Molecular Mechanics of Enzymes

Lead Research Organisation: University of Exeter
Department Name: Physics and Astronomy

Abstract

Laser light can be used to perform multiple roles, including sensing, manipulating and moving objects within a laser trap (so-called optical tweezers). It is remarkable that the application of light allows one to exert minute optical forces on individual protein molecules. By pulling on individual molecules it has been possible to study DNA and protein structures in great detail. The pulling and unfolding of proteins has revealed the intramolecular forces that give them their three-dimensional structure. Optical tweezer experiments have also allowed the direct measurement of pico-Newton forces that are exerted by individual motor proteins. However, optical tweezers and other single-molecule techniques are currently not sensitive enough to resolve femto-Newton (fN) forces, and hence not all molecular forces can yet be investigated. An important, but so far poorly understood example is the miniscule fN forces that are exerted by active enzymes when they are catalysing reactions in living systems.

This research programme will develop an entirely novel and much more sensitive alternative optical tweezer technology. The nanosensors developed in this programme will provide optical 'hands' that can probe and feel-out fN forces of enzymes. This allows precise sensing of the energetics of conformational changes of enzymes, i.e. their own deforming motion, for the first time. Such measurements will provide fundamental insights into the forces that drive the conformational changes that are required for catalysis. We will visualise the enzyme movements and this will allow us to develop more accurate models to predict how these very important molecular machines function. Our approach will unravel nature's design principles for a class of nanomachines that carry out most of the important biochemistry and molecular signalling that make our bodies work.

The technology developed in this programme will not only sense forces exerted by enzymes, but allows us to manipulate the complex motions of active enzymes. Such control offers the possibility of making some patterns of molecular organisation in an enzyme more likely than another, and can be used to control enzymatic activity. Demonstrating this capability will prepare the ground for future manipulation and exploitation of synthetic biomolecular machinery and designing enzymes for specific chemical or medical tasks.

Our pathway to impact work will demonstrate the extreme sensitivity of our technology in healthcare diagnostic tests that we will develop for human pathogens. Nanosensors will be modified by attaching enzymes. This will allow us to measure pathogen-specific signals during enzymatic breakdown of different sugars present on cell-walls of the human fungal pathogen Candida albicans - a pathogenic fungus that causes around 250,000 blood stream infections per year. This measurement will enable a more rapid identification of fungal pathogens than current microbial diagnostics of infections based on cell cultures. This approach will be tested on samples provided by the Fungal Immunology Group, AFGrica, located in Cape Town, South Africa.

Planned Impact

This research programme will develop a breakthrough nanosensor technology that allows us to visualise processes at the nanoscale, and watch and manipulate enzymes at work. The application of this technology will instigate entirely new domains for 1) biomolecular analysis, 2) optical control of enzymes, and 3) the treatment of human disease.

1) The ability to directly visualise enzyme activity on nanosensors opens up new areas for enzyme-based biomolecular analysis. For example, by monitoring the activity of enzymes such as glucosyl hydrolases directly with light one can realise novel ways of rapidly detecting carbohydrates and analysing their molecular composition. This capability will translate into various important applications. We will demonstrate one of these applications in our pathway to impact work (aim 9) by detecting and analysing carbohydrates from the cell walls of fungal pathogens. We will use our nanosensors to diagnose human fungal infections more rapidly than current microbial diagnostics of infections based on cell cultures. We will construct a portable analysis device as part of our pathway to impact work so that we can introduce this bioanalytical capability to various industrial laboratories. Future industrial application areas include veterinary and plant biotechnology industries, and the area of biofuels.

2) The technology developed in this programme can provide novel means to optically control enzymatic activity, a capability that sets the stage for future, potentially high-value applications of enzyme-linked nanoparticles: in bioreactors; for controlling enzymatic activity in drug delivery; and for various photodynamic healthcare applications.

3) The enzyme-linked nanoparticles developed in this programme can furthermore find use in the treatment of human disease. As part of aim 9, we will target the enzyme-linked nanoparticles onto the human pathogen Candida albicans to study the rapid break-down of the cell wall by nanoparticle sensors now acting as antifungal agents. This opens up the important application of our technology for addressing antimicrobial resistance (AMR).

UK and international markets

Taken together, these various applications can have an impact on UK markets which are part of the international medical sensors market which is expected to reach USD 15.01 Billion by 2022 (MarketsandMarkets). A multitude of other industries will benefit from our programme in nanosensing sensing, including analytical sensing (USD48.4 billion international market), analysis instrumentation (USD10.2 billion international market) and more. In the longer term multiplexed nanosensors will benefit from sensor signal analysis based on artificial intelligence, a combination that will allow us to realise advanced applications in health, environment, and security. For more details on this exciting trend we refer to the recent article "Sensor Intelligence enabling Industry 4.0", http://www.industryweek.com/technology/preparing-manufacturing-s-future-industry-40.

