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Wang L, Ding B, Hu X, Li G, Deng Y. Rationally Engineering pH Adaptation of Acid-Induced Arginine Decarboxylase from Escherichia coli to Alkaline Environments to Efficiently Biosynthesize Putrescine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307779. [PMID: 38569221 PMCID: PMC11186044 DOI: 10.1002/advs.202307779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Acid-induced arginine decarboxylase AdiA is a typical homo-oligomeric protein biosynthesizing alkaline nylon monomer putrescine. However, upon loss of the AdiA decamer oligomeric state at neutral and alkaline conditions the activity also diminishes, obstructing the whole-cell biosynthesis of alkaline putrescine. Here, a structure cohesion strategy is proposed to change the pH adaptation of AdiA to alkaline environments based on the rational engineering of meridional and latitudinal oligomerization interfaces. After integrating substitutions of E467K at the latitudinal interface and H736E at the meridional channel interface, the structural stability of AdiA decamer and its substrate transport efficiency at neutral and alkaline conditions are improved. Finally, E467K_H736E is well adapted to neutral and alkaline environments (pH 7.0-9.0), and its enzymatic activity is 35-fold higher than that of wild AdiA at pH 8.0. Using E467K_H736E in the putrescine synthesis pathway, the titer of putrescine is up to 128.9 g·L-1 with a conversion of 0.94 mol·mol-1 in whole-cell catalysis. Additionally, the neutral pH adaptation of lysine decarboxylase, with a decamer structure similar to AdiA, is also improved using this cohesion strategy, providing an option for pH-adaptation engineering of other oligomeric decarboxylases.
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Affiliation(s)
- Li Wang
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Bo Ding
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Xiangyang Hu
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Guohui Li
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
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2
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Lang L, Böhler H, Wagler H, Beck T. Assembly Requirements for the Construction of Large-Scale Binary Protein Structures. Biomacromolecules 2024; 25:177-187. [PMID: 38059469 DOI: 10.1021/acs.biomac.3c00891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The precise assembly of multiple biomacromolecules into well-defined structures and materials is of great importance for various biomedical and nanobiotechnological applications. In this study, we investigate the assembly requirements for two-component materials using charged protein nanocages as building blocks. To achieve this, we designed several variants of ferritin nanocages to determine the surface characteristics necessary for the formation of large-scale binary three-dimensional (3D) assemblies. These nanocage variants were employed in protein crystallization experiments and macromolecular crystallography analyses, complemented by computational methods. Through the screening of nanocage variant combinations at various ionic strengths, we identified three essential features for successful assembly: (1) the presence of a favored crystal contact region, (2) the presence of a charged patch not involved in crystal contacts, and (3) sufficient distinctiveness between the nanocages. Surprisingly, the absence of noncrystal contact mediating patches had a detrimental effect on the assemblies, highlighting their unexpected importance. Intriguingly, we observed the formation of not only binary structures but also both negatively and positively charged unitary structures under previously exclusively binary conditions. Overall, our findings will inform future design strategies by providing some design rules, showcasing the utility of supercharging symmetric building blocks in facilitating the assembly of biomacromolecules into large-scale binary 3D assemblies.
