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Suder DS, Gonen S. Mitigating the Blurring Effect of CryoEM Averaging on a Flexible and Highly Symmetric Protein Complex through Sub-Particle Reconstruction. Int J Mol Sci 2024; 25:5665. [PMID: 38891853 PMCID: PMC11171969 DOI: 10.3390/ijms25115665] [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: 03/31/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Many macromolecules are inherently flexible as a feature of their structure and function. During single-particle CryoEM processing, flexible protein regions can be detrimental to high-resolution reconstruction as signals from thousands of particles are averaged together. This "blurring" effect can be difficult to overcome and is possibly more pronounced when averaging highly symmetric complexes. Approaches to mitigating flexibility during CryoEM processing are becoming increasingly critical as the technique advances and is applied to more dynamic proteins and complexes. Here, we detail the use of sub-particle averaging and signal subtraction techniques to precisely target and resolve flexible DARPin protein attachments on a designed tetrahedrally symmetric protein scaffold called DARP14. Particles are first aligned as full complexes, and then the symmetry is reduced by alignment and focused refinement of the constituent subunits. The final reconstructions we obtained were vastly improved over the fully symmetric reconstructions, with observable secondary structure and side-chain placement. Additionally, we were also able to reconstruct the core region of the scaffold to 2.7 Å. The data processing protocol outlined here is applicable to other dynamic and symmetric protein complexes, and our improved maps could allow for new structure-guided variant designs of DARP14.
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Affiliation(s)
| | - Shane Gonen
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
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Ding J, Deme J, Stagno JR, Yu P, Lea S, Wang YX. Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. Nucleic Acids Res 2023; 51:9952-9960. [PMID: 37534568 PMCID: PMC10570017 DOI: 10.1093/nar/gkad651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.
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Affiliation(s)
- Jienyu Ding
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Justin C Deme
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ping Yu
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Susan M Lea
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Forsberg BO, Shah PNM, Burt A. A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps. Nat Commun 2023; 14:5802. [PMID: 37726277 PMCID: PMC10509264 DOI: 10.1038/s41467-023-41478-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023] Open
Abstract
Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction.
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Affiliation(s)
- Björn O Forsberg
- Department of Physiology and Pharmacology, Karolinska Institute, 171 77, Stockholm, Sweden.
- Division of Structural Biology, University of Oxford, OX3 7BN, Oxford, UK.
| | - Pranav N M Shah
- Division of Structural Biology, University of Oxford, OX3 7BN, Oxford, UK
| | - Alister Burt
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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Lee JK, Liu YT, Hu JJ, Aphasizheva I, Aphasizhev R, Zhou ZH. CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics. J Struct Biol X 2023; 7:100088. [PMID: 37128595 PMCID: PMC10148081 DOI: 10.1016/j.yjsbx.2023.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/13/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan Leishmania tarentolae (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
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Affiliation(s)
- Jane K.J. Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jason J. Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
- Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
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Fernandez JJ, Martinez-Sanchez A. Computational methods for three-dimensional electron microscopy (3DEM). COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 225:107039. [PMID: 35917713 DOI: 10.1016/j.cmpb.2022.107039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Jose-Jesus Fernandez
- Spanish National Research Council (CINN-CSIC) and Health Research Institute of Asturias (ISPA), Av Hospital Universitario s/n, Oviedo 33011, Spain.
| | - A Martinez-Sanchez
- Computer Science Dept, University of Oviedo (UniOvi) and Health Research Institute of Asturias (ISPA), Campus Llamaquique, Oviedo 33007, Spain.
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