Pierre Aller

My main research interests are structural biology and beamline instrumentation development.

With the rise of XFEL technology and serial synchrotron crystallography (SSX) 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 methods on demand for XFEL and synchrotron sources. Our aim is to reduce significantly the amount of sample needed for an experiment. The accoustic method on demand has already been used successfully at XFELs and we are working to adapt and miniaturize this technique for synchrotron and XFEL for time resolved studies.

One of the accoustic methods we are using is PolyPico. In collaboration with i24 we used picolitre dispenser PolyPico to load chips for fixed target. We were able to reduce the sample needed by more than one order of magnitude (Davy et al., 2019).

My main collaborators are:

• I24 team at Diamond
• Dr James Foadi, Bath University
• Dr Jan Kern from the Yano/Yachandra lab
• Dr Gabriel Leen from PolyPico
• Dials East (Diamond) and West (Berkeley) 

Orlans J, Vincent-Monegat C, Rahioui I, Sivignon C, Butryn A, Soulère L, Zaidman-Remy A, Orville AM, Heddi A, Aller P*, Da Silva P*. PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction. Int J Mol Sci. 2021 May; 22(9): 4957.

Aller P, Orville AM. Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol. 2021;2305:203-228. doi: 10.1007/978-1-0716-1406-8_11. PMID: 33950392

Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J*, Aller P*. High-throughput in situ experimental phasing. Acta Crystallogr D Struct Biol. 2020 Aug 1;76(Pt 8):790-801. doi: 10.1107/S2059798320009109

Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL. Anaerobic fixed-target serial crystallography. IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374

Burgie ES, Clinger JA, Miller MD, Brewster AS, Aller P, Butryn A, Fuller FD, Gul S, Young ID, Pham CC, Kim IS, Bhowmick A, O'Riordan LJ, Sutherlin KD, Heinemann JV, Batyuk A, Alonso-Mori R, Hunter MS, Koglin JE, Yano J, Yachandra VK, Sauter NK, Cohen AE, Kern J, Orville AM, Phillips GN Jr, Vierstra RD. Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):300-307. DOI: 10.1073/pnas.1912041116

Davy B, Axford D, Beale JH, Butryn A, Docker P, Ebrahim A, Leen G, Orville AM, Owen RL*, Aller P*. Reducing sample consumption for serial crystallography using acoustic drop ejection. J Synchrotron Radiat. 2019 Sep 1;26(Pt 5):1820-1825. DOI: 10.1107/S1600577519009329.

Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK. Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature. 2018 Nov;563(7731):421-425. DOI: 10.1038/s41586-018-0681-2

Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. Crystals (Basel). 2017 Aug 4;7(8):242. DOI: 10.3390/cryst7080242.

Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM Jr, Krebs C, Högbom M, Phillips GN Jr, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods. 2017 Apr;14(4):443-449. DOI: 10.1038/nmeth.4195

Kwon H, Basran J, Casadei CM, Fielding AJ, Schrader TE, Ostermann A, Devos JM, Aller P, Blakeley MP, Moody PCE, Raven EL. Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme. Nat Commun. 2016 Nov 29;7:13445. DOI: 10.1038/ncomms13445

Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature. 2016 Dec 15;540(7633):453-457. DOI: 10.1038/nature20161

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.

Warren AJ, Crawshaw AD, Trincao J, Aller P, Alcock S, Nistea I, Salgado PS, Evans G. In vacuo X-ray data collection from graphene-wrapped protein crystals. Acta Crystallogr D Biol Crystallogr. 2015 Oct;71(Pt 10):2079-88. 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. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases. 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.