151
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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152
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Christiansen A, Weiel M, Winkler A, Schug A, Reinstein J. The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly. J Mol Biol 2021; 433:166859. [PMID: 33539884 DOI: 10.1016/j.jmb.2021.166859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Icosahedral viral capsids assemble with high fidelity from a large number of identical buildings blocks. The mechanisms that enable individual capsid proteins to form stable oligomeric units (capsomers) while affording structural adaptability required for further assembly into capsids are mostly unknown. Understanding these mechanisms requires knowledge of the capsomers' dynamics, especially for viruses where no additional helper proteins are needed during capsid assembly like for the Mavirus virophage that despite its complexity (triangulation number T = 27) can assemble from its major capsid protein (MCP) alone. This protein forms the basic building block of the capsid namely a trimer (MCP3) of double-jelly roll protomers with highly intertwined N-terminal arms of each protomer wrapping around the other two at the base of the capsomer, secured by a clasp that is formed by part of the C-terminus. Probing the dynamics of the capsomer with HDX mass spectrometry we observed differences in conformational flexibility between functional elements of the MCP trimer. While the N-terminal arm and clasp regions show above average deuterium incorporation, the two jelly-roll units in each protomer also differ in their structural plasticity, which might be needed for efficient assembly. Assessing the role of the N-terminal arm in maintaining capsomer stability showed that its detachment is required for capsomer dissociation, constituting a barrier towards capsomer monomerisation. Surprisingly, capsomer dissociation was irreversible since it was followed by a global structural rearrangement of the protomers as indicated by computational studies showing a rearrangement of the N-terminus blocking part of the capsomer forming interface.
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Affiliation(s)
- Alexander Christiansen
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany
| | - Marie Weiel
- Karlsruhe Institute of Technology, Steinbuch Centre for Computing and Department of Physics, Eggenstein-Leopoldshafen, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology. Graz, Austria
| | - Alexander Schug
- Institute for Advanced Simulation, Jülich Supercomputing Center, Jülich, Germany
| | - Jochen Reinstein
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany.
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153
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Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry. Nat Commun 2021; 12:589. [PMID: 33500404 PMCID: PMC7838286 DOI: 10.1038/s41467-020-20862-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022] Open
Abstract
Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.
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154
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Rahikainen R, Rijal P, Tan TK, Wu H, Andersson AC, Barrett JR, Bowden TA, Draper SJ, Townsend AR, Howarth M. Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation. Angew Chem Int Ed Engl 2021; 60:321-330. [PMID: 32886840 PMCID: PMC7821241 DOI: 10.1002/anie.202009663] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus-like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid-19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre-existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer-designed VLP not only to monomers (SARS-CoV-2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag-mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.
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Affiliation(s)
- Rolle Rahikainen
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Pramila Rijal
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Tiong Kit Tan
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Hung‐Jen Wu
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Anne‐Marie C. Andersson
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- Current address: InProTher ApsOle Maaløes Vej 32200KøbenhavnDenmark
| | | | - Thomas A. Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | - Alain R. Townsend
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Mark Howarth
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
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155
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Seychell BC, Beck T. Molecular basis for protein-protein interactions. Beilstein J Org Chem 2021; 17:1-10. [PMID: 33488826 PMCID: PMC7801801 DOI: 10.3762/bjoc.17.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work.
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Affiliation(s)
- Brandon Charles Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
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156
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Rahikainen R, Rijal P, Tan TK, Wu H, Andersson AC, Barrett JR, Bowden TA, Draper SJ, Townsend AR, Howarth M. Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:325-334. [PMID: 38504824 PMCID: PMC10947127 DOI: 10.1002/ange.202009663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 11/10/2022]
Abstract
Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus-like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid-19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre-existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer-designed VLP not only to monomers (SARS-CoV-2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag-mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.