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Affiliation(s)
- Laurin Lang
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Böhler
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Henrike Wagler
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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3
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Kinkar OU, Singh R, Prashar A, Kumar A, Hire RS, Makde RD. 20-kDa accessory protein (P20) from Bacillus thuringiensis subsp. israelensis ISPC-12: Purification, characterization, solution scattering and structural analysis. Int J Biol Macromol 2024; 254:127985. [PMID: 37949263 DOI: 10.1016/j.ijbiomac.2023.127985] [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: 09/16/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
The 20-kDa accessory protein (P20) from Bacillus thuringiensis subsp. israelensis (Bti) has been identified as an essential molecular chaperone in the enhancement of Cry11Aa and Cyt1Aa toxins production and their bio-crystallization. Additionally, P20 plays a vital role in suppressing the toxic effect of Cyt toxin on the host bacterium and also enhances insecticidal activity of Cry1Ac protein. Thus, the function of P20 is more specific than that of the chaperones. However, P20 is poorly investigated and insufficiently characterized. In the present study, we recombinantly expressed p20 from local isolate Bti ISPC-12 in heterologous bacterium E. coli and P20 protein was purified to homogeneity. Detailed biochemical and biophysical characterization provides crucial insights about in-vitro behavior as well as spatial conformations of P20 protein. Further, structural modelling and analysis provides insights into three-dimensional organization of the protein and shows that P20 is a non-toxic member of cytolytic (Cyt) toxin family similar to Cyt1Ca, with presence of conserved cytolysin fold. Additionally, solution scattering reveals that P20 is present as a dimer in the solution and probable dimeric assembly of P20 is presented. The findings reported here reveal engaging facts about P20 thereby advancing our understanding about this protein, which will expedite future studies.
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Affiliation(s)
- Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Rahul Singh
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ramesh S Hire
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
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4
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Kinkar OU, Prashar A, Yadav B, Kumar A, Hadapad AB, Hire RS, Makde RD. Purification, characterization and proteolytic processing of mosquito larvicidal protein Cry11Aa from Bacillus thuringensis subsp. isralensis ISPC-12. Int J Biol Macromol 2023:124979. [PMID: 37245748 DOI: 10.1016/j.ijbiomac.2023.124979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023]
Abstract
Cry11Aa is the most potent mosquito larvicidal protein of Bacillus thuringiensis subsp. israelensis (Bti). Development of resistance against insecticidal proteins including Cry11Aa is known but no field resistance was observed with Bti. The phenomenon of increasing resistance in insect pests necessitates the development of new strategies and techniques to enhance efficacy of insecticidal proteins. Recombinant technology offers better control over the molecule and allows modification of protein to achieve maximal effect against target pests. In this study, we standardised protocol for recombinant purification of Cry11Aa. Recombinant Cry11Aa found active against larvae of Aedes and Culex mosquito species and LC50 were estimated. Detailed biophysical characterization provides crucial insights into stability and in-vitro behaviour of the recombinant Cry11Aa. Moreover, trypsin hydrolysis doesn't improve overall toxicity of recombinant Cry11Aa. Proteolytic processing suggests domain I and II are more prone to proteolysis in comparison to domain III. Significance of structural features for proteolysis of Cry11Aa was observed after performing molecular dynamics simulations. Findings reported here are contributing significantly in method for purification, understanding in-vitro behaviour and proteolytic processing of Cry11Aa which could facilitate in efficient utilisation of Bti for insect pests and vectors control.
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Affiliation(s)
- Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Beena Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ashok B Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ramesh S Hire
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
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5
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Allen JR, Wilkinson EG, Strader LC. Creativity comes from interactions: modules of protein interactions in plants. FEBS J 2022; 289:1492-1514. [PMID: 33774929 PMCID: PMC8476656 DOI: 10.1111/febs.15847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
Protein interactions are the foundation of cell biology. For robust signal transduction to occur, proteins interact selectively and modulate their behavior to direct specific biological outcomes. Frequently, modular protein interaction domains are central to these processes. Some of these domains bind proteins bearing post-translational modifications, such as phosphorylation, whereas other domains recognize and bind to specific amino acid motifs. Other modules act as diverse protein interaction scaffolds or can be multifunctional, forming head-to-head homodimers and binding specific peptide sequences or membrane phospholipids. Additionally, the so-called head-to-tail oligomerization domains (SAM, DIX, and PB1) can form extended polymers to regulate diverse aspects of biology. Although the mechanism and structures of these domains are diverse, they are united by their modularity. Together, these domains are versatile and facilitate the evolution of complex protein interaction networks. In this review, we will highlight the role of select modular protein interaction domains in various aspects of plant biology.
