Workshops time!

Lucas attended the “Advanced Methods for the Integration of Diverse Structural Data” workshop in Florence. Lucas says: “The workshop covered the foundations and software associated with widely used and upcoming structual biology techniques; including SAXS, NMR, cryo-EM and crystallography in the context of integrative modelling. The days were jam packed with information, and really enlightened a newly christened biophysist such as myself. And of course, the beautiful city of Florence set the backdrop – with good food and wine, which warmed us up in spite of the cold weather from Siberia!”


In the meantime, Matteo travelled to the Freie Universität Berlin to attended the workshop “Computer Tutorial in Markov Modeling“. Some excellent work from the the pyEMMA team, really good to learn about what this Python package can do for the interpretation of MD simulations!

New article published on Science!

The article “Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions” has been published today in Science!

Most proteins assemble into complexes to achieve a specific biological function. In this work, we show how small Heat Shock Proteins assemble selectively according to mechanisms away from the typical shape and charge complementarity, and that this phenomenon might in fact be widespread. Our results indicate an economical mechanism for duplicated proteins to evolve distinct functions: modification of a minimal amount of amino acids, altering protein dynamics but not their structure, allows preventing co-assembly.

This work is the fruit of several years of collaboration between researchers from areas as diverse as molecular and plant biology, molecular dynamics and modelling and crystallography.  For more information, see the University of Oxford blog post.

Georg K. A. Hochberg et al., Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions, Science, Vol. 359, Issue 6378, pp. 930-935, 2018 [Supplemental data is available here]

New publication: Mineral surface chemistry control for origin of prebiotic peptides


Our study, in collaboration with Durham and Oxford Earth Sciences departments, has been published in Nature Communications. Herein we demonstrate how, in early Earth conditions, layered double-hydroxides could have adsorbed amino acids, favouring the formation of peptidic bonds. We propose that successive wetting-drying cycles could have enabled the formation of peptidic chains having a length compatible to  that of simple functional proteins.

Erastova, V., Degiacomi, M.T., Fraser, D.G., Greenwell, H.C. (2017). Mineral surface control for origin of prebiotic peptides, Nature Communications.

All datasets related to this work are available here.

Lunchtime research meeting

image1.gifMatteo presented his past and current research during the weekly lunchtime seminar of Durham’s department of Chemistry.

In the gif: an interpretative dance representing  the assembly of a small heat shock protein complex.

COST action working group retreat

tuscany1After 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.

New publication: accommodating protein dynamics in the modeling of chemical crosslinks

GAWe 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

Postdoctoral position available

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).

German tour

IMG_3227Matteo 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.