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Meinhold S, Zdanowicz R, Giese C, Glockshuber R. Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex. SCIENCE ADVANCES 2024; 10:eadj6358. [PMID: 38324697 PMCID: PMC10849603 DOI: 10.1126/sciadv.adj6358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
The Escherichia coli pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The PDHc core is a cubic complex of eight E2 homotrimers. Homodimers of the peripheral subunits E1 and E3 associate with the core by binding to the peripheral subunit binding domain (PSBD) of E2. Previous reports indicated that 12 E1 dimers and 6 E3 dimers bind to the 24-meric E2 core. Using an assembly arrested E2 homotrimer (E23), we show that two of the three PSBDs in the E23 dimerize, that each PSBD dimer cooperatively binds two E1 dimers, and that E3 dimers only bind to the unpaired PSBD in E23. This mechanism is preserved in wild-type PDHc, with an E1 dimer:E2 monomer:E3 dimer stoichiometry of 16:24:8. The conserved PSBD dimer interface indicates that PSBD dimerization is the previously unrecognized architectural determinant of gammaproteobacterial PDHc megacomplexes.
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Affiliation(s)
| | | | - Christoph Giese
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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Lu C, Peng X, Lu D. Molecular Dynamics Simulation of Protein Cages. Methods Mol Biol 2023; 2671:273-305. [PMID: 37308651 DOI: 10.1007/978-1-0716-3222-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular dynamics (MD) simulations enable the description of the physical movement of the system over time based on classical mechanics at various scales depending on the models. Protein cages are a particular group of different-size proteins with hollow, spherical structures and are widely found in nature, which have vast applications in numerous fields. The MD simulation of cage proteins is particularly important as a powerful tool to unveil their structures and dynamics for various properties, assembly behavior, and molecular transport mechanisms. Here, we describe how to conduct MD simulations for cage proteins, especially technical details, and analyze some of the properties of interest using GROMACS/NAMD packages.
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Affiliation(s)
- Chenlin Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Xue Peng
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China.
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Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11020242. [PMID: 35203843 PMCID: PMC8868475 DOI: 10.3390/antibiotics11020242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 02/05/2023] Open
Abstract
In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.
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Babaei M, Jones IC, Dayal K, Mauter MS. Computing the Diamagnetic Susceptibility and Diamagnetic Anisotropy of Membrane Proteins from Structural Subunits. J Chem Theory Comput 2017; 13:2945-2953. [PMID: 28418668 DOI: 10.1021/acs.jctc.6b01251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of large, complex molecules in the presence of magnetic fields is experimentally challenging to measure and computationally intensive to predict. This work proposes a novel, mixed-methods approach for efficiently computing the principal magnetic susceptibilities and diamagnetic anisotropy of membrane proteins. The hierarchical primary (amino acid), secondary (α helical and β sheet), and tertiary (α helix and β barrel) structure of transmembrane proteins enables analysis of a complex molecule using discrete subunits of varying size and resolution. The proposed method converts the magnetic susceptibility tensor for all protein subunits to a unit coordinate system and sums them to build the magnetic susceptibility tensor for the membrane protein. Using this approach, we calculate the diamagnetic anisotropy for all transmembrane proteins of known structure and investigate the effect of different subunit resolutions on the resulting predictions of diamagnetic anisotropy. We demonstrate that amino acid residues with aromatic side groups exhibit higher diamagnetic anisotropies. On average, high percentages of aromatic amino acid subunits, a β barrel tertiary structure, and a small volume are correlated with high volumetric diamagnetic anisotropy. Finally, we demonstrate that accounting for the spatial position of the residues with respect to one another is critical to accurately computing the magnetic properties of the complex protein molecule.
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Affiliation(s)
- Mahnoush Babaei
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Isaac C Jones
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Kaushik Dayal
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Meagan S Mauter
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States.,Department of Engineering and Public Policy, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
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Reengineering of the human pyruvate dehydrogenase complex: from disintegration to highly active agglomerates. Biochem J 2017; 474:865-875. [PMID: 27986918 DOI: 10.1042/bcj20160916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 11/17/2022]
Abstract
The pyruvate dehydrogenase complex (PDC) plays a central role in cellular metabolism and regulation. As a metabolite-channeling multi-enzyme complex it acts as a complete nanomachine due to its unique geometry and by coupling a cascade of catalytic reactions using 'swinging arms'. Mammalian and specifically human PDC (hPDC) is assembled from multiple copies of E1 and E3 bound to a large E2/E3BP 60-meric core. A less restrictive and smaller catalytic core, which is still active, is highly desired for both fundamental research on channeling mechanisms and also to create a basis for further modification and engineering of new enzyme cascades. Here, we present the first experimental results of the successful disintegration of the E2/E3BP core while retaining its activity. This was achieved by C-terminal α-helixes double truncations (eight residues from E2 and seven residues from E3BP). Disintegration of the hPDC core via double truncations led to the formation of highly active (approximately 70% of wildtype) apparently unordered clusters or agglomerates and inactive non-agglomerated species (hexamer/trimer). After additional deletion of N-terminal 'swinging arms', the aforementioned C-terminal truncations also caused the formation of agglomerates of minimized E2/E3BP complexes. It is likely that these 'swinging arm' regions are not solely responsible for the formation of the large agglomerates.
