Lucy, Physics student in Durham, joins us for her Masters project. She will work on using molecular simulations and convolutional neural networks to sample protein conformational spaces.
Mass spectrometry, structural biology and computational methods: 3 articles!
This week we celebrate the publication of three articles in Analytical Chemistry!
In the scope of the EU COST Action BM1403 on Native MS and Related Methods for Structural Biology, we have contributed to the redaction of two articles. These review existing methods and software to analyse and interpret native mass spectrometry data, and highlight state of the art and current challenges in the area. We hope these works will stimulate discussions within the community, and serve as help for newcomers to the area
- T. Allison et al. (2020). Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology, Analytical Chemistry
- T. Allison et al. (2020). Software requirements for the analysis and interpretation of native mass spectrometry data, Analytical Chemistry
In related news, in collaboration with Michael Landreh (Karolinska Instituet) and Erik Marklund (Uppsala University) we have figured out that ion mobility can tell more than one would think about the shape of protein complexes. Coupling collision cross section and mass measurements with protein databank searches, we have shown that it is possible to determine whether a protein complex is prolate (like a cigar) or oblate (like a disk).
M. Landreh et al. (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searches, Analytical Chemistry
Welcome back Sam!
Sam joins our group again for his PhD project! After having spent his masters project with us, he now comes back sponsored by the SOFI2 CDT. Sam will develop methods leveraging on convolutional neural networks to study protein conformational spaces. While currently Sam can only join us in an unusual “virtual” way, he is already at work. Looking forward to welcoming him in Durham, hopefully soon!
Scientist Next Door
In this period of lock down caused by COVID-19, children are home schooled. We have joined the “Scientist Next Door ” project, organised by scientists from the university of Edinburgh and Durham, to share our excitement for science with them!
We hope to hold group video calls with families and discuss things we find interesting, share ideas and resources. And, as Scientists Next Door, after the lockdown is over, it would be great to meet in person!
If you are a scientist, consider joining too. If you are parent, get in touch! www.scientist-next-door.org
mass spectrometry for structural biology
Eager to learn about how mass spectrometry can help structural biology? Join us in Bordeaux on the 5-7 October 2020 to learn everything about top-down and native MS, ion mobility, HDX, cross-linking and, of course, integrative modelling!
Welcome Holly and George!
This week two Masters students joined our group. George, from Chemistry department, will work on expanding JabberDock capabilities while Holly, from Physics, will study protein conformational spaces via deep learning. Welcome both!
Moving to Physics
Today the group moves to Durham University Department of Physics, where Matteo will take the position of Assistant Professor in Condensed Matter Physics!
Protein docking with JabberDock
We are very excited to present JabberDock, our new protein-protein docking algorithm. JabberDock is capable of accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility. To do this, it leverages Spatial and Temporal Intensity (STID) maps, our single volumetric representation for proteins surface, electrostatics and local dynamics. JabberDock is freely available on Github, and is presented in the following article:
Rudden L.P., Degiacomi M.T. (2019), Protein docking using a single representation for protein surface, electrostatics and local dynamics. Journal of Chemical Theory and Computation
This publication not only complies to the Palatinate Challenge but, more importantly, it is the first article of Lucas Rudden, PhD student in our group. Congratulations!
Today we welcome Lorenza Pacini, PhD student in ENS Lyon under the supervision of Dr. Claire Lesieur and Prof. Laurent Vuillon (Université Savoie Mont Blanc). Lorenza will spend one month with us, developing methods to model protein fibrils. Looking forward to some collaborative software development!
Well done Sam!
Sam successfully completed his Masters project with us, presenting a great poster on his study of peptide-lipid interactions by molecular dynamics simulations. Congratulations!