1
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Lučić M, Allport T, Clarke TA, Williams LJ, Wilson MT, Chaplin AK, Worrall JAR. The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation. Protein Sci 2024; 33:e5073. [PMID: 38864770 PMCID: PMC11168072 DOI: 10.1002/pro.5073] [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] [Received: 02/22/2024] [Revised: 05/18/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexColchesterUK
| | - Thomas Allport
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Amanda K. Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
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2
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Abstract
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase behavior of heterogeneous biomolecular mixtures are only beginning to be explored. Theory and simulation provide invaluable tools for probing the relationship between molecular determinants, such as protein and RNA sequences, and the emergence of phase-separated condensates in such complex environments. This review covers recent advances in the prediction and computational design of biomolecular mixtures that phase-separate into many coexisting phases. First, we review efforts to understand the phase behavior of mixtures with hundreds or thousands of species using theoretical models and statistical approaches. We then describe progress in developing analytical theories and coarse-grained simulation models to predict multiphase condensates with the molecular detail required to make contact with biophysical experiments. We conclude by summarizing the challenges ahead for modeling the inhomogeneous spatial organization of biomolecular mixtures in living cells.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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3
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Kleiner D, Shapiro Tuchman Z, Shmulevich F, Shahar A, Zarivach R, Kosloff M, Bershtein S. Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Protein Sci 2022; 31:e4352. [PMID: 35762725 PMCID: PMC9202080 DOI: 10.1002/pro.4352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/14/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
Homomers are prevalent in bacterial proteomes, particularly among core metabolic enzymes. Homomerization is often key to function and regulation, and interfaces that facilitate the formation of homomeric enzymes are subject to intense evolutionary change. However, our understanding of the molecular mechanisms that drive evolutionary variation in homomeric complexes is still lacking. How is the diversification of protein interfaces linked to variation in functional regulation and structural integrity of homomeric complexes? To address this question, we studied quaternary structure evolution of bacterial methionine S‐adenosyltransferases (MATs)—dihedral homotetramers formed along a large and conserved dimeric interface harboring two active sites, and a small, recently evolved, interdimeric interface. Here, we show that diversity in the physicochemical properties of small interfaces is directly linked to variability in the kinetic stability of MAT quaternary complexes and in modes of their functional regulation. Specifically, hydrophobic interactions within the small interface of Escherichia coli MAT render the functional homotetramer kinetically stable yet impose severe aggregation constraints on complex assembly. These constraints are alleviated by electrostatic interactions that accelerate dimer‐dimer assembly. In contrast, Neisseria gonorrhoeae MAT adopts a nonfunctional dimeric state due to the low hydrophobicity of its small interface and the high flexibility of its active site loops, which perturbs small interface integrity. Remarkably, in the presence of methionine and ATP, N. gonorrhoeae MAT undergoes substrate‐induced assembly into a functional tetrameric state. We suggest that evolution acts on the interdimeric interfaces of MATs to tailor the regulation of their activity and stability to unique organismal needs. PDB Code(s): 7R2W;7R3B;
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Affiliation(s)
- Daniel Kleiner
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ziva Shapiro Tuchman
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Fannia Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Shahar
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Macromolecular Crystallography and Cryo-EM Research Center, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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4
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Kleiner D, Shmulevich F, Zarivach R, Shahar A, Sharon M, Ben-Nissan G, Bershtein S. The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase. J Mol Biol 2019; 431:4796-4816. [PMID: 31520601 DOI: 10.1016/j.jmb.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
Methionine S-adenosyltransferases (MATs) are predominantly homotetramers, comprised of dimers of dimers. The larger, highly conserved intradimeric interface harbors two active sites, making the dimer the obligatory functional unit. However, functionality of the smaller, more diverged, and recently evolved interdimeric interface is largely unknown. Here, we show that the interdimeric interface of Ureaplasmaurealiticum MAT has evolved to control the catalytic activity and structural integrity of the homotetramer in response to product accumulation. When all four active sites are occupied with the product, S-adenosylmethionine (SAM), binding of four additional SAM molecules to the interdimeric interface prompts a ∼45° shift in the dimer orientation and a concomitant ∼60% increase in the interface area. This rearrangement inhibits the enzymatic activity by locking the flexible active site loops in a closed state and renders the tetramer resistant to proteolytic degradation. Our findings suggest that the interdimeric interface of MATs is subject to rapid evolutionary changes that tailor the molecular properties of the entire homotetramer to the specific needs of the organism.