Carbohydrate sensing and analysis is vital to a broad range of fields in medicine, biology, chemistry, and pharmacology. The analytical sensing instrumentation international market is estimated to be 48.4 billion Euros for 2016 (L1, and growing). The Personalized Medicine Drive Protein Analysis international market is expected to reach USD19 billion in 2023 [L2].

Links to web sites (L):

L1: http://www.marketsandmarkets.com/Market-Reports/life-science-chemical-biotech-instrumentation-market-38.html)
L2: https://globenewswire.com/news-release/2018/10/01/1587517/0/en/Applications-in-Personalized-Medicine-Drive-Protein-Analysis-Market.html
 
Description Key findings 2023:

We achieved the main objective of the research programme: we developed the optical instrumentation to visualise the dynamics of enzymes and detect their femtoNewton forces. The findings are prepared for publications in high impact journals.

Our result is a breakthrough in fundamental research which is seeking new ways for measuring the kinetics and energetics of biomolecular reactions beyond the current capabilities of single-molecule sensing and imaging techniques. Our optical technology advances our fundamental understanding of the physics of life, specifically the molecular mechanics of enzymes, and can lead to new ways of controlling biomolecular reactions in optical nanoreactors for precise biomolecular synthesis. This will be explored in the follow on EPSRC Fellowship (to Dr Koji Masuda) starting this year in Exeter where he apply the technology platform developed with the help of this grant to specific biomolecular systems and to develop an application for de novo DNA synthesis.

Also, the outstanding aim9 of this research programme is being completed by bringing the technology platform to commercialisation, as a biosensor for sensing fungal infections of blood. We are currently preparing IP and patent application with Exeter's Innovation Centre. The completion of aim9 is supported by an EPSRC IAA award that we received recently.

From previous reporting:
The Physics of Life (PoL) grant proposes to develop (1) mark I sensors to detect and visualise changes in enzymes, (2) mark II sensors that apply optical forces to enzyme movements, (3) to measure femtoNewton fN forces, (4) to influence motional patterns of enzymes, (5) to develop theoretical analysis, (6) to detect fungal pathogen from enzymatic breakdown of fungal cell wall constituents, and (7) to extract further structural information by Raman. We are in year two of the PoL grant which effectively started June 2019. Staffing is complete. Laser installation is complete. Laboratory refurbishment in complete.

Progress

(1) Mark I sensor

We have assembled optoplasmonic sensor instruments capable of detecting movements of single enzymes. In close collaboration with biochemistry Co-PI Prof Littlechild, we have cloned, over-expressed and purified several enzymes including 3-phosphoglycerate kinase (pgk) that undergoes large conformational changes during catalysis which is robust to temperature change. We established a surface chemistry method to attach pgk to the sensor so that it remains active. We have made mutant forms of pgk to study effects on different methods to immobilise onto the sensor and to reduce the flexibility of the enzyme. We have cloned, over-expressed and purified two thermophilic transaminase enzymes and have immobilised onto the sensor on an active form via their his -tag and are currently looking for loop movements during turnover on the sensor. We have demonstrated first recording of sensor signals from the active pgk enzyme. We selected thermostable enzymes because of their known crystallographic structures and different conformational changes on turnover for rationalisation of signals obtained on single molecule sensor.
Some of these studies were delayed by two months due to unexpected building construction at the Living Systems Institute and the subsequent COVID pandemic 3 month shutdown and subsequent limited laboratory access,
Theoretical approaches with Janet Anders and her postdoc regarding the fitting of the signals observed from the nanosensor during pgk turnover (opening and closing the enzyme).

(2) Mark II Sensor to apply optical forces

We are integrating an advanced laser source purchased from MSquared. We have started to vary laser light intensity which controls forces exerted on enzymes. We have started to simulate these forces as part of a split-side studentship programme with the Institute of High Performance Computing IHPC at ASTAR Singapore where we have access to supercomputers and predictive algorithms

(3) Measure femtoNewton forces
With Prof Anders, theoretical progress has been made towards providing a quantitative characterisation of the experimental traces of our sensor; now it is possible not only to identify and verify single-molecule events, but also characterise the underlying signal structure, which is done via auto-correlation functions and other statistical descriptors often employed for time series. In the short term, this may shed light on the important question of establishing the existence of a hierarchy of molecular movements. In the long term, it is expected that this formal approach to the analysis of experimental data paves the way towards the connection with the theory of stochastic thermodynamics, a crucial milestone in the later stages of this project.

