People

 

Current members:

Franca Fraternali

Group Leader

Franca Fraternali, Group Leader / Professor of Bioinformatics and Computational Biology, Randall Division, King’s College London

Tel (direct): +44 (0) 207 848 6843
Fax: +44 (0) 207 8486 435
Email: franca [dot] fraternali@kcl.ac.uk

Biography

  • Professor of Bioinformatics and Computational Biology, Randall Division, King’s College London
  • Staff Scientist, National Institute for Medical Research of London
  • Research Associate, EMBL Heidelberg
  • Post Doctoral Research Fellow, University of Strasbourg
  • EMBO Fellowship, ETHZ, Zurich
  • PhD in Physical Chemistry, University of Naples

Research Interests : Structural Bioinformatics of Proteins and Nucleic acids; Protein Structure Prediction; Molecular Dynamics of folded and misfolded proteins; Systems Biology; Statistical Analysis of Protein Interaction Networks.

 

The research of the group aims at identifying the molecular determinants in the functioning or misfunctioning of protein structures and protein-protein interactions. The wider objective is to understand, at a molecular level, the nature of the interactions occurring in the cell.

I am particularly interested in the study of the physical nature of the interactions between protein-protein, protein-solvent, protein-lipid and protein-nucleic acid. We develop methods in Bioinformatics and Computational Biology to analyse the available data on such interactions and molecular simulations and to characterize and determine their stability. Once these key molecular signatures have been identified, one can propose ‘rescue’ mutants to restore the protein function, one can design proteins with enhanced binding; one can design inhibitors to disrupt the binding.

Christian Margreitter

Research Associate

Christian Margreitter, Research Associate / Post Doc
Researchgate: https://www.researchgate.net/profile/Christian_Margreitter
ORCID: 0000-0002-5473-6318

Tel (direct): +44 (0) 207 848 6843
Fax: +44 (0) 207 8486 435
Email: christian [dot] margreitter@kcl.ac.uk

Biography

  • 2017 – now Research Associate / PostDoc in the lab of Prof. Franca Fraternali
  • 2012 – 2016 PhD studies in Compuational Biophysics, University of Natural Resources and Life Sciences, Vienna,
    Thesis written under supervision of Prof. Chris Oostenbrink
  • 2006 – 2012 Diploma studies in Molecular Biology, University of Vienna, Vienna,
    Thesis written under supervision of Dr Bojan Zagrovic
  • 2007 – 2015 Bachelor studies in Bioinformatics, University of Vienna, rests

Research interests

  • classical atomistic molecular dynamics simulations of proteins (especially anti-bodies)
  • (method-independent) force field parameter development
  • tool development (bioinformatics, biophysics)
  • data feature extraction by means of machine learning approaches
  • in general, elucidating links between different levels of information on biomolecules
Publications
[6] C. Margreitter and C. Oostenbrink, “MDplot: Visualise Molecular Dynamics”, The R Journal, in press
[5] C. Margreitter, M. Reif and C. Oostenbrink, “Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field”, Journal of Computational Chemistry, vol. 38, 10.1002/jcc.24733, January 2017
[4] C. Margreitter and C. Oostenbrink, “On the Optimization of the Protein Backbone Dihedral Angles by 
Means of Hamiltonian Reweighting”, Journal of Chemical Information and Modeling, 10.1021/acs.jcim.6b00399, Aug. 2016
[3] C. Margreitter*, P. Mayrhofer*, R. Kunert, and C. Oostenbrink, “Antibody humanization
by molecular dynamics simulations – in-silico guided selection of critical backmutations”, Journal of Molecular Recognition, vol. 29, pp. 266–275, 10.1002/jmr.2527, June 2016
[2] D. Petrov*, C. Margreitter*, M. Grandits, C. Oostenbrink, and B. Zagrovic, “A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications”, PLoS Computational Biology, vol. 9, p. e1003154, 10.1371/journal.pcbi.1003154, July 2013
[1] C. Margreitter*, D. Petrov*, and B. Zagrovic, “Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications”, Nucleic Acids Research, vol. 41, pp. W422–W426, 10.1093/nar/gkt416, 2013

Sun Sook Chung

PhD Student

Sun Sook Chung, Bloodwise PhD Student
Researchgate : https://www.researchgate.net/profile/Sun_Sook_Chung
Email: sun_sook [dot] chung@kcl.ac.uk

