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Lynch EM, Hansen H, Salay L, Cooper M, Timr S, Kollman JM, Webb BA. Structural basis for allosteric regulation of human phosphofructokinase-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585110. [PMID: 38559074 PMCID: PMC10980016 DOI: 10.1101/2024.03.15.585110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington
| | - Heather Hansen
- Department of Biochemistry and Molecular Medicine, West Virginia University
| | - Lauren Salay
- Department of Biochemistry, University of Washington
| | - Madison Cooper
- Department of Biochemistry and Molecular Medicine, West Virginia University
| | - Stepan Timr
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences
| | | | - Bradley A Webb
- Department of Biochemistry and Molecular Medicine, West Virginia University
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2
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Olson DG, Maloney MI, Lanahan AA, Cervenka ND, Xia Y, Pech-Canul A, Hon S, Tian L, Ziegler SJ, Bomble YJ, Lynd LR. Ethanol tolerance in engineered strains of Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:137. [PMID: 37710260 PMCID: PMC10503014 DOI: 10.1186/s13068-023-02379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/05/2023] [Indexed: 09/16/2023]
Abstract
Clostridium thermocellum is a natively cellulolytic bacterium that is promising candidate for cellulosic biofuel production, and can produce ethanol at high yields (75-80% of theoretical) but the ethanol titers produced thus far are too low for commercial application. In several strains of C. thermocellum engineered for increased ethanol yield, ethanol titer seems to be limited by ethanol tolerance. Previous work to improve ethanol tolerance has focused on the WT organism. In this work, we focused on understanding ethanol tolerance in several engineered strains of C. thermocellum. We observed a tradeoff between ethanol tolerance and production. Adaptation for increased ethanol tolerance decreases ethanol production. Second, we observed a consistent genetic response to ethanol stress involving mutations at the AdhE locus. These mutations typically reduced NADH-linked ADH activity. About half of the ethanol tolerance phenotype could be attributed to the elimination of NADH-linked activity based on a targeted deletion of adhE. Finally, we observed that rich growth medium increases ethanol tolerance, but this effect is eliminated in an adhE deletion strain. Together, these suggest that ethanol inhibits growth and metabolism via a redox-imbalance mechanism. The improved understanding of mechanisms of ethanol tolerance described here lays a foundation for developing strains of C. thermocellum with improved ethanol production.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
| | - Marybeth I Maloney
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Anthony A Lanahan
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Nicholas D Cervenka
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Ying Xia
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Angel Pech-Canul
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Shuen Hon
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Liang Tian
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Youth Olympic Village, #1-1-602, Jianye District, Nanjing, Jiangsu, China
| | - Samantha J Ziegler
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Yannick J Bomble
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Lee R Lynd
- Thayer School of Engineering at Dartmouth College, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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3
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Hvorecny KL, Kollman JM. Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments. Curr Opin Struct Biol 2023; 79:102530. [PMID: 36709625 PMCID: PMC10023394 DOI: 10.1016/j.sbi.2023.102530] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
Abstract
Recent work in structural biology is shedding light on how many of the enzymes of intermediary metabolism are self- and co-assembling into large, filamentous polymers or agglomerates to organize and regulate the complex and essential biochemical pathways in cells. Filament assembly provides an additional layer of regulation by modulating the intrinsic allostery of the enzyme protomers which tunes activity in response to a variety of environmental cues. Enzyme filaments dynamically assemble and disassemble in response to changes in metabolite levels and environmental cues, shifting metabolic flux on a more rapid timescale than transcriptional or translational reprogramming. Here we present recent examples of high-resolution structures of filaments from proteins in intermediary metabolism and we discuss how filament assembly modulates the activities of these and other proteins.
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Affiliation(s)
- Kelli L Hvorecny
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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4
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Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
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5
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Mao Q, Jiang J, Wu X, Ma Y, Zhang Y, Zhao Y, Zhang Y, Wang Q. Bifunctional alcohol/aldehyde dehydrogenase AdhE controls phospho-transferase system sugar utilization and virulence gene expression by interacting PtsH in Edwardsiella piscicida. Microbiol Res 2022; 260:127018. [DOI: 10.1016/j.micres.2022.127018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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Chen H, Peng L, Zhao C, Cai Z, Zhou X. Protective Mechanism of Polygonum perfoliatum L. Extract on Chronic Alcoholic Liver Injury Based on UHPLC-QExactive Plus Mass Spectrometry Lipidomics and MALDI-TOF/TOF Mass Spectrometry Imaging. Foods 2022; 11:foods11111583. [PMID: 35681333 PMCID: PMC9179971 DOI: 10.3390/foods11111583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 02/07/2023] Open
Abstract
Polygonum perfoliatum L. has a long history of medicinal and edible applications. Studies have shown that it can significantly protect liver injury, but the mechanism is unclear. The purpose of this study was to explore the protective mechanism of P. perfoliatum on chronic alcoholic liver injury from the perspective of lipid metabolism. After 8 weeks of alcohol exposure in male Wister mice, the levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP) in serum were significantly increased, and the activities of alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH) in liver were significantly decreased. Meanwhile, pathological changes of liver tissue in mice were observed by histopathology. Then, Ultra-High Performance Liquid Chromatography (UHPLC) QExactive Plus Mass Spectrometer lipidomics and matrix-assisted laser desorption/ionization time-of-flight/time -of-flight (MALDI-TOF/TOF) mass spectrometry imaging methods were established to analyze lipid metabolism in mice. Ten different lipids were identified by statistical analysis, including Fatty Acyls, Glycerophospholipids, Prenol lipids and Sphingomyelins. After intervention with P. perfoliatum extracts at different doses (25 to 100 mg/kg), levels of AST, ALT, ALP in serum, and activities of ADH and ALDH in liver were significantly corrected. The hepatic cord structure was clear, and the liver cells were closely arranged without other obvious abnormalities. Non-target lipidomics analysis showed that P. perfoliatum extract could regulate the metabolic disorders of the 10 different lipids caused by continuous alcohol exposure. Pathway analysis suggested that the mechanism of P. perfoliatum extract on chronic alcoholic liver injury may be related to the regulation of linoleic acid and α-linolenic acid.
