PhD student profiles

     
     
Millie Pang

Camilla S. M. Pang
Wellcome Trust 4-year Interdisciplinary PhD Programme, beginning in Autumn 2013

Project title
Developing a Computational Platform to Investigate the Effects of Disease Causing Mutations on protein Structure and Function.

Principle investigators: Professor Christine Orengo and Dr Andrew Martin

 
Background

Preceding my studies at UCL, I read a Bsc (Hons) in Biochemistry at the University of Bristol in 2013. Here I encountered a variety of fields ranging from the techniques of cell biology including confocal microscopy and FACS, to those investigating protein structure and function using X-ray crystallography and enzyme assays. The latter techniques were introduced during a summer project within Professor Leo Brady’s group where I focused on elucidating the structure of a bacterial membrane complex for antibiotic targeting. My 2 dissertations at Bristol involved the study of a GTPase in Salmonella infection, along with investigating the regulation of the globin switch to make adult haemoglobin.

During my undergraduate, I attended 3 other summer internships, 2 of which were held at Imperial College London, where I performed drug activity assays of the Aromatase and sulphatase inhibitor in breast cancer cells, along with investigating the role of salmonella infection in Hela Cells. The last internship I did was at UCL in professor John Christodoulou’s group, where I purified the bacterial chaperone, Trigger Factor, and was introduced to NMR spectroscopy.

The great opportunity to study a multi-disciplinary project at UCL really appealed to me, as it would enable me to use and integrate the many sides of science that were both familiar and new to me, expanding my choices and providing a sound basis to finally choose a path in science.

 
Rotation projects

Chemical Biology: Rotation 1 (Professor Stephen Caddick)
The Production of Homogeneous Antibody Drug Conjugates a Novel Anti-cancer Therapeutics

Structural Biology: Rotation 2 (Dr Cara Vaughan and Dr Chris Kay)
Revealing the Structural Intermediates of the Hsp90-cdc37 Complex using EPR Spectroscopy

Computational Biology: Rotation 3 (Professor Francesco Gervasio)
Investigating the Conformational Dynamics and Allosteric Effects of the B-Raf Oncogene

 
PhD Project

After the opportunity to experience the 3 different labs the PhD course offered, along with an inspiring talk from professor Christine Orengo, I decided that I wanted to be within the computational field. I decided to create my own project from the aspects that I enjoyed most from my experiences, which encompassed bioinformatic analysis of cancer and disease mutations and the use of molecular dynamics to enable their further characterisation. The aims of this project are to establish new approaches for determining the impacts of disease associated mutations on protein structure and function. The different types of disease causing mutations considered include those in germline diseases, somatic cancer mutations in oncogenes and tumour-suppressors, along with known activating and inactivating mutations in kinases.

The proximity of disease-associated mutations has been analysed with respect to known functional sites reported by CSA, IBIS and ELMS, along with predicted functional sites derived from the CATH classification of domain structure superfamilies. The latter are called FunSites, and are highly conserved residues within a CATH functional family (FunFam) – which is a functionally coherent subset of a CATH superfamily. Such sites include key catalytic residues as well as specificity determining residues and interface residues. Clear differences were found between oncogenes, tumour suppressor and germ-line mutations with oncogene mutations more likely to locate close to FunSites.

We have also identified functional families that are highly enriched in disease mutations and exploited structural data to identify clusters within proteins in these families that are enriched in mutations (using our MutClust program). We examined the tendencies of these clusters to lie close to the functional sites discussed above.

For selected genes, the stability effects of disease mutations in cancer have also been investigated with particular focus on activating mutations in FGFR3. These studies, which were supported by experimental validation, showed that activating mutations implicated in cancer tend to cause stabilisation of the active FGFR3 form, leading to its abnormal activity and oncogenesis (Patani et al. OncoTarget 2016).

 
Figure 1
 
Oncogenic mutation in a signalling kinase causes abnormal activation by mimicking native hydrogen bonding networks.
 
Publications
Patani, H, Bunney, TD, Thiyagarajan, N, Norman, RA, Ogg, D, Breed, J, Ashford, P, Potterton, A, Edwards, M, Williams, SV, Thomson, GS, Pang, CSM, Knowles, MA, Breeze, AL, Orengo, C, Phillips, C and Katan, M. Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use. Oncotarget 1949–2553 (2016).

 

 

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