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Affiliation(s)
- Jeffrey R. Allen
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Edward G. Wilkinson
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Lucia C. Strader
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
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6
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Rossino G, Rui M, Linciano P, Rossi D, Boiocchi M, Peviani M, Poggio E, Curti D, Schepmann D, Wünsch B, González-Avendaño M, Vergara-Jaque A, Caballero J, Collina S. Bitopic Sigma 1 Receptor Modulators to Shed Light on Molecular Mechanisms Underpinning Ligand Binding and Receptor Oligomerization. J Med Chem 2021; 64:14997-15016. [PMID: 34624193 DOI: 10.1021/acs.jmedchem.1c00886] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The sigma 1 receptor (S1R) is an enigmatic ligand-operated chaperone involved in many important biological processes, and its functions are not fully understood yet. Herein, we developed a novel series of bitopic S1R ligands as versatile tools to investigate binding processes, allosteric modulation, and the oligomerization mechanism. These molecules have been prepared in the enantiopure form and subjected to a preliminary biological evaluation, while in silico investigations helped to rationalize the results. Compound 7 emerged as the first bitopic S1R ligand endowed with low nanomolar affinity (Ki = 2.6 nM) reported thus far. Computational analyses suggested that 7 may stabilize the open conformation of the S1R by simultaneously binding the occluded primary binding site and a peripheral site on the cytosol-exposed surface. These findings pave the way to new S1R ligands with enhanced activity and/or selectivity, which could also be used as probes for the identification of a potential allosteric site.
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Affiliation(s)
- Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Marta Rui
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Massimo Boiocchi
- Centro Grandi Strumenti, University of Pavia, via Bassi 21, 27100 Pavia, Italy
| | - Marco Peviani
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Elena Poggio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Daniela Curti
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Dirk Schepmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Correnstraße 48, 48149 Münster, Germany
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Correnstraße 48, 48149 Münster, Germany
| | - Mariela González-Avendaño
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Ariela Vergara-Jaque
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
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7
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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8
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Bu W, Levitskaya Z, Tan SM, Gao YG. Emerging evidence for kindlin oligomerization and its role in regulating kindlin function. J Cell Sci 2021; 134:256567. [PMID: 33912917 DOI: 10.1242/jcs.256115] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrin-mediated cell-extracellular matrix (ECM) interactions play crucial roles in a broad range of physiological and pathological processes. Kindlins are important positive regulators of integrin activation. The FERM-domain-containing kindlin family comprises three members, kindlin-1, kindlin-2 and kindlin-3 (also known as FERMT1, FERMT2 and FERMT3), which share high sequence similarity (identity >50%), as well as domain organization, but exhibit diverse tissue-specific expression patterns and cellular functions. Given the significance of kindlins, analysis of their atomic structures has been an attractive field for decades. Recently, the structures of kindlin and its β-integrin-bound form have been obtained, which greatly advance our understanding of the molecular functions that involve kindlins. In particular, emerging evidence indicates that oligomerization of kindlins might affect their integrin binding and focal adhesion localization, positively or negatively. In this Review, we presented an update on the recent progress of obtaining kindlin structures, and discuss the implication for integrin activation based on kindlin oligomerization, as well as the possible regulation of this process.
