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Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JFR, Bommer M, Brewster AS, Browne MC, Chatterjee R, Cho E, Cohen AE, Cowan M, Datwani S, Davidson VL, Defever J, Eaton B, Ellson R, Feng Y, Ghislain LP, Glownia JM, Han G, Hattne J, Hellmich J, Héroux A, Ibrahim M, Kern J, Kuczewski A, Lemke HT, Liu P, Majlof L, McClintock WM, Myers S, Nelsen S, Olechno J, Orville AM, Sauter NK, Soares AS, Soltis SM, Song H, Stearns RG, Tran R, Tsai Y, Uervirojnangkoorn M, Wilmot CM, Yachandra V, Yano J, Yukl ET, Zhu D, Zouni A. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 2016; 24:631-640. [PMID: 26996959 DOI: 10.1016/j.str.2016.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/25/2015] [Accepted: 02/17/2016] [Indexed: 02/01/2023]
Abstract
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
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Affiliation(s)
- Christian G Roessler
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Babak Andi
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - José F R Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, CEP: 13560-970, Brazil
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Michael C Browne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Eunsun Cho
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew Cowan
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Victor L Davidson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816-2364, USA
| | - Jim Defever
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | | | - Yiping Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Annie Héroux
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anthony Kuczewski
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | | | - Stuart Myers
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Silke Nelsen
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Allen M Orville
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Alexei S Soares
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Heng Song
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Yingssu Tsai
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Chemistry, Stanford University, Stanford, CA 94305-4401, USA
| | | | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vittal Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Erik T Yukl
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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Kenney GE, Rosenzweig AC. Genome mining for methanobactins. BMC Biol 2013; 11:17. [PMID: 23442874 PMCID: PMC3621798 DOI: 10.1186/1741-7007-11-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/26/2013] [Indexed: 01/27/2023] Open
Abstract
Background Methanobactins (Mbns) are a family of copper-binding natural products involved in copper uptake by methanotrophic bacteria. The few Mbns that have been structurally characterized feature copper coordination by two nitrogen-containing heterocycles next to thioamide groups embedded in a peptidic backbone of varying composition. Mbns are proposed to derive from post-translational modification of ribosomally synthesized peptides, but only a few genes encoding potential precursor peptides have been identified. Moreover, the relevance of neighboring genes in these genomes has been unclear. Results The potential for Mbn production in a wider range of bacterial species was assessed by mining microbial genomes. Operons encoding Mbn-like precursor peptides, MbnAs, were identified in 16 new species, including both methanotrophs and, surprisingly, non-methanotrophs. Along with MbnA, the core of the operon is formed by two putative biosynthetic genes denoted MbnB and MbnC. The species can be divided into five groups on the basis of their MbnA and MbnB sequences and their operon compositions. Additional biosynthetic proteins, including aminotransferases, sulfotransferases and flavin adenine dinucleotide (FAD)-dependent oxidoreductases were also identified in some families. Beyond biosynthetic machinery, a conserved set of transporters was identified, including MATE multidrug exporters and TonB-dependent transporters. Additional proteins of interest include a di-heme cytochrome c peroxidase and a partner protein, the roles of which remain a mystery. Conclusions This study indicates that Mbn-like compounds may be more widespread than previously thought, but are not present in all methanotrophs. This distribution of species suggests a broader role in metal homeostasis. These data provide a link between precursor peptide sequence and Mbn structure, facilitating predictions of new Mbn structures and supporting a post-translational modification biosynthetic pathway. In addition, testable models for Mbn transport and for methanotrophic copper regulation have emerged. Given the unusual modifications observed in Mbns characterized thus far, understanding the roles of the putative biosynthetic proteins is likely to reveal novel pathways and chemistry.
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Affiliation(s)
- Grace E Kenney
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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