Sun Sook Chung is a Ph.D student co-supervised by Prof. Nicholas Shaun Thomas in Haematological medicine and Prof. Franca Fraternali in Randall division. Her project is ‘Protein interaction abnormalities in leukaemia : effects of patient-specific genetic variation’ funded by Bloodwise (formerly Leukaemia Lymphoma Research foundation). She aims to investigate patient-specific genetic variation protein complexes containing proteins in mutated in Acute Myeloid Leukaemia, and ultimately identify new drug targets from such protein complexes. She is conducting large-scale data analyses from protein-protein interaction networks to 3D structural models and also wet-lab experiments to probe their functional associations on cellular processes.
Before joining the Ph.D programme, she graduated in honour from Ajou University in South Korea majoring in Information & Computer Engineering. She took an MSc degree in Computer Science from State University of New York at Stony Brook. She also obtained another MSc degree (Distinction; Best performance prize) in Bioinformatics from KCL with her thesis, ‘Information-theoretic approach to extract topological and functional motifs in Protein-Protein Interaction Networks’.

Publications

Kordasti S, Costantini B, Seidl T, Perez Abellan P, Martinez Llordella M, McLornan D, Diggins KE, Kulasekararaj A, Benfatto C, Feng X, Smith A, Mian SA, Melchiotti R, de Rinaldis E, Ellis R, Petrov N, Povoleri GA, Chung SS, Thomas NS, Farzaneh F, Irish JM, Heck S, Young NS, Marsh JC, Mufti GJ. Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment. Blood. 2016 Sep 1;128(9):1193-205. doi:10.1182/blood-2016-03-703702. Epub 2016 Jun 8. PubMed PMID: 27281795; PubMed Central PMCID: PMC5009512.

Lu HC, Chung SS, Fornili A, Fraternali F. Anatomy of protein disorder, flexibility and disease-related mutations. Front Mol Biosci. 2015 Aug 12;2:47. doi: 10.3389/fmolb.2015.00047. eCollection 2015 Aug 12. PubMed PMID: 26322316; PubMed Central PMCID: PMC4532925.

Chung SS, Pandini A, Annibale A, Coolen AC, Thomas NS, Fraternali F. Bridging topological and functional information in protein interaction networks by short loops profiling. Sci Rep. 2015 Feb 23;5:8540. doi: 10.1038/srep08540. PubMed PMID: 25703051; PubMed Central PMCID: PMC5224520.

Anna Laddach

PhD Student

Anna Laddach, British Heart Foundation PhD Student
Researchgate: https://www.researchgate.net/profile/Anna_Laddach
Email: anna [dot] laddach@kcl.ac.uk

Anna is a BHF funded PhD student undertaking a project entitled ‘Novel bioinformatics tools for assessing the impact of titin sequence variants in hypertrophic cardiomyopathy and core myopathies on protein structure and function’, supervised by Prof. Franca Fraternali and Prof. Mathias Gautel. She has developed the web application TITINdb, which integrates titin structure, sequence and variant information. Currently she is exploring whether machine learning can be used to create better predictors of titin nsSNP pathogenicity, alongside the development of tools for the largescale annotation of NGS variant data with protein structural and network features. In particular she is interested in exploring the combinatorial effect of variants, and believes this may play an important role in deciphering the mechanisms underlying complex diseases such as hypertrophic cardiomyopathy (HCM).

Previously she gained a first class BSc(Hons) in Molecular Science from the Open University and was awarded the RSC Mid-Anglia Section Prize for the top Molecular Science Honours Degree graduate (2013). She then completed an MRes in Bioinformatics with Systems Biology at Birkbeck (awarded distinction); her research, as part of the Shepherd group, involved the large scale analysis of Ig-seq data with a focus on the properties of antibody CDR3s.

Jamie Macpherson

PhD Student

Jamie Macpherson, King’s/Crick PhD Student
Email: James [dot] Macpherson@crick.ac.uk

Jamie completed his B.Sc. in Biochemistry at King’s College London in 2014 before joining the group in September 2014 as an MPhil-PhD student. In the third year of his PhD studies, he is jointly supervised by Prof. Fraternali (KCL) and Dr. Anastasiou (Francis Crick Institute, London), and uses computational and experimental structural and biophysical techniques to investigate protein dynamics. Additionally, he has developed methods for estimating entropy of macromolecular systems.

