Blog

Welcome to Lucas Powell-Rudden, the first PhD student of the group! Lucas has obtained joint honours in Physics and Chemistry from Durham University, and his work with us will focus on the characterization of integrin structure and dynamics by integrative modelling.

After having attended the Physics of Life Town Meeting in London, Matteo flew to Pisa to join a COST action working group retreat discussing the use and development of computational methods in native mass spectrometry. The three days-long event, on the beautiful Tuscan hills, centred on producing two manuscripts reviewing currently available computational resources, identifying their shortcomings, and defining a roadmap for the whole community. We hope this work will contribute facilitating the uptake of native mass spectrometry approaches, and nucleate the community around a set of commonly shared goals.

We present a new method and associated software, DynamXL, that accommodates intrinsic protein dynamics in the modelling of cross-linking data. Our approach substantially reduces error rates, leading to higher confidence in structure assessment and improved protein-protein docking.

M.T. Degiacomi, C. Schmidt, A.J. Baldwin, J.L.P. Benesch, Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, 2017

All data produced in this work are available here: doi:10.15128/r27s75dc36z

The PDRA position is in the scope of the EPSRC-funded project entitled Software for Experimentally Driven Macromolecular Modelling, and is funded for two years. The work will revolve around the development and application of novel integrative modelling methodologies for the study of flexible protein monomers and the prediction of their multimeric arrangement. The position is available from 01/11/2017, or as soon as possible thereafter.  Full information (and application form) on Durham University vacancies site (job ID: 008549).

Matteo visited Prof. Carla Schmidt in Halle Martin Luther University. There, he gave a presentation about integrative modelling of heat shock proteins guided by cross-linking, SAXS and IM data, and delivered a 6 hour-long Python scientific programming workshop.

He then travelled to Berlin to attend the Biophysical Society conference “Conformational Ensembles from Experimental Data and Computer Simulations“, where he presented a poster.

Matteo moved in, computers are installed, login to the Hamilton supercomputer granted… let the modelling begin!