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Affiliation(s)
- Wenting Bu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551.,Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China518055
| | - Zarina Levitskaya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551
| | - Suet-Mien Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore639798
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9
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Dindo M, Ambrosini G, Oppici E, Pey AL, O’Toole PJ, Marrison JL, Morrison IEG, Butturini E, Grottelli S, Costantini C, Cellini B. Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting. J Pers Med 2021; 11:jpm11040273. [PMID: 33917320 PMCID: PMC8067440 DOI: 10.3390/jpm11040273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
Peroxisomal matrix proteins are transported into peroxisomes in a fully-folded state, but whether multimeric proteins are imported as monomers or oligomers is still disputed. Here, we used alanine:glyoxylate aminotransferase (AGT), a homodimeric pyridoxal 5′-phosphate (PLP)-dependent enzyme, whose deficit causes primary hyperoxaluria type I (PH1), as a model protein and compared the intracellular behavior and peroxisomal import of native dimeric and artificial monomeric forms. Monomerization strongly reduces AGT intracellular stability and increases its aggregation/degradation propensity. In addition, monomers are partly retained in the cytosol. To assess possible differences in import kinetics, we engineered AGT to allow binding of a membrane-permeable dye and followed its intracellular trafficking without interfering with its biochemical properties. By fluorescence recovery after photobleaching, we measured the import rate in live cells. Dimeric and monomeric AGT displayed a similar import rate, suggesting that the oligomeric state per se does not influence import kinetics. However, when dimerization is compromised, monomers are prone to misfolding events that can prevent peroxisomal import, a finding crucial to predicting the consequences of PH1-causing mutations that destabilize the dimer. Treatment with pyridoxine of cells expressing monomeric AGT promotes dimerization and folding, thus, demonstrating the chaperone role of PLP. Our data support a model in which dimerization represents a potential key checkpoint in the cytosol at the crossroad between misfolding and correct targeting, a possible general mechanism for other oligomeric peroxisomal proteins.
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Affiliation(s)
- Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Joanne L. Marrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Ian E. G. Morrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Elena Butturini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Silvia Grottelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
- Correspondence: ; Tel.: +39-075-585-8339
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10
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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11
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Frieden C. Protein oligomerization as a metabolic control mechanism: Application to apoE. Protein Sci 2019; 28:837-842. [PMID: 30701627 DOI: 10.1002/pro.3583] [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: 12/18/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 02/03/2023]
Abstract
It has been estimated that 30%-50% of proteins self-assemble to form complexes consisting of multiple copies of themselves. If there is a functional difference between different molecular weight forms and if these forms interconvert on a reasonable time scale then oligomerization could be an important metabolic control mechanism. The example given here is of apoE for which the oligomerization process is measured in minutes to hours and the monomer binds lipids while the tetramer does not. Examination of the literature reveals few reports on the rate constants that control the interconversion of different molecular weight forms. Perhaps it is time to collect such data.
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Affiliation(s)
- Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
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12
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Pandhare A, Stuebler AG, Pirayesh E, Jansen M. A modified clear-native polyacrylamide gel electrophoresis technique to investigate the oligomeric state of MBP-5-HT 3A-intracellular domain chimeras. Protein Expr Purif 2018; 153:45-52. [PMID: 30130580 DOI: 10.1016/j.pep.2018.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 11/27/2022]
Abstract
The main principles of higher-order protein oligomerization are elucidated by many structural and biophysical studies. An astonishing number of proteins self-associate to form dimers or higher-order quaternary structures which further interact with other biomolecules to elicit complex cellular responses. In this study, we describe a simple and convenient approach to determine the oligomeric state of purified protein complexes that combines implementation of a novel form of clear-native gel electrophoresis and size exclusion chromatography in line with multi-angle light scattering. Here, we demonstrate the accuracy of this ensemble approach by characterizing the previously established pentameric state of the intracellular domain of serotonin type 3A (5-HT3A) receptors.
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Affiliation(s)
- Akash Pandhare
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Antonia G Stuebler
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Elham Pirayesh
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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13
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Ma G, Zhang Q, He L, Nguyen NT, Liu S, Gong Z, Huang Y, Zhou Y. Genetically encoded tags for real time dissection of protein assembly in living cells. Chem Sci 2018; 9:5551-5555. [PMID: 30061986 PMCID: PMC6048692 DOI: 10.1039/c8sc00839f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
Simple methods with straightforward readouts that enable real-time interrogation of protein quaternary structure are much needed to facilitate the physicochemical characterization of proteins at the single-cell level. After screening over a series of microtubule (MT) binders, we report herein the development of two genetically encoded tags (designated as "MoTags" for the monomer/oligomer detection tag) that can be conveniently fused to a given protein to probe its oligomeric state in cellulo when combined with routine fluorescence microscopy. In their monomeric form, MoTags are evenly distributed in the cytosol; whereas oligomerization enables MoTags to label MT or track MT tips in an oligomeric state-dependent manner. We demonstrate here the broad utility of engineered MoTags to aid the determination of protein oligomeric states, dissection of protein structure and function, and monitoring of protein-target interactions under physiological conditions in living cells.
