1
|
Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc Natl Acad Sci U S A 2024; 121:e2318527121. [PMID: 39190355 PMCID: PMC11388330 DOI: 10.1073/pnas.2318527121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and, more importantly, a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
Collapse
Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| |
Collapse
|
2
|
Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559052. [PMID: 37790421 PMCID: PMC10543002 DOI: 10.1101/2023.09.22.559052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
Collapse
Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston MA 02115 USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260 USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| |
Collapse
|
3
|
Weiss S, Vergara S, Lin G, Calero G. Detection of Microcrystals for CryoEM. Methods Mol Biol 2020; 2215:299-307. [PMID: 33368010 DOI: 10.1007/978-1-0716-0966-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Here, we present a strategy to identify microcrystals from initial protein crystallization screen experiments and to optimize diffraction quality of those crystals using negative stain transmission electron microscopy (TEM) as a guiding technique. The use of negative stain TEM allows visualization along the process and thus enables optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nanocrystals bearing perfect lattices are seeded and can be used for MicroED as well as growing larger crystals for X-ray and free electron laser (FEL) data collection.
Collapse
Affiliation(s)
- Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| |
Collapse
|
4
|
Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
Collapse
|
5
|
Lin G, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals. Methods 2019; 159-160:23-28. [PMID: 31029767 DOI: 10.1016/j.ymeth.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
Well-diffracting crystals are essential to obtain relevant structural data that will lead to understanding of RNA Polymerase II (Pol II) transcriptional processes at a molecular level. Here we present a strategy to study Pol II crystals using negative stain transmission electron microscopy (TEM) and a methodology to optimize radiation damage free data collection using free electron laser (FEL) at the Linac Coherent Light Source (LCLS). The use of negative stain TEM allowed visualization and optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nano crystals bearing perfect lattices were seeded and used to grow larger crystals for FEL data collection. Moreover, the use of in house designed crystal loops together with ultra-violet (UV) microscopy for crystal detection facilitated data collection. Such strategy permitted collection of multiple crystals of radiation-free-damage data, resulting in the highest resolution of wild type (WT) Pol II crystals ever observed.
Collapse
Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Carlos Camacho
- Department of Computanional and Systems Biology, University of Pittsburgh School of Medicine, United States
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States.
| |
Collapse
|
6
|
Martiel I, Müller-Werkmeister HM, Cohen AE. Strategies for sample delivery for femtosecond crystallography. Acta Crystallogr D Struct Biol 2019; 75:160-177. [PMID: 30821705 PMCID: PMC6400256 DOI: 10.1107/s2059798318017953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 11/11/2022] Open
Abstract
Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.
Collapse
Affiliation(s)
- Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Henrike M. Müller-Werkmeister
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| |
Collapse
|
7
|
Mathews II, Allison K, Robbins T, Lyubimov AY, Uervirojnangkoorn M, Brunger AT, Khosla C, DeMirci H, McPhillips SE, Hollenbeck M, Soltis M, Cohen AE. The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography. Biochemistry 2017; 56:4751-4756. [PMID: 28832129 PMCID: PMC5721673 DOI: 10.1021/acs.biochem.7b00711] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of the trans-acyltransferase (AT) from the disorazole polyketide synthase (PKS) was determined at room temperature to a resolution of 2.5 Å using a new method for the direct delivery of the sample into an X-ray free-electron laser. A novel sample extractor efficiently delivered limited quantities of microcrystals directly from the native crystallization solution into the X-ray beam at room temperature. The AT structure revealed important catalytic features of this core PKS enzyme, including the occurrence of conformational changes around the active site. The implications of these conformational changes for polyketide synthase reaction dynamics are discussed.
Collapse
Affiliation(s)
- Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Kim Allison
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | | | | | - Hasan DeMirci
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Hollenbeck
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Soltis
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
8
|
Abstract
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection. Additionally, we describe the protein quality-control assays that are often instrumental as a guideline for a shorter path toward the structure.
Collapse
Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Enrique E Abola
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
9
|
Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol 2016; 72:603-15. [PMID: 27139624 PMCID: PMC4854312 DOI: 10.1107/s2059798316001546] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.