Aside from his studies, Jamie is interested in economic and current-affair topics, with a particular intrigue in understanding extreme financial events. He additionally, takes great interest in political issues and is an active member of the Liberal Democrat party.

Publications

  • Gehrig S, Macpherson JA, Driscoll PC, Symon AC, Martin SR, MacRae JI, Kleinjung J, Fraternali F. and Anastasiou D. An engineered photoswitchable mammalian pyruvate kinase. FEBS J. 2017 (Accepted)
  • Macpherson JA and Anastasiou D, Allosteric regulation of metabolism in cancer: endogenous mechanisms and considerations for drug design. Curr Opin Biotech. 2017 Dec;48.
  • Schmidt C, Macpherson JA, Lau AM, Tan KW, Fraternali F, Politis A. Surface Accessibility and Dynamics of Macromolecular Assemblies Probed by Covalent Labeling Mass Spectrometry and Integrative Modeling. Anal Chem. 2017 Feb 7;89(3):1459-1468.
  • Morena P, Francesca C, Macpherson JA, Michaelis M, Fraternali F, Wass MN. Investigating Ebola virus Dynamics. BMC Genomics. (In Press).
  • Macpherson JA. To steer the course, or capsize the ship? The macroeconomic policies of the Clinton and Trump campaigns. Perspectives J. 2016 Nov 27.
  • Laffy JM, Dodev T, Macpherson JA, Townsend C, Lu HC, Dunn-Walters D, Fraternali F. Promiscuous antibodies characterised by their physico-chemical properties: From sequence to structure and back. Prog Biophys Mol Biol. 2016 Sep 14.
  • Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, Brugiroux S, Keller I, Macpherson JA, Rupp S, Stolp B, Stein JV, Stecher B, Sauer U, McCoy KD, Macpherson AJ. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun. 2015 Sep 22;6:8292.
  • Juillerat P, Andrew P, Macpherson JA, Cahenzli J, Patuto N, Slack E, Seibold F, McCoy KD, Macpherson AJ. Measurement of Functional Blocade of TNF-Alpha by Anti-TNF Agents Is a Stronger Predictor Than Trough Levels and Anti-Drug Antibodies: 2-Year Prospective Clinical Data. Gastroenterology 2015 148(4):S-850-S-851.
  • Juillerat P, Andrew P, Macpherson JA, Cahenzli J, Patuto N, Slack E, Seibold F, McCoy KD, Macpherson AJ. CD62L (L-Selectin) Shedding for Assessment of Functional Blockade of TNFAlpha in Anti-TNF Treated Inflammatory Bowel Disease Patients: Clinical Feasibility and Perspectives. Gastroenterology 2014 May 146(5):S-239.

Marius Kausas

PhD Student

Marius Kausas, King’s/Crick PhD Student
Email: marius [dot] kausas@kcl.ac.uk

Marius completed his MSc in Biochemistry with Industrial Placement in Computational Chemistry (First Class) at University of Aberdeen in 2016. Following, he began his PhD in a collaboration between Prof Franca Fraternali (King’s College London) and Dr Katrin Rittinger (The Francis Crick Institute). His research interests are focused on investigating multidomain protein dynamics using combination of experimental and computational methods. The aim of the PhD project is to characterize intrinsic dynamic phenomena of the Ring-Between-Ring (RBR) E3 ligase ubiquitin transfer mechanism using enhanced sampling molecular dynamics and solution-based biophysical characterization.

Joseph Ng

PhD Student

Joseph (Chi-Fung) Ng, PhD student / Croucher scholar
Email: chi_fung_joseph [dot] ng@kcl.ac.uk

Joseph graduated with first class honours the degree of Bachelor of Biomedical Sciences at the University of Hong Kong (HKU). He is broadly interested in cancer, structural biology and the “-omics” sciences; and in particular, mechanistic exploration of effectors that drive tumour development. This primes him to pursue an interdisciplinary path in integrating bioinformatics analysis with traditional experimental approaches to study key players of tumour evolution and development. Joseph is now a PhD student, supported by the Croucher Foundation from Hong Kong, supervised by Prof Fraternali and Prof Michael Malim (DIIID, KCL) working on the APOBEC3 family of proteins. He is interdisciplinary, working on both bioinformatics and wet-lab experiments that explore the mechanistic aspect of this critical family of proteins in mutagenesis.