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Affiliation(s)
- Guolin Ma
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Qian Zhang
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
- Department of Infectious Diseases , Renmin Hospital of Wuhan University , Wuhan 430060 , China
| | - Lian He
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Nhung T Nguyen
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Shuzhong Liu
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
| | - Zuojiong Gong
- Department of Infectious Diseases , Renmin Hospital of Wuhan University , Wuhan 430060 , China
| | - Yun Huang
- Center for Epigenetics and Disease Prevention , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA .
- Department of Molecular and Cellular Medicine , College of Medicine , Texas A&M University , College Station , TX 77843 , USA
| | - Yubin Zhou
- Center for Translational Cancer Research , Institute of Biosciences and Technology , College of Medicine , Texas A&M University , 2121 W Holcombe Blvd , Houston , TX 77030 , USA . ;
- Department of Medical Physiology , College of Medicine , Texas A&M University , Temple , TX 76504 , USA
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14
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Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018; 1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.
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Affiliation(s)
- Sucharita Dey
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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15
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Kolesnikova S, Hubálek M, Bednárová L, Cvacka J, Curtis EA. Multimerization rules for G-quadruplexes. Nucleic Acids Res 2017; 45:8684-8696. [PMID: 28911118 PMCID: PMC5587800 DOI: 10.1093/nar/gkx637] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
G-quadruplexes can multimerize under certain conditions, but the sequence requirements of such structures are not well understood. In this study, we investigated the ability of all possible variants of the central tetrad in a monomeric, parallel-strand G-quadruplex to form higher-order structures. Although most of these 256 variants existed primarily as monomers under the conditions of our screen, ∼10% formed dimers or tetramers. These structures could form in a wide range of monovalent and divalent metal ions, and folding was highly cooperative in both KCl and MgCl2. As was previously shown for G-quadruplexes that bind GTP and promote peroxidase reactions, G-quadruplexes that form dimers and tetramers have distinct sequence requirements. Some mutants could also form heteromultimers, and a second screen was performed to characterize the sequence requirements of these structures. Taken together, these experiments provide new insights into the sequence requirements and structures of both homomultimeric and heteromultimeric G-quadruplexes.
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Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Martin Hubálek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Josef Cvacka
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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16
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Mishra SK, Sankar K, Jernigan RL. Altered dynamics upon oligomerization corresponds to key functional sites. Proteins 2017; 85:1422-1434. [PMID: 28383162 DOI: 10.1002/prot.25302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
Abstract
It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422-1434. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sambit Kumar Mishra
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
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17
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Grant Pearce F, Hudson AO, Loomes K, Dobson RCJ. Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution. Subcell Biochem 2017; 83:271-289. [PMID: 28271480 DOI: 10.1007/978-3-319-46503-6_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Enzymes are usually comprised of multiple subunits and more often than not they are made up of identical subunits. In this review we examine lysine biosynthesis and focus on the enzyme dihydrodipicolinate synthase in terms of its structure, function and the evolution of its varied number of subunits (quaternary structure). Dihydrodipicolinate synthase is the first committed step in the biosynthesis of lysine, which occurs naturally in plants, bacteria, archaea and fungi, but is not synthesized in mammals. In bacteria, there have been four separate pathways identified from tetrahydrodipicolinate to meso-diaminopimelate, which is the immediate precursor to lysine. Dihydrodipicolinate synthases from many bacterial and plant species have been structurally characterised and the results show considerable variability with respect to their quaternary structure, hinting at their evolution. The oligomeric state of the enzyme plays a key role, both in catalysis and in the allosteric regulation of the enzyme by lysine. While most bacteria and plants have tetrameric enzymes, where the structure of the dimeric building blocks is conserved, the arrangement of the dimers differs. We also review a key development in the field, namely the discovery of a human dihydrodipicolinate synthase-like enzyme, now known as 4-hydroxy-2-oxoglutarate aldolase . This discovery complicates the rationale underpinning drug development against bacterial dihydrodipicolinate synthases, since genetic errors in 4-hydroxy-2-oxoglutarate aldolase cause the disease Primary Hyperoxaluria Type 3 and therefore compounds that are geared towards the inhibition of bacterial dihydrodipicolinate synthase may be toxic to mammalian cells.
