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Yusuf Hamied Department of Chemistry

 
Portrait of dk10012
Royal Society GSK Research Professor

Watching single molecules in action

We are physical scientists interested in developing and applying a range of new quantitative biophysical methods, based on single molecule  fluorescence  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 important and disease relevant  biological processes at  the level of single molecules. While our experiments range from experiments in  test-tubes to imaging  living cells, no previous biological background is required for our research since  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.

For a recent review  of our work on neurodegenerative disease see: Imaging individual protein aggregates to follow aggregation and determine the role of aggregates in neurodegenerative disease. Biochimica et Biophysica Acta - Proteins and Proteomics 1867,870 (2019).

Two recent talks are also available on Youtube which provide an overview of the work in the group  : https://www.youtube.com/watch?v=S6Dxzajz5iM    and https://www.youtube.com/watch?v=S6Dxzajz5iM

Watch Professor Klenerman discuss his research

Take a tour of the Klenerman Lab

Selected Publications

Different soluble aggregates of Abeta 42 can give rise to cellular toxicity through different mechanisms.Nat Commun 10,1541 (2019).

A cell-topography based mechanism for ligand discrimination by the T-cell receptor. PNAS 116,14002, (2019).

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).

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

A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-labelled Oligonucleotides.
J Konč, L Brown, DR Whiten, Y Zuo, P Ravn, D Klenerman, GJL Bernardes
– Angewandte Chemie (International ed. in English)
(2021)
Trapping or slowing the diffusion of T cell receptors at close contacts initiates T cell signaling.
KY Chen, E Jenkins, M Körbel, A Ponjavic, AH Lippert, AM Santos, N Ashman, C O'Brien-Ball, J McBride, D Klenerman, SJ Davis
– Proceedings of the National Academy of Sciences
(2021)
118,
e2024250118
Deformable and Robust Core–Shell Protein Microcapsules Templated by Liquid–Liquid Phase-Separated Microdroplets
Y Xu, Y Shen, TCT Michaels, KN Baumann, D Vigolo, Q Peter, Y Lu, KL Saar, D Vella, H Zhu, B Li, H Yang, APM Guttenplan, M Rodriguez-Garcia, D Klenerman, TPJ Knowles
– Advanced Materials Interfaces
(2021)
8,
2101071
Alpha synuclein only forms fibrils in vitro when larger than its critical size of 70 monomers.
SE Sanchez, DR Whiten, G Meisl, FS Ruggeri, E Hidari, D Klenerman
– ChemBioChem
(2021)
22,
2867
Imaging protein aggregates in the serum and cerebrospinal fluid in Parkinson’s disease
E Lobanova, D Whiten, FS Ruggeri, C Taylor, A Kouli, Z Xia, D Emin, YP Zhang, JYL Lam, CH Williams-Gray, D Klenerman
– Brain : a journal of neurology
(2021)
awab306-
Liquid–Liquid Phase‐Separated Systems from Reversible Gel–Sol Transition of Protein Microgels (Adv. Mater. 33/2021)
Y Xu, R Qi, H Zhu, B Li, Y Shen, G Krainer, D Klenerman, TPJ Knowles
– Advanced Materials
(2021)
33,
2170258
Noncontact Nanoscale Imaging of Cells.
D Klenerman, Y Korchev, P Novak, A Shevchuk
– ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 14, 2021
(2021)
14,
347
Liquid-liquid phase separated systems from reversible gel-sol transition of protein microgels
Y Xu, R Qi, H Zhu, B Li, Y Shen, G Krainer, D Klenerman, TPJ Knowles
– Adv Mater
(2021)
33,
2008670
Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer's disease.
DI Sideris, JSH Danial, D Emin, FS Ruggeri, Z Xia, YP Zhang, E Lobanova, H Dakin, S De, A Miller, JC Sang, TPJ Knowles, M Vendruscolo, G Fraser, D Crowther, D Klenerman
– Brain Commun
(2021)
3,
fcab147-
Single molecule imaging of protein aggregation in Dementia: Methods, insights and prospects
JSH Danial, D Klenerman
– Neurobiol Dis
(2021)
153,
105327
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Research Interest Groups

Telephone number

01223 336481

Email address

dk10012@cam.ac.uk