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Hezaveh S, Zeng AP, Jandt U. Human Pyruvate Dehydrogenase Complex E2 and E3BP Core Subunits: New Models and Insights from Molecular Dynamics Simulations. J Phys Chem B 2016; 120:4399-409. [DOI: 10.1021/acs.jpcb.6b02698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Samira Hezaveh
- Institute of Bioprocess and
Biosystem Engineering, Hamburg University of Technology, Denickestrasse
15, 21071 Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and
Biosystem Engineering, Hamburg University of Technology, Denickestrasse
15, 21071 Hamburg, Germany
| | - Uwe Jandt
- Institute of Bioprocess and
Biosystem Engineering, Hamburg University of Technology, Denickestrasse
15, 21071 Hamburg, Germany
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Holmes K, Shepherd DA, Ashcroft AE, Whelan M, Rowlands DJ, Stonehouse NJ. Assembly Pathway of Hepatitis B Core Virus-like Particles from Genetically Fused Dimers. J Biol Chem 2015; 290:16238-45. [PMID: 25953902 PMCID: PMC4481223 DOI: 10.1074/jbc.m114.622035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/08/2015] [Indexed: 01/17/2023] Open
Abstract
Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation.
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Affiliation(s)
- Kris Holmes
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Dale A Shepherd
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Alison E Ashcroft
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Mike Whelan
- iQur Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, United Kingdom
| | - David J Rowlands
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Nicola J Stonehouse
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
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Miyagawa M, Yamaguchi M. Helicene-Grafted Silica Nanoparticles Capture Hetero-Double-Helix Intermediates during Self-Assembly Gelation. Chemistry 2015; 21:8408-15. [DOI: 10.1002/chem.201406482] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 12/12/2022]
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Abstract
Controlling the self-assembly behavior of caged proteins expands their potential applications in nanotechnology. While the structure of a caged E2 protein from pyruvate dehydrogenase is inert to any pH change, the incorporation of switchable GALA peptide that undergoes a coil-to-helix transition at acidic pH modulates its self-assembly property. By substituting the native α-helix at the C-terminus of the E2 protein with the GALA peptide, we report the first engineered caged protein with reversible inversed pH-responsive behavior. The redesigned caged E2 protein assumes an assembly profile that is distinct from the native state; it disassembles at pH 7.0 and self-assembles at pH 4.0 in a reversible manner. This unique reversible pH trigger suggests the applicability of the self-assembly control on other multi-subunit macromolecules.
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Affiliation(s)
- Tao Peng
- Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457.
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Why are the 2-oxoacid dehydrogenase complexes so large? Generation of an active trimeric complex. Biochem J 2014; 463:405-12. [DOI: 10.1042/bj20140359] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A trimeric core of the 42-mer 2-oxoacid dehydrogenase complex of the thermophilic archaeon Thermoplasma has been generated and its structure determined. This trimeric core binds both E1 and E3 component enzymes to form for the first time a catalytically active mini-complex.
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Peng T, Paramelle D, Sana B, Lee CF, Lim S. Designing non-native iron-binding site on a protein cage for biological synthesis of nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3131-3138. [PMID: 24788938 DOI: 10.1002/smll.201303516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 06/03/2023]
Abstract
In biomineralization processes, a supramolecular organic structure is often used as a template for inorganic nanomaterial synthesis. The E2 protein cage derived from Geobacillus stearothermophilus pyruvate dehydrogenase and formed by the self-assembly of 60 subunits, has been functionalized with non-native iron-mineralization capability by incorporating two types of iron-binding peptides. The non-native peptides introduced at the interior surface do not affect the self-assembly of E2 protein subunits. In contrast to the wild-type, the engineered E2 protein cages can serve as size- and shape-constrained reactors for the synthesis of iron nanoparticles. Electrostatic interactions between anionic amino acids and cationic iron molecules drive the formation of iron oxide nanoparticles within the engineered E2 protein cages. The work expands the investigations on nanomaterial biosynthesis using engineered host-guest encapsulation properties of protein cages.
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Affiliation(s)
- Tao Peng
- Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637457
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