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Affiliation(s)
- F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Kerry Loomes
- School of Biological Sciences & Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia.
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18
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Affiliation(s)
- Cintia Jozefkowicz
- a Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires , Buenos Aires , Argentina.,b Instituto de Genética Ewald A. Favret (CICVyA-INTA) , Buenos Aires , Argentina
| | - Florencia Scochera
- c Instituto de Química y Fisicoquímica Biológica "Alejandro C. Paladini" (IQUIFIB) UBA-CONICET , and Departamento de Fisicomatemática, Facultad de Farmacia y Bioquímica, UBA , Buenos Aires , Argentina
| | - Karina Alleva
- a Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires , Buenos Aires , Argentina.,c Instituto de Química y Fisicoquímica Biológica "Alejandro C. Paladini" (IQUIFIB) UBA-CONICET , and Departamento de Fisicomatemática, Facultad de Farmacia y Bioquímica, UBA , Buenos Aires , Argentina
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19
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Healy EF. A model for non-obligate oligomer formation in protein aggregration. Biochem Biophys Res Commun 2015; 465:523-7. [PMID: 26282203 PMCID: PMC4564312 DOI: 10.1016/j.bbrc.2015.08.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022]
Abstract
Using solvent-exposed intramolecular backbone hydrogen bonds as physico-chemical descriptors for protein packing, a role for transient, non-obligate oligomers in the formation of aberrant protein aggregates is presented. Oligomeric models of the both wild type (wt) and select mutant variants of superoxide dismutase (SOD1) are proposed to provide a structural basis for investigating the etiology of Amyotrophic Lateral Sclerosis (ALS).
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Affiliation(s)
- Eamonn F Healy
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA.
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20
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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21
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Are Aquaporins the Missing Transmembrane Osmosensors? J Membr Biol 2015; 248:753-65. [PMID: 25791748 DOI: 10.1007/s00232-015-9790-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/12/2015] [Indexed: 01/08/2023]
Abstract
Regulation of cell volume is central to homeostasis. It is assumed to begin with the detection of a change in water potential across the bounding membrane, but it is not clear how this is accomplished. While examples of general osmoreceptors (which sense osmotic pressure in one phase) and stretch-activated ion channels (which require swelling of a cell or organelle) are known, effective volume regulation requires true transmembrane osmosensors (TMOs) which directly detect a water potential difference spanning a membrane. At present, no TMO molecule has been unambiguously identified, and clear evidence for mammalian TMOs is notably lacking. In this paper, we set out a theory of TMOs which requires a water channel spanning the membrane that excludes the major osmotic solutes, responds directly without the need for any other process such as swelling, and signals to other molecules associated with the magnitude of changing osmotic differences. The most likely molecules that are fit for this purpose and which are also ubiquitous in eukaryotic cells are aquaporins (AQPs). We review experimental evidence from several systems which indicates that AQPs are essential elements in regulation and may be functioning as TMOs; i.e. the first step in an osmosensing sequence that signals osmotic imbalance in a cell or organelle. We extend this concept to several systems of current interest in which the cellular involvement of AQPs as simple water channels is puzzling or counter-intuitive. We suggest that, apart from regulatory volume changes in cells, AQPs may also be acting as TMOs in red cells, secretory granules and microorganisms.