Outside science, Joseph is also interested in ethical and policy questions surrounding medicine. He is particularly fascinated by directed-to-consumer genomic testing.

Link to Joseph’s page on Croucher was at the top of this window. Read also his featured article on Croucher.

Publications

Cheng CWH, Chung MWH & *Ng JCF. (2016) “Structural dynamics of Alzheimer’s amyloid-? aggregation: computational and experimental approaches.” Journal of Young Investigators. doi: 10.22186/jyi.31.6.44-50.  (Equal contribution from all authors)

Chung MWH & *Ng JCF. (2016) “Personal utility is inherent to direct-to-consumer genomic testing.” Journal of Medical Ethics, 42:649-652. doi:10.1136/medethics-2015-103057. (Equal contribution from all authors)

Irene Marzuoli

PhD Student

Irene Marzuoli, PhD Student / CANES Student
Email: irene [dot] marzuoli@kcl.ac.uk

Irene pursued a Master in Theoretical Physics at the University of Padova, focussing on statistical mechanics and its applications to soft matter systems. She then joined the CANES master programme at King’s College of London, to gain a more interdisciplinary approach to research, developing an interest for biological problems.  Irene now works on Molecular Dynamics simulations of self-assembling antimicrobial peptides, applying her physical and mathematical expertise in the field of biophysics. She is co-funded by the National Physics Laboratories which provide experimental support, the aim of the project being the design of new functional antimicrobial molecule. She still pursue her interest in abstract statistical mechanics models, in particular in extreme events.

Affiliated members:

Enrico Spiga

Affiliated member

Enrico Spiga, Research Associate / Post Doc
Google Scholar: https://scholar.google.co.uk/citations?user=RWNukWoAAAAJ&hl=en

Email: enrico [dot] spiga@crick.ac.uk

Biography

  • 2014 – now Research Associate / PostDoc in the lab of Dr. William R. Taylor (The Francis Crick Institute)
  • 2008 – 2013 PhD studies in Bioengineering and Biotechnology, Swiss Federal Institute of Technology in Lausanne (EPFL), Lausanne, Switzerland; Research developed under the supervision of Prof. Matteo Dal Peraro
  • 2004 – 2008 MSc in Physics (Major in Theoretical Condensed Matter), University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli
  • 2000 – 2004 BSc in General Physics, University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli and Prof Paolo Ruggerone

Research interests

  • Development and application of coarse-grained models for molecular dynamics simulations of biomolecules
  • Rationalising the binding of homeodomain transcription factors to DNA by using molecular modelling tools
  • Probing the elastic properties of Structural Maintenance Complexes by using atomistic molecular dynamics simulations
  • Development of non-standard analysis of molecular dynamics simulations

Other Interest

  • Swimming
  • Smiling

 

Francesca Collu

Affiliated member

Francesca Collu
Researchgate: https://www.researchgate.net/profile/Francesca_Collu/publications
Email: Francesca [dot] collu@gmail.com

Biography

  • 2017 – now Imaging Clinical Operation Coordinator at Bioclinica
  • 2013 – 2016 Research Associate / PostDoc in Computational Chemistry in the lab of Prof. Franca Fraternali
  • 2012 – 2013 Research Associate / PostDoc in Computational Chemistry in the lab of Prof. Michele Cascella
  • 2008 – 2012 PhD studies in Chemistry, University of Bern, Switzerland; Research developed under the supervision of Prof. Michele Cascella
  • 2004 – 2008 MSc in Physics (Major in Theoretical Condensed Matter), University of Cagliari, Italy; Thesis written under the supervision of Prof Paolo Ruggerone
  • 2000 – 2004 BSc in General Physics, University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli and Prof Paolo Ruggerone

Research interests

Alumni:

Grace Lu

Grace (Hui-chun) Lu

Hui-chun joined the Fraternali group in 2010 for her PhD studies. Her research project applies computational methods to large scale studies of protein-protein interaction networks (PPINs). In particular by mapping these interactions on 3D-structural data and to non-synonymous SNPs data occurring at protein interacting interfaces. This type of SNPs are thought to be more likely to have impact on protein functions or even to be related to genetic diseases. The project aimed at building structure-integrated PPINs within an automated procedure which can integrate multiple datasets. Hui-Chun also worked on the Human immune system. Ageing of immune system increases susceptibility to infection and decreases responses to vaccination. Previous studies show that antibodies from older people tend to have lower binding affinity, lower specificity and longer CDRH3 region. In order to understand intrinsic age-related deficiencies of antibody repertoires, we aim to characterise the molecular features of the B cell antibodies obtained from the old and young cohorts.