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Affiliation(s)
- Daniel Kleiner
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Fannia Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel; Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel.
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5
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Marklund EG, Zhang Y, Basha E, Benesch JLP, Vierling E. Structural and functional aspects of the interaction partners of the small heat-shock protein in Synechocystis. Cell Stress Chaperones 2018; 23:723-732. [PMID: 29476342 PMCID: PMC6045555 DOI: 10.1007/s12192-018-0884-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/09/2018] [Accepted: 02/01/2018] [Indexed: 01/28/2023] Open
Abstract
The canonical function of small heat-shock proteins (sHSPs) is to interact with proteins destabilized under conditions of cellular stress. While the breadth of interactions made by many sHSPs is well-known, there is currently little knowledge about what structural features of the interactors form the basis for their recognition. Here, we have identified 83 in vivo interactors of the sole sHSP in the cyanobacterium Synechocystis sp. PCC 6803, HSP16.6, reflective of stable associations with soluble proteins made under heat-shock conditions. By performing bioinformatic analyses on these interactors, we identify primary and secondary structural elements that are enriched relative to expectations from the cyanobacterial genome. In addition, by examining the Synechocystis interactors and comparing them with those identified to bind sHSPs in other prokaryotes, we show that sHSPs associate with specific proteins and biological processes. Our data are therefore consistent with a picture of sHSPs being broadly specific molecular chaperones that act to protect multiple cellular pathways.
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Affiliation(s)
- Erik G Marklund
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
| | - Yichen Zhang
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
- Alorica, Inc., Irvine, CA, USA
| | - Eman Basha
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
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6
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Wright MA, Aprile FA, Bellaiche MMJ, Michaels TCT, Müller T, Arosio P, Vendruscolo M, Dobson CM, Knowles TPJ. Cooperative Assembly of Hsp70 Subdomain Clusters. Biochemistry 2018; 57:3641-3649. [PMID: 29763298 PMCID: PMC6202011 DOI: 10.1021/acs.biochem.8b00151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Many molecular chaperones exist as oligomeric complexes in their functional states, yet the physical determinants underlying such self-assembly behavior, as well as the role of oligomerization in the activity of molecular chaperones in inhibiting protein aggregation, have proven to be difficult to define. Here, we demonstrate direct measurements under native conditions of the changes in the average oligomer populations of a chaperone system as a function of concentration and time and thus determine the thermodynamic and kinetic parameters governing the self-assembly process. We access this self-assembly behavior in real time under native-like conditions by monitoring the changes in the micrometer-scale diffusion of the different complexes in time and space using a microfluidic platform. Using this approach, we find that the oligomerization mechanism of the Hsp70 subdomain occurs in a cooperative manner and involves structural constraints that limit the size of the species formed beyond the limits imposed by mass balance. These results illustrate the ability of microfluidic methods to probe polydisperse protein self-assembly in real time in solution and to shed light on the nature and dynamics of oligomerization processes.
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Affiliation(s)
- Maya A Wright
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Fluidic Analytics Ltd. , Cambridge , U.K
| | - Francesco A Aprile
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Mathias M J Bellaiche
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Thomas Müller
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Fluidic Analytics Ltd. , Cambridge , U.K
| | - Paolo Arosio
- Institute for Chemical and Bioengineering , ETH Zurich , Vladimir-Prelog-Weg 1, ETH Hönggerberg, HCI F 105 , 8093 Zurich , Switzerland
| | - Michele Vendruscolo
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Cavendish Laboratory, Department of Physics , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
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7
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Bergendahl LT, Marsh JA. Functional determinants of protein assembly into homomeric complexes. Sci Rep 2017; 7:4932. [PMID: 28694495 PMCID: PMC5504011 DOI: 10.1038/s41598-017-05084-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/24/2017] [Indexed: 11/24/2022] Open
Abstract
Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions. We observe that homomers from different symmetry groups are significantly enriched in distinct functions, and can often provide simple physical and geometrical explanations for these associations in regards to substrate recognition or physical environment. One of the strongest associations is the tendency for metabolic enzymes to form dihedral complexes, which we suggest is closely related to allosteric regulation. We provide a physical explanation for why allostery is related to dihedral complexes: it allows for efficient propagation of conformational changes across isologous (i.e. symmetric) interfaces. Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.
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Affiliation(s)
- L Therese Bergendahl
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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