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Affiliation(s)
- Huaguo Chen
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, China; (H.C.); (L.P.); (C.Z.)
- Guizhou Engineering Laboratory for Quality Control & Evaluation Technology of Medicine, Guizhou Normal University, 116 Baoshan North Rd., Guiyang 550001, China
| | - Lei Peng
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, China; (H.C.); (L.P.); (C.Z.)
- Guizhou Engineering Laboratory for Quality Control & Evaluation Technology of Medicine, Guizhou Normal University, 116 Baoshan North Rd., Guiyang 550001, China
| | - Chao Zhao
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, China; (H.C.); (L.P.); (C.Z.)
- Guizhou Engineering Laboratory for Quality Control & Evaluation Technology of Medicine, Guizhou Normal University, 116 Baoshan North Rd., Guiyang 550001, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Correspondence: (Z.C.); (X.Z.); Tel./Fax: +86-851-8669-0018 (X.Z.)
| | - Xin Zhou
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, China; (H.C.); (L.P.); (C.Z.)
- Guizhou Engineering Laboratory for Quality Control & Evaluation Technology of Medicine, Guizhou Normal University, 116 Baoshan North Rd., Guiyang 550001, China
- Correspondence: (Z.C.); (X.Z.); Tel./Fax: +86-851-8669-0018 (X.Z.)
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7
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De la Fuente IM, Martínez L, Carrasco-Pujante J, Fedetz M, López JI, Malaina I. Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior. Front Genet 2021; 12:644615. [PMID: 34093645 PMCID: PMC8176287 DOI: 10.3389/fgene.2021.644615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Basque Center of Applied Mathematics (BCAM), Bilbao, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
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8
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Shortall K, Djeghader A, Magner E, Soulimane T. Insights into Aldehyde Dehydrogenase Enzymes: A Structural Perspective. Front Mol Biosci 2021; 8:659550. [PMID: 34055881 PMCID: PMC8160307 DOI: 10.3389/fmolb.2021.659550] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Aldehyde dehydrogenases engage in many cellular functions, however their dysfunction resulting in accumulation of their substrates can be cytotoxic. ALDHs are responsible for the NAD(P)-dependent oxidation of aldehydes to carboxylic acids, participating in detoxification, biosynthesis, antioxidant and regulatory functions. Severe diseases, including alcohol intolerance, cancer, cardiovascular and neurological diseases, were linked to dysfunctional ALDH enzymes, relating back to key enzyme structure. An in-depth understanding of the ALDH structure-function relationship and mechanism of action is key to the understanding of associated diseases. Principal structural features 1) cofactor binding domain, 2) active site and 3) oligomerization mechanism proved critical in maintaining ALDH normal activity. Emerging research based on the combination of structural, functional and biophysical studies of bacterial and eukaryotic ALDHs contributed to the appreciation of diversity within the superfamily. Herewith, we discuss these studies and provide our interpretation for a global understanding of ALDH structure and its purpose–including correct function and role in disease. Our analysis provides a synopsis of a common structure-function relationship to bridge the gap between the highly studied human ALDHs and lesser so prokaryotic models.
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Affiliation(s)
- Kim Shortall
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Edmond Magner
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
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9
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Cho S, Kim G, Song JJ, Cho C. Cryo-EM structure of Vibrio cholerae aldehyde-alcohol dehydrogenase spirosomes. Biochem Biophys Res Commun 2020; 536:38-44. [PMID: 33360541 DOI: 10.1016/j.bbrc.2020.12.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/13/2020] [Indexed: 01/10/2023]
Abstract
Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it is unknown whether AdhE structure is conserved in divergent bacteria. Here, we present the cryo-EM structure of AdhE (vAdhE) from Vibrio cholerae to 4.31 Å resolution. Overall, vAdhE spirosomes are similar to eAdhE with conserved subunit arrangement. However, divergences in key oligomerization residues cause vAdhE to form labile spirosomes with lower enzymatic activity. Mutating the vAdhE oligomerization interface to mimic eAdhE increases spirosome stability and enzymatic activity to levels comparable to eAdhE. These results support the generality of AdhE spirosome structures, and provide a structural basis to target vAdhE to attenuate bacterial virulence.
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Affiliation(s)
- Saehyun Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea
| | - Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea.
| | - Carol Cho
- Center for Natural Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea.
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10
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Kim G, Jang S, Lee E, Song JJ. EMPAS: Electron Microscopy Screening for Endogenous Protein Architectures. Mol Cells 2020; 43:804-812. [PMID: 32975210 PMCID: PMC7528680 DOI: 10.14348/molcells.2020.0163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 11/27/2022] Open
Abstract
In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.
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Affiliation(s)
- Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
- These authors contributed equally to this work
| | - Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
- These authors contributed equally to this work
| | - Eunhye Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
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