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Department of Chemistry

 
Portrait of dk10012

Watching single molecules in action

We are physical scientists interested in developing and applying a range of new quantitative biophysical methods, based on laser fluorescence spectroscopy and scanning probe microscopy, to important problems in biology, which have not been addressed to date due to the lack of suitable tools and hence  directly image biological processes down to  the level of single molecules. While our experiments range from studies of individual biomolecules to living cells, no previous biological background is required for our research and we work closely with a range of biological and clinical collaborators. We are also part of the Cambridge Dementia Research centre.

Single molecule fluorescence

By studying molecules one at time, using fluorescence, specific complexes in a mixture can be identified and analysed without the need for any separation. With our collaborators we are exploiting single molecule fluorescence spectroscopy to study a range of biologically important molecules and processes. At present our main projects are:

  • Imaging the early molecular events that lead to the triggering of T-cells, a process that underpins the adaptive immune response and is remarkably  sensitive and selective.
  • Imaging the early molecular events that lead to the triggering of Toll-like receptors, a key process in the innate immune response which plays an important role in causing inflammation in neurodegenerative diseases such as Alzheimer’s disease.
  • Imaging and characterising the protein aggregates formed in the test-tube during aggregation reactions of disease-associated proteins and those present in human samples such as cerebral spinal fluid and brain tissue. We want to determine the aggregates responsible for causing neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease in humans and the mechanisms by which they damage cells and spread through the brain.
  • Determining the structure and organisation of DNA in the nucleus of cells and  how this is regulated and changes during  cell differentiation.
  • Imaging aggregates of P53 and determining the role of these aggregates in the development and spreading of cancer.  
  • Developing and improving our imaging methods. At present our focus is developing methods to image protein aggregates at 20 nm spatial resolution and determine their composition and structure.

Scanning nanopipette

In collaboration with Professor Korchev at Imperial College we have developed a method based on a scanning nanopipette that allows robust, high resolution, non- contact imaging of living cells, down to the level of individual protein complexes. It can also be used to probe function by performing nanoscale assays such as locally deliver controlled amounts of reagents or performing single ion channel recording. The figure shows the University of Cambridge crest written in fluorescent DNA. We are using this method to watch the details of biological process taking place on the surface of living cells and to directly observe protein aggregates damage neuronal cells.

 

New postdoctoral position available

We  have a  position available imaging liquid droplet formation. For more information and to apply see:

 

PhD positions

We have positions for PhD students to work in the group starting in October 2019 in the areas of imaging the protein aggregates in neurodegenerative disease, studying the molecular basis of the innate and adaptive immune response and studying the organisation of DNA in the cell nucleus and how this changes during cell differentiation. For further information and to arrange a visit to look round the group please contact Professor Klenerman (dk10012@cam.ac.uk). 

 

Selected Publications

Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hubeLife 7, (2018) . 

 Inhibiting the Ca2+ Influx Induced by Human CSFCell Rep 21, 3310 (2017)

Initiation of T cell signalling by CD45 segregation at "close contacts". Nature Immunology 17, 574 (2016).

Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading. PNAS 113, E1206 (2016).

A mechanistic model of tau amyloid aggregation based on the direct observation of oligomers. Nature Communication 6, 7025 (2015).

Single molecule imaging reveals that small amyloid-beta (1-42) oligomers interact with the cellular prion protein. Chembiochem 15, 2515 (2014).

Local delivery of molecules from a nanopipette for quantitative receptor mapping on live cells. Analytical chemistry 85, 9333 (2013).

Ubiquitin chain conformation regulates recognition and activity of interacting proteins. Nature  492, 266-270 (2012).

Direct Observation of the Interconversion of Normal and Toxic Forms of alpha-Synuclein. Cell  149, 1048-1059 (2012).

Publications

Simple and ultrafast resonance frequency and dissipation shift measurements using a fixed frequency drive
A Guha, N Sandström, VP Ostanin, W van der Wijngaart, D Klenerman, SK Ghosh
– Sensors and Actuators, B: Chemical
(2019)
281,
960
α-synuclein oligomers interact with ATP synthase and open the permeability transition pore in Parkinson's disease
MHR Ludtmann, PR Angelova, MH Horrocks, ML Choi, M Rodrigues, AY Baev, AV Berezhnov, Z Yao, D Little, B Banushi, AS Al-Menhali, RT Ranasinghe, DR Whiten, R Yapom, KS Dolt, MJ Devine, P Gissen, T Kunath, M Jaganjac, EV Pavlov, D Klenerman, AY Abramov, S Gandhi
– Nature Communications
(2018)
9,
2293
Quantifying Co-Oligomer Formation by α-Synuclein.
M Iljina, AJ Dear, GA Garcia, S De, L Tosatto, P Flagmeier, DR Whiten, TCT Michaels, D Frenkel, CM Dobson, TPJ Knowles, D Klenerman
– ACS nano
(2018)
12,
10855
Mapping Surface Hydrophobicity of α-Synuclein Oligomers at the Nanoscale
J-E Lee, JC Sang, M Rodrigues, AR Carr, MH Horrocks, S De, MN Bongiovanni, P Flagmeier, CM Dobson, DJ Wales, SF Lee, D Klenerman
– Nano Lett
(2018)
Sensitive light-sheet microscopy in multiwell plates using an AFM cantilever
A Ponjavic, Y Ye, E Laue, S Lee, D Klenerman
– Biomedical Optics Express
(2018)
Characterisation of particle-surface interactions via anharmonic acoustic transduction
C da Silva Granja, N Sandström, I Efimov, VP Ostanin, W van der Wijngaart, D Klenerman, SK Ghosh
– Sensors and Actuators B: Chemical
(2018)
272,
175
Correction to: Picomolar concentrations of oligomeric alpha-synuclein sensitizes TLR4 to play an initiating role in Parkinson’s disease pathogenesis (Acta Neuropathologica, (2018), 10.1007/s00401-018-1907-y)
CD Hughes, ML Choi, M Ryten, L Hopkins, A Drews, JA Botía, M Iljina, M Rodrigues, SA Gagliano, S Gandhi, C Bryant, D Klenerman
– Acta neuropathologica
(2018)
Direct observation of murine prion protein replication in vitro
JC Sang, G Meisl, AM Thackray, L Hong, A Ponjavic, TPJ Knowles, R Bujdoso, D Klenerman
– J Am Chem Soc
(2018)
140,
14789
Nanoscopic characterization of individual endogenous protein aggregates in human neuronal cells
DR Whiten, Y Zuo, L Calo, M-L Choi, S De, P Flagmeier, DC Wirthensohn, F Kundel, RT Ranasinghe, SE Sanchez, D Athauda, SF Lee, CM Dobson, S Gandhi, M-G Spillantini, D Klenerman, MH Horrocks
– Chembiochem : a European journal of chemical biology
(2018)
19,
2033
Extrinsic Amyloid-Binding Dyes for the Detection of Individual Protein Aggregates in Solution
CG Taylor, G Meisl, MH Horrocks, H Zetterberg, TPJ Knowles, D Klenerman
– Analytical chemistry
(2018)
90,
10385
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Research Interest Groups

Telephone number

01223 336481

Email address

dk10012@cam.ac.uk