properties and catalytic efficiency of enzymes. To ensure a broad uptake of the tools, we will actively develop and engage with the user community. The project will deliver three main outputs: 1) Computationally inexpensive protocols for use on standard computers and HPC facilities. The protocols will use state-of-the-art simulation techniques, in particular molecular dynamics simulation and quantum mechanical / molecular mechanical (QM/MM) calculations, and provide relevant analysis of the simulation data. 2) A core software program that links together simulation setup and driving of software for MM and QM calculations, to seamlessly run the protocols mentioned above. The program will be set up such that interfaces to different external software packages can be written easily. The software will be released under an open-source (GPL) licence. 3) User-friendly plugins to molecular visualization software popular with structural biologists. With the plugins, released as open-source (GPL licence), users can run the core software program and then display the results in the molecular viewer.

Summary

It is becoming increasingly popular to use the powerful principles present in nature to our advantage. A key example is the extraordinary ability of organisms to make molecules with high specificity (pure, potentially complex molecules are obtained) and efficiency (little energy is used). Nature uses enzymes, proteins that act as catalysts, to achieve this. These enzymes typically work under mild conditions. Enzymes are already used in industry to make molecules that we require in cost-efficient, comparatively green and sustainable processes. However, nature has not provided us with an enzyme to suit the production of every desired molecule; typically enzymes only catalyze specific chemical reactions with specific starting materials. But the process of evolution teaches us that enzymes may be malleable for engineering different properties. For example, making small changes (mutations) in specific amino acids (the building blocks of proteins) of enzymes can allow these enzymes to accept different substrates and thereby catalyze the formation of new, desired molecules. Even though it is possible to determine the positions of atoms in an enzyme with great detail (e.g. using X-ray crystallography), the full effects of making changes to amino acids are not evident. This limits researchers in assessing what the (beneficial or non-beneficial) effects of such mutations are. It is possible to predict these effects with sophisticated computer simulation methods, but performing the necessary simulations requires expert knowledge. The researchers that are involved in optimizing enzymes to obtain new catalysts for making desired molecules are therefore usually limited to guessing what the effect of mutations is based on static structures alone. To bridge the gap between such experimental researchers and those that are experts in computer simulation, we aim to make expert simulation methods available through an interface that is familiar to the experimental researchers. Our project will involve the development of simulation protocols that assess the effects of mutations, using state-of-the-art methods that include molecular dynamics simulations and quantum chemistry calculations. The protocols will be designed such that they can be run on standard computers and they will be made accessible through an easy and familiar interface for experimental researchers (without the need for in-depth training in computer simulation). In addition, the protocols will allow high-throughput screening of 100s of mutations on high-performance computer clusters. The end result will be that researchers not skilled in computer simulation can easily assess the potential influence of mutations using their own computers, and that high-throughput screening of enzyme variants can be performed computationally. This can potentially save a lot of time and resources in the process of adapting an enzyme for a desired reaction. In addition, collaboration between researchers with complementary skills will be encouraged. The tools developed will also be beneficial in related fields, for example in designing effective drugs and understanding inheritable diseases.

Impact Summary

This project will lead to new, easy-to-use and intuitive software designed to suit experimental researchers with no or little expertise in computational modelling and simulation. The software will thus facilitate basic and applied biochemical research by helping experimental scientists better understand and predict the effect of mutations. The software, related protocols and demonstration cases are primarily aimed at those interested in (re)designing enzymes for use as biocatalysts; this is an area of research that is also actively being pursued in industry, due to its ability to enhance the cost-effectiveness and sustainability of synthesis of chemical compounds and production of biofuels, for example. The tools produced are therefore expected to be taken up in industry as well as academia. In the short term, the proposed project will deliver tools to help increase understanding and successful engineering of enzymes. The same tools will similarly help related biochemical research, such as protein and drug design. Significant efforts will be made to introduce interested experimental researchers to the tools developed, and train them in their use. By giving researchers with primarily experimental expertise access to and explanation of expert simulation methods, the skill-sets of these researchers will be increased. Outreach to experimental researchers will also encourage further cross-disciplinary research and related transfer of knowledge and skills. In addition, the researcher responsible for software development will obtain valuable programming experience that will be useful in his future academic or non-academic career. In the medium term, the protocols and software that will be developed as part of the project (especially those for computational high-throughput screening of enzyme variants) should significantly reduce the time and resources spent to optimize biocatalysts for particular reactions. This has direct economic and environmental benefits (biocatalysts can be brought to market sooner, with reduced use of chemicals and energy in the development process). Similarly, computational assessment of the effect of mutations may avoid spending on producing and testing protein variants or drug lead compounds that subsequently prove ineffective. In the long term, the commercial availability of biocatalysts optimized with help of the developed tools can potentially have enormous economic and environmental benefits by allowing the sustainable production of desired molecules, including fine-chemicals, drugs and biofuels. Biocatalysts are already starting to transform our current chemical industry by improvements in the methods, cost-effectiveness, safety, health, and environmental impact of the processes involved, and these impacts will be extended by the availability of additional biocatalysts. In addition, the application of the tools to help with and speed up drug design, for example to develop anti-viral and antibiotic compounds active against species that are currently drug-resistant, has obvious significant benefits for health in addition to the economic benefits. Similarly, the tools should contribute in helping to fulfil the enormous potential of synthetic biology to deliver societal and economic benefits.

Committee	Research Committee D (Molecules, cells and industrial biotechnology)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	Tools and Resources Development Fund (TRDF) [2006-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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