Collapse
Affiliation(s)
- Hilary P. Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ieva Sutkeviciute
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shelley Reynolds
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ying Wu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | | | - Alexander M. Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Robert Lawrence
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Emily Lamm
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Lisa Clark
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Craig M. Ogata
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 60439, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Angela M. Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jean-Pierre Vilardaga
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| |
Collapse
|
10
|
Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
Collapse
Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
| |
Collapse
|
11
|
Barnes CO, Kovaleva EG, Fu X, Stevenson HP, Brewster AS, DePonte DP, Baxter EL, Cohen AE, Calero G. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography. Arch Biochem Biophys 2016; 602:61-68. [PMID: 26944553 DOI: 10.1016/j.abb.2016.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL) sources has enabled structural studies on microcrystalline protein samples at non-cryogenic temperatures. However, the identification and optimization of conditions that produce well diffracting microcrystals remains an experimental challenge. Here, we report parallel SFX and transmission electron microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate 2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions and morphology, as well as similar crystal size and density, the indexing efficiency of the diffraction data collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the H200Q variant sample. While not reported herein, the 1.75 Å resolution structure of the H200Q variant was determined from ∼16 min of beam time, demonstrating the utility of TEM analysis in evaluating sample monodispersity and lattice quality, parameters critical to the efficiency of SFX experiments.
Collapse
Affiliation(s)
- Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Aaron S Brewster
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| |
Collapse
|
12
|
Gao A, Wu Q, Wang D, Ha Y, Chen Z, Yang P. A Superhydrophobic Surface Templated by Protein Self-Assembly and Emerging Application toward Protein Crystallization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:579-87. [PMID: 26607764 DOI: 10.1002/adma.201504769] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/10/2015] [Indexed: 05/06/2023]
Abstract
A proteinaceous superhydrophobic material for facile protein crystallization is reported. The lysozyme phase transition is rationally manipulated to form a reliable superhydrophobic coating on virtually arbitrary material surfaces with good thermostability and mechanical robustness. Such a surface exhibits a fascinating capability to drive protein crystallization, and the protein crystal array can be facilitated in a large area at an ultralow protein concentration.
Collapse
Affiliation(s)
- Aiting Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Qian Wu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Dehui Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yuan Ha
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure, Jilin University, Changchun, 130012, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| |
Collapse
|
13
|
Li C, Schmidt K, Spence JC. Data collection strategies for time-resolved X-ray free-electron laser diffraction, and 2-color methods. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041714. [PMID: 26798813 PMCID: PMC4711652 DOI: 10.1063/1.4922433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/29/2015] [Indexed: 05/29/2023]
Abstract
We compare three schemes for time-resolved X-ray diffraction from protein nanocrystals using an X-ray free-electron laser. We find expressions for the errors in structure factor measurement using the Monte Carlo pump-probe method of data analysis with a liquid jet, the fixed sample pump-probe (goniometer) method (both diffract-and-destroy, and below the safe damage dose), and a proposed two-color method. Here, an optical pump pulse arrives between X-ray pulses of slightly different energies which hit the same nanocrystal, using a weak first X-ray pulse which does not damage the sample. (Radiation damage is outrun in the other cases.) This two-color method, in which separated Bragg spots are impressed on the same detector readout, eliminates stochastic fluctuations in crystal size, shape, and orientation and is found to require two orders of magnitude fewer diffraction patterns than the currently used Monte Carlo liquid jet method, for 1% accuracy. Expressions are given for errors in structure factor measurement for the four approaches, and detailed simulations provided for cathepsin B and IC3 crystals. While the error is independent of the number of shots for the dose-limited goniometer method, it falls off inversely as the square root of the number of shots for the two-color and Monte Carlo methods, with a much smaller pre-factor for the two-color mode, when the first shot is below the damage threshold.
Collapse
Affiliation(s)
- Chufeng Li
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
| | - Kevin Schmidt
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
| | - John C Spence
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
| |
Collapse
|
14
|
Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B, Burghammer M, Colletier JP. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1184-96. [PMID: 25945583 PMCID: PMC4427202 DOI: 10.1107/s1399004715004514] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023]
Abstract
High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.
Collapse
Affiliation(s)
- Nicolas Coquelle
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ulrike Kapp
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Britta Weinhausen
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Jacques-Philippe Colletier
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| |
Collapse
|
15
|
Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:928-40. [PMID: 25849403 PMCID: PMC4388268 DOI: 10.1107/s1399004715002308] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.
Collapse
Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismail Emre Araci
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aina E. Cohen
- SLAC National Accelerator Laboratory, Stanford, CA 94305, USA
| | | | | | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85282, USA
| | - Henry N Chapman
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
| |
Collapse
|
17
|
Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A 2014; 111:17122-7. [PMID: 25362050 PMCID: PMC4260607 DOI: 10.1073/pnas.1418733111] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.
Collapse
Affiliation(s)
| | | | | | | | | | - Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | | | | | | | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | | | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | | | | | | | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Artem Y Lyubimov
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | | | | | | | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Soichi Wakatsuki
- Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; Structural Biology, and
| | - William I Weis
- Molecular and Cellular Physiology, and Structural Biology, and
| | - Oleg A Zadvornyy
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Oliver B Zeldin
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry,
| |
Collapse
|