Publications

  • Setta-Kaffetzi, N, Simpson, MA, Navarini, AA, Patel, VM, Lu, H-C, Allen, MH, Duckworth, M, Bachelez, H, Burden, AD, Choon, S-E, Griffiths, CEM, Kirby, B, Kolios, A, Seyger, MMB, Prins, C, Smahi, A, Trembath, RC, Fraternali, F, Smith, CH, Barker, JN & Capon, F. AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking. Am. J. Hum. Genet. 94, 790–797 (2014)
  • Lu, H.-C., Fornili, A. & Fraternali, F. Protein-protein interaction networks studies and importance of 3D structure knowledge. Expert Rev Proteomics 10, 511–520 (2013)
  • Fornili, A., Pandini, A., Lu, H.-C. & Fraternali, F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J. Chem. Theory Comput. 9, 5127–5147 (2013)
  • Scharner, J., Lu, H.-C., Fraternali, F., Ellis, J. A. & Zammit, P. S. Mapping disease-related missense mutations in the immunoglobulin-like fold domain of lamin A/C reveals novel genotype-phenotype associations for laminopathies. Proteins (2013). doi:10.1002/prot.24465
  • Baines, A. J., Lu, H.-C. & Bennett, P. M. The Protein 4.1 family: Hub proteins in animals for organizing membrane proteins. Biochim. Biophys. Acta (2013). doi:10.1016/j.bbamem.2013.05.030
  • Satoh, T, Smith, A, Sarde, A, Lu, H, Mian, S, Trouillet, C, Mufti, G, Emile, J-F, Fraternali, F, Donadieu, J & Geissmann, F. B-RAF mutant alleles associated with Langerhans cell histiocytosis, a granulomatous pediatric disease. PLoS ONE 7, e33891 (2012)

Flavia Autore

Flavia Autore

Flavia Autore gained a PhD in Biotechnology at the University of Naples “Federico II” Italy, in January 2008 with a thesis entitled Computational investigations of molecular complexes of biotechnological interest. She was a Post-doctoral fellow in the Fraternali lab, funded by the British Heart Foundation (BHF) to elucidate the structural and biophysical properties of Nesprin Spectrin Repeats to understand of the mechanisms leading to cardiac muscle dysfunction. She use a multidisciplinary approach combining computational biology, cell biology and biophysical techniques to investigate the protein-protein interactions and the molecular determinants leading to the cellular phenotypes associated with nesprin mutations. Understanding how these scaffolding proteins interact with their binding partners will provide important targets for interfering with cellular signaling pathways and will impact on the design of novel strategies to combat the Emery Dreifuss muscular dystrophy (EDMD) and dilated cardiomyopathy (DCM).

Publications

  • Autore F, Pfuhl M, Quan X, Williams A, Roberts RG, Shanahan CM, Fraternali F. Large-Scale Modelling of the Divergent Spectrin Repeats in Nesprins: Giant Modular Proteins. PLoS ONE 8(5): e63633
  • Rajgor D, Mellad JA, Autore F, Zhang Q, Shanahan CM. Multiple novel nesprin-1 and nesprin-2 variants act as versatile tissue-specific intracellular scaffolds. PLoS One. 2012;7(7):e40098
  • Autore F, Pagano B, Fornili A, Rittinger K, Fraternali F. In silico phosphorylation of the autoinhibited form of p47(phox): insights into the mechanism of activation. Biophys J. 2010 Dec 1;99(11):3716-25
  • Autore F, Bergeron JR, Malim MH, Fraternali F, Huthoff H. Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies  by molecular dynamics simulations. PLoS One. 2010 Jul 12;5(7):e11515
  • Vaz F, Hanenberg H, Schuster B, Barker K, Wiek C, Erven V, Neveling K, Endt D, Kesterton I, Autore F, Fraternali F, Freund M, Hartmann L, Grimwade D, Roberts RG, Schaal H, Mohammed S, Rahman N, Schindler D, Mathew CG. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Nat Genet. 2010 May;42(5):406-9
  • Huthoff H, Autore F, Gallois-Montbrun S, Fraternali F, Malim MH. RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1. PLoS Pathog. 2009 Mar;5(3):e1000330