Pierre Aller

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Pierre Aller is a beamline scientist with the UK XFEL-Hub. After a Ph.D. on Molecular Dynamic Simulation, Pierre moved to the University of Vermont (Burlington, USA) for a post-doc. He studied protein crystallography for 6 years on DNA polymerase, before joining Diamond in August 2011 as support scientist for MX village. Since July 2016 he has become beamline scientist working for the UK XFEL Hub led by Allen Orville.

Email: pierre.aller@diamond.ac.uk
Tel: +44 (0) 123577 8183

Key Research Area

Latest Publications

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  1. Research Expertise
  2. Collaborations
  3. Publications
Research Expertise -

Current Research Interests

 
My main research interests are structural biology and beamline instrumentation development.
 XFEL: With the rise of XFEL technology we are facing several challenges from sample preparation and delivery and data processing. All these area need to be optimised and one of my focus is sample delivery using acoustic droplet ejection. I have also a keen interest in data processing especially with DIALS, ctbx.xfel and ccpxfel.

Multi-crystals analysis with DIALS and BLEND:
The recent developments of micro-focus beamlines and in situ data collection have led to a renewed interest in multiple crystal dataset analysis. For a typical experiment on a micro-focus or sub micro-focus beamline we should expect to merge small wedges of data collected on multiple crystals in order to get a complete set. Programs such as DIALS and BLEND will help to get the best of the data.

My current research work is focusing on XFEL technology. As part of the XFEL-Hub our aim is to facilitate access to UK community to XFEL instruments in the world. My current work is focusing on the sample delivery method we can use during XFEL beamtime. The aim is to reduce the amount of sample needed for an experiment. The Acoustic Droplet Ejection method has already been used at LCLS and we are working to adapt and miniaturize this technique for synchrotron and XFEL for time resolved studies.

My other interest is the multi-crystals analysis with DIALS and BLEND. Collecting small wedges of data and merging them together to obtain a complete dataset is not always straightforward. Using joint refinement in DIALS to obtain more accurate cell parameters and merging the datasets with BLEND is particularly useful to get the best of the data.



 
 

 

Collaborations - +

Collaborations

My main collaborators are:

Professor Sylvie Doublié, University of Vermont (USA)
Dr James Foadi, MPL / Diamond (UK)
Professor Mark Moloney, University of Oxford (UK)
 

 

Publications - +

Publications

Aller P, Geng T, Evans G, Foadi J. Applications of the BLEND Software to Crystallographic Data from Membrane Proteins Adv Exp Med Biol. 2016;922:119-35.
DOI: 10.1007/978-3-319-35072-1_9

Axford D, Aller P, Sanchez-Weatherby J, Sandy J. Applications of thin-film sandwich crystallization platforms Acta Crystallogr F Struct Biol Commun. 2016 Apr;72(Pt 4):313-9. Epub 2016 Mar 24.
DOI: 10.1107/S2053230X16004386.

Acta Crystallogr D Biol Crystallogr. 2015 Oct;71(Pt 10):2079-88. In vacuo X-ray data collection from graphene-wrapped protein crystals
Epub 2015 Sep 26.
DOI: 10.1107/S1399004715014194.

Zahn KE, Averill AM, Aller P, Wood RD, Doublié S. Human DNA polymerase θ grasps the primer terminus to mediate DNA repair
Nat Struct Mol Biol. 2015 Apr;22(4):304-11. Epub 2015 Mar 16.
DOI: 10.1038/nsmb.2993.

Aller P, Sanchez-Weatherby J, Foadi J, Winter G, Lobley CM, Axford D, Ashton AW, Bellini D, Brandao-Neto J, Culurgioni S, Douangamath A, Duman R, Evans G, Fisher S, Flaig R, Hall DR, Lukacik P, Mazzorana M, McAuley KE, Mykhaylyk V, Owen RL, Paterson NG, Romano P, Sandy J, Sorensen T, von Delft F, Wagner A, Warren A, Williams M, Stuart DI, Walsh MA. Application of in situ diffraction in high-throughput structure determination platforms Methods Mol Biol. 2015;1261:233-53.
DOI: 10.1007/978-1-4939-2230-7_13. Review.

Foadi J, Aller P, Alguel Y, Cameron A, Axford D, Owen RL, Armour W, Waterman DG, Iwata S, Evans G. Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1617-32. Epub 2013 Jul 20.
DOI: 10.1107/S0907444913012274.

Byrne RT, Whelan F, Aller P, Bird LE, Dowle A, Lobley CM, Reddivari Y, Nettleship JE, Owens RJ, Antson AA, Waterman DG.S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):1090-8. Epub 2013 May 15.
DOI: 10.1107/S0907444913004939.

Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Moraes I, Brandao-Neto J. Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):920-3.Epub 2013 Apr 19. 
DOI: 10.1107/S0907444913002412.
 
Lobley CM, Aller P, Douangamath A, Reddivari Y, Bumann M, Bird LE, Nettleship JE, Brandao-Neto J, Owens RJ, O'Toole PW, Walsh MA.Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118 Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1427-33.
DOI: 10.1107/S174430911204273X. Epub 2012 Nov 14.

Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace SS, Doublié S. Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine DNA Repair (Amst). 2012 Sep 1;11(9):714-25. Epub 2012 Jul 11.
doi: 10.1016/j.dnarep.2012.06.004.

Aller P, Duclos S, Wallace SS, Doublié S. A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex J Mol Biol. 2011 Sep 9;412(1):22-34. Epub 2011 Jul 18.
DOI: 10.1016/j.jmb.2011.07.007.

Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B. Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12.
DOI: 10.1093/nar/gkr215.

Aller P, Ye Y, Wallace SS, Burrows CJ, Doublié
S. Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin Biochemistry. 2010 Mar 23;49(11):2502-9.
doi: 10.1021/bi902195p

Aller P, Rould MA, Hogg M, Wallace SS, Doublié S. A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):814-8. Epub 2007 Jan 8.

Hogg M, Aller P, Konigsberg W, Wallace SS, Doublié S. Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family J Biol Chem. 2007 Jan 12;282(2):1432-44. Epub 2006 Nov 9.

Aller P, Garnier N, Genest M. Transmembrane helix packing of ErbB/Neu receptor in membrane environment: a molecular dynamics study J Biomol Struct Dyn. 2006 Dec;24(3):209-28.

Samna Soumana O, Aller P, Garnier N, Genest M.Transmembrane peptides from tyrosine kinase receptor. Mutation-related behavior in a lipid bilayer investigated by molecular dynamics simulations J Biomol Struct Dyn. 2005 Aug;23(1):91-100.
 
Aller P, Voiry L, Garnier N, Genest M. Molecular dynamics (MD) investigations of preformed structures of the transmembrane domain of the oncogenic Neu receptor dimer in a DMPC bilayer Biopolymers. 2005 Mar;77(4):184-97.