(4) This work will start soon

(5) This work is ongoing, see (3)

(6) We are developing various nanoparticles modified with enzymes for bulk and single-molecule optical sensing applications. We have also started to develop electrochemical methods with microbiology collaborator Prof Gow. We are now starting to modify the nanoparticles with enzymes and biomaterials relevant for the detection of fungal pathogen Candida albicans. A protein known to be located on the surface of C albicans (Xog 1) has been cloned, over-expressed and purified. This has been found to be active when attached to gold nanoparticles. It is known to modify glycans involved in infection and could be used as a biomarker. This work is carried out by Prof Littlechild and postdoc to use for sensor technology with co-applicant Prof Neil Gow.


(7) In close collaboration with Prof Winlove we have observed Raman signatures specific to different enzymes attached to nanoparticles. We are starting to interpret these Raman signals so that these may become a guide for developing surface chemistries.
Exploitation Route The outcomes of this funding are taken forward in the following way:

- technology is basis for work of EPSRC Fellowship to Koji Masuda starting Sept. 2023 who will develop a de novo DNA writer for error free synthesis of DNA, a direct further development and application of the technology platform and methodologies developed with help of the PoL grant.
- commercialisation of the technology developed as part of this research programme as sensor for fungal infections in blood, supported by EPSRC-IAA award
- programme grant application in new area of quantum biology (full proposal stage): the connection formed to one of the advisory board members on this grant led to the formation of the consortium for the programme grant and developing the new idea for the programme grant application which will be submitted 16 March 2023.
- Ms Jialun Han was awarded a CSC PhD Scholarship from the Chinese government and is currently working in Exeter towards the goals of the Scholarship supported by a 6 month CSC research project grant and using some of the technology and methodology developed by this PoL grant.



From previous report
Academic advancement next step is to develop a Mark II sensor to measure forces of enzymes and control their activity directly with light.

The development of sensor technology, to be used for rapid and specific detection as medical biosensors for different fungal diseases. This will be of benefit to the general public and reduce hospital deaths from fungal infection.
Sectors Electronics,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL https://www.exeter.ac.uk/research/livingsystems/research/mmi/
 
Description In line with work package aim9 of this grant we are bringing the sensor technology to commercial application, with the next step being patent filing with Exeter's Innovation Centre . The work package is planned to be completed within the next couple of months and supported by a recent EPSRC-IAA award. Work package aim9 details: We develop a commercial assay for detecting fungal C.Albicans infections in patient blood serum, as a commercially viable alternative to the only FDA (U.S. Food and drug administration)-approved assay Fungitell currently in use in clinics throughout the USA and UK. We have invented a bespoke electrochemical sensor that generates pathogen-specific signals via the breakdown of sugars present on a Candida albicans' cell wall. This fungus causes around 250,000 bloodstream infections (~40% mortality), and more than 100 million women suffer from 4+ episodes of mucosal thrush per year. Dr Pedireddy now funded by EPSRC-IAA is completing the data collection that demonstrates a detection sensitivity of 102 to 104 pg/ml, the typical serum glucan levels in subjects with candidemia. This data shows the commercial viability and will be included in the patent filing with Exeter IIB Dr Norouzi. The clinical samples for this test have been provided by Public Health England Mycology Reference Laboratory. In parallel, our test results are confirmed by testing serum samples with the Fungitell assay.
First Year Of Impact 2022
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description EPSRC IAA
Amount £28,872 (GBP)
Organisation University of Exeter 
Sector Academic/University
Country United Kingdom
Start 03/2023 
End 08/2023
 
Description The quantum avian compass probed on the single molecule level
Amount £200,889 (GBP)
Funding ID EP/X018822/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2022 
End 04/2024
 
Title Mark I Single Molecule Sensor 
Description Single-molecule technique to visualise functional movements and structural/conformational changes in enzymes 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact Two collaborative PhD Studentship projects 1. SWBioDTP Bath 2. UoE Studentship co-supervised by Prof Tamara Galloway, Exeter 
URL https://www.vollmerlab.com/copy-of-student-2-1
 
Description Molecular Mechanics Initiative MMI @ University of Exeter UoE and INIFTA in Argentina 
Organisation University of La Plata
Department Institute of Theoretical and Applied Physicochemical Research
Country Argentina 
Sector Public 
PI Contribution We are providing access to single-molecule detection capabilities for INIFTA visiting researchers from Argentina (Dr Matias Rafti, Dr Mariana Serrano.
Collaborator Contribution Argentina collaborators Mariana Serrano and Matias Rafti; we will leverage their key expertise in chemistry and photochemistry for the MMI initiative, to explore new research areas building upon the grant
Impact year one in progress......
Start Year 2019
 
Description Split Side PhD Studentship with Institute of High Performance Computation ASTAR Singapore, student Katya Zossimova 
Organisation Agency for Science, Technology and Research (A*STAR)
Department Singapore Institute for Clinical Sciences
Country Singapore 
Sector Academic/University 
PI Contribution Our student Katya Zossimova is working with ASTAR Singapore to help with simulating our sensor response.
Collaborator Contribution Dr Khuong Ong Phuong is providing invaluable input for the computational simulations, access to computational resources, ASTAR fellowship provides financial support which Katya can spend on materials and travel.
Impact Ongoing, I expect outcomes and outputs this year and next year. Preliminary data on small molecule interactions with our sensor to interpret sensor data Longer term: simulation of our sensor data for proteins.
Start Year 2019
 