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22
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Lansky S, Alalouf O, Solomon HV, Alhassid A, Govada L, Chayen NE, Belrhali H, Shoham Y, Shoham G. A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus. ACTA ACUST UNITED AC 2014; 70:261-78. [PMID: 24531461 DOI: 10.1107/s139900471302840x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/15/2013] [Indexed: 08/26/2023]
Abstract
Geobacillus stearothermophilus T6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xylan, arabinan and galactan. As part of the xylan-degradation system, the bacterium uses a number of side-chain-cleaving enzymes, one of which is Axe2, a 219-amino-acid intracellular serine acetylxylan esterase that removes acetyl side groups from xylooligosaccharides. Bioinformatic analyses suggest that Axe2 belongs to the lipase GDSL family and represents a new family of carbohydrate esterases. In the current study, the detailed three-dimensional structure of Axe2 is reported, as determined by X-ray crystallography. The structure of the selenomethionine derivative Axe2-Se was initially determined by single-wavelength anomalous diffraction techniques at 1.70 Å resolution and was used for the structure determination of wild-type Axe2 (Axe2-WT) and the catalytic mutant Axe2-S15A at 1.85 and 1.90 Å resolution, respectively. These structures demonstrate that the three-dimensional structure of the Axe2 monomer generally corresponds to the SGNH hydrolase fold, consisting of five central parallel β-sheets flanked by two layers of helices (eight α-helices and five 310-helices). The catalytic triad residues, Ser15, His194 and Asp191, are lined up along a substrate channel situated on the concave surface of the monomer. Interestingly, the Axe2 monomers are assembled as a `doughnut-shaped' homo-octamer, presenting a unique quaternary structure built of two staggered tetrameric rings. The eight active sites are organized in four closely situated pairs, which face the relatively wide internal cavity. The biological relevance of this octameric structure is supported by independent results obtained from gel-filtration, TEM and SAXS experiments. These data and their comparison to the structural data of related hydrolases are used for a more general discussion focusing on the structure-function relationships of enzymes of this category.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Onit Alalouf
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Hodaya Vered Solomon
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Anat Alhassid
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lata Govada
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Naomi E Chayen
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Hassan Belrhali
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Abstract
One of the most striking features of proteins is their common assembly into multimeric structures, usually homomers with even numbers of subunits all derived from the same genetic locus. However, although substantial structural variation for orthologous proteins exists within and among major phylogenetic lineages, in striking contrast to patterns of gene structure and genome organization, there appears to be no correlation between the level of protein structural complexity and organismal complexity. In addition, there is no evidence that protein architectural differences are driven by lineage-specific differences in selective pressures. Here, it is suggested that variation in the multimeric states of proteins can readily arise from stochastic transitions resulting from the joint processes of mutation and random genetic drift, even in the face of constant directional selection for one particular protein architecture across all lineages. Under the proposed hypothesis, on a long evolutionary timescale, the numbers of transitions from monomers to dimers should approximate the numbers in the opposite direction and similarly for transitions between higher-order structures.
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24
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Levy ED, Teichmann S. Structural, evolutionary, and assembly principles of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:25-51. [PMID: 23663964 DOI: 10.1016/b978-0-12-386931-9.00002-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In the protein universe, 30-50% of proteins self-assemble to form symmetrical complexes consisting of multiple copies of themselves, called homomers. The prevalence of homomers motivates us to review many of their properties. In Section 1, we describe the methods and challenges associated with quaternary structure inference-these methods are indeed at the basis of any analysis on homomers. In Section 2, we describe the morphological properties of homomers, as well as the database 3DComplex, which provides a taxonomy for both homomeric and heteromeric protein complexes. In Section 3, we review interface properties of homomeric complexes. In Section 4, we then present recent findings on the evolution of homomer interfaces, which we link in Section 5 to the evolution of homomers as entire entities. In Section 6, we discuss mechanisms involved in their assembly and how these mechanisms can be linked to evolution.
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Affiliation(s)
- Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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