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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCRJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Diffuse X-ray scattering from correlated motions in a protein crystal. Nat Commun 2020; 11:1271. [PMID: 32152274 PMCID: PMC7062842 DOI: 10.1038/s41467-020-14933-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/07/2020] [Indexed: 11/29/2022] Open
Abstract
Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions. Protein motion in crystals causes diffuse X-ray scattering, which so far has been very challenging to measure and interpret. Here the authors present a finely sampled diffuse scattering map from triclinic lysozyme, which allows them to resolve inter- and intramolecular correlations and they further analyze the maps using all-atom molecular dynamics simulations and simple vibrational models, revealing the contribution of internal protein motion.
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Candoni N, Grossier R, Lagaize M, Veesler S. Advances in the Use of Microfluidics to Study Crystallization Fundamentals. Annu Rev Chem Biomol Eng 2019; 10:59-83. [PMID: 31018097 DOI: 10.1146/annurev-chembioeng-060718-030312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review compares droplet-based microfluidic systems used to study crystallization fundamentals in chemistry and biology. An original high-throughput droplet-based microfluidic platform is presented. It uses nanoliter droplets, generates a chemical library, and directly solubilizes powder, thus economizing both material and time. It is compatible with all solvents without the need for surfactant. Its flexibility permits phase diagram determination and crystallization studies (screening and optimizing experiments) and makes it easy to use for nonspecialists in microfluidics. Moreover, it allows concentration measurement via ultraviolet spectroscopy and solid characterization via X-ray diffraction analysis.
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Affiliation(s)
- Nadine Candoni
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Romain Grossier
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Mehdi Lagaize
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Stéphane Veesler
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
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