Description collaboration with research group Imperial College 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration with advisory board member at Imperial; we have prepared programme grant application with Exeter in the lead on 'Quantum Sensing of Quantum Biology' which will be submitted as full proposal on 16 March 2023.
Collaborator Contribution co-PI on programme grant application
Impact submission full proposal programme grant on 16 March 2023 on Quantum Sensing of Quantum Biology.
Start Year 2023
 
Description Dissemination event at Royal Society, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Special event at Royal Society London to disseminate projects which had been funded by UKRI in the Physics of Life call
Year(s) Of Engagement Activity 2019
 
Description Exeter Microfluidics working group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Study participants or study members
Results and Impact we are launching the Exeter Microfluidics Network
Year(s) Of Engagement Activity 2020
 
Description International Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This conference brings togethers researchers in the rapidly advancing field of Single Molecule Sensors and nanoSystems, it was held in 2019, 2020 and next will be in November 22-24, 2023 in Barcelona. The conference focusses on the most recent advances in micro and nano-sensing techniques that have either demonstrated single-molecule detection or that claim single-molecule detection capability on sensor chips in the longer term.

https://premc.org/conferences/s3ic-single-molecule-sensors-nanosystems/
Year(s) Of Engagement Activity 2023
URL https://premc.org/conferences/s3ic-single-molecule-sensors-nanosystems/
 
Description Invited Talk Single-Molecule Biophysics Meeting Les Houches France Winter School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prestigous Single-Molecule conference

added our technique to established mix of single molecule techniques: optical tweezer, magnetic tweezer, FRET, AFM
Year(s) Of Engagement Activity 2020
URL https://smbleshouches.com/
 
Description Physics of life early career researcher symposium - Dr Daniel Mitchell gave talk and helped organise on line conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Physics of life early career researcher symposium, online - talk and organiser
Title: Molecular mechanics of enzymes
Dr Daniel Mitchell, Dr Nikita Toporov, Dr Jesús Rubio
Year(s) Of Engagement Activity 2021
 
Description Poster Presentation by Dr Daniel Mitchell at British Society for Medical Mycology Annual Conference September 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster at British Society for Medical Mycology Annual Conference September 2022
Describing studies with Xog1 located in the cell wall of C. albicans towards a marker for fungal infection.
Title: Measuring femto-Newton forces in enzyme turnover and its potential in highly specific pathogen diagnostic,
Author(s): Daniel Mitchell, Sivaraman Subramanian, Srikanth Pedireddy, Simona Frustaci, Frank Vollmer, Neil Gow, Jennifer Littlechild
Year(s) Of Engagement Activity 2022
 
Description Poster at Virtual Conference Single-Molecule Sensors and NanoSystems International Conference 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Single-Molecule Sensors and NanoSystems International Conference
Title: Measuring femto-Newton forces in enzyme turnover and its potential in highly specific pathogen detection,
Daniel Mitchell, Simona Frustaci, Frank Vollmer, Neil Gow, Jennifer Littlechild
Year(s) Of Engagement Activity 2020
 
Description Presentation at IMTB Meeting in Solvenia 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation
Molecular Mechanics of Enzymes International conference on Immobilisation in Microbioreactors in Biotechnology
Year(s) Of Engagement Activity 2022
 
Description S3IC 2020 Single-Molecule Sensors and nanoSystems conference Nov 1-9 2020 online 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sensor systems have emerged that exhibit extraordinary sensitivity for detecting physical, chemical, and biological entities at the micro/nanoscale. This conference will bring together researchers in the rapidly advancing field of Single Molecule Sensors and nanoSystems. The conference focusses on the most recent advances in micro and nano-sensing techniques that have either demonstrated single-molecule detection or that claim single-molecule detection capability on sensor chips in the longer term.

21 high profile speakers
250 attendees
2 afterworks
Year(s) Of Engagement Activity 2020
URL https://premc.org/conferences/s3ic-single-molecule-sensors-nanosystems/
 
Description collaboration with Fungal Pathogen groups in France and Brazil 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact PoL sensing of fungal pathogens is expanding:

ongoing discussion with Prof Bernard Henrissat (CNRS, France)
and Prof Igor Polikarpov (Sao Paolo, Brazil)

targeting collaboration on CAZymes and BBSRC-FAPESP proposal
Year(s) Of Engagement Activity 2020
 
Description physics seminar Cardiff 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact invited seminar, physics department Cardiff
Year(s) Of Engagement Activity 2020