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Affiliation(s)
- Rolle Rahikainen
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Pramila Rijal
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Tiong Kit Tan
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Hung‐Jen Wu
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Anne‐Marie C. Andersson
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- Current address: InProTher ApsOle Maaløes Vej 32200KøbenhavnDenmark
| | | | - Thomas A. Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | - Alain R. Townsend
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Mark Howarth
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
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157
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Zeng H. Self-assembling Properties. Food Hydrocoll 2021. [DOI: 10.1007/978-981-16-0320-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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158
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Srinivasan B. Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery*. ChemMedChem 2020; 16:899-918. [PMID: 33231926 DOI: 10.1002/cmdc.202000791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/27/2022]
Abstract
Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential to sustain life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were mostly tested and implemented for cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more-complex systems (for instance, multiprotein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate, and the development of a new kind of kinetic analysis to study these systems is required. This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling Discovery Sciences, R&D, AstraZeneca, 310, Milton Rd, Milton CB4 0WG, Cambridge, UK
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159
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Hertle R, Nazet J, Semmelmann F, Schlee S, Funke F, Merkl R, Sterner R. Reprogramming the Specificity of a Protein Interface by Computational and Data-Driven Design. Structure 2020; 29:292-304.e3. [PMID: 33296666 DOI: 10.1016/j.str.2020.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/21/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The formation of specific protein complexes in a cell is a non-trivial problem given the co-existence of thousands of different polypeptide chains. A particularly difficult case are two glutamine amidotransferase complexes (anthranilate synthase [AS] and aminodeoxychorismate synthase [ADCS]), which are composed of homologous pairs of synthase and glutaminase subunits. We have attempted to identify discriminating interface residues of the glutaminase subunit TrpG from AS, which are responsible for its specific interaction with the synthase subunit TrpEx and prevent binding to the closely related synthase subunit PabB from ADCS. For this purpose, TrpG-specific interface residues were grafted into the glutaminase subunit PabA from ADCS by two different approaches, namely a computational and a data-driven one. Both approaches resulted in PabA variants that bound TrpEx with higher affinity than PabB. Hence, we have accomplished a reprogramming of protein-protein interaction specificity that provides insights into the evolutionary adaptation of protein interfaces.
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Affiliation(s)
- Regina Hertle
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
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160
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Kalomoiri P, Rodríguez-Rodríguez C, Sørensen KK, Bergamo M, Saatchi K, Häfeli UO, Jensen KJ. Bioimaging and Biodistribution of the Metal-Ion-Controlled Self-Assembly of PYY 3-36 Studied by SPECT/CT. Chembiochem 2020; 21:3338-3348. [PMID: 32667131 DOI: 10.1002/cbic.202000266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/10/2020] [Indexed: 12/11/2022]
Abstract
The controlled self-assembly of peptide- and protein-based pharmaceuticals is of central importance for their mode of action and tuning of their properties. Peptide YY3-36 (PYY3-36 ) is a 36-residue peptide hormone that reduces food intake when peripherally administered. Herein, we describe the synthesis of a PYY3-36 analogue functionalized with a metal-ion-binding 2,2'-bipyridine ligand that enables self-assembly through metal complexation. Upon addition of CuII , the bipyridine-modified PYY3-36 peptide binds stoichiometric quantities of metal ions in solution and contributes to the organization of higher-order assemblies. In this study, we aimed to explore the size effect of the self-assembly in vivo by using non-invasive quantitative single-photon emission computed tomography/computed tomography (SPECT/CT) imaging. For this purpose, bipyridine-modified PYY3-36 was radiolabeled with a chelator holding 111 InIII , followed by the addition of CuII to the bipyridine ligand. SPECT/CT imaging and biodistribution studies showed fast renal clearance and accumulation in the kidney cortex. The radiolabeled bipyridyl-PYY3-36 conjugates with and without CuII presented a slightly slower excretion 1 h post injection compared to the unmodified-PYY3-36 , thus demonstrating that higher self-assemblies of the peptide might have an effect on the pharmacokinetics.
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Affiliation(s)
- Panagiota Kalomoiri
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Cristina Rodríguez-Rodríguez
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Kasper K Sørensen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Marta Bergamo
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Katayoun Saatchi
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Urs O Häfeli
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.,Center for Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Knud J Jensen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
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161
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Hochberg GKA, Liu Y, Marklund EG, Metzger BPH, Laganowsky A, Thornton JW. A hydrophobic ratchet entrenches molecular complexes. Nature 2020; 588:503-508. [PMID: 33299178 PMCID: PMC8168016 DOI: 10.1038/s41586-020-3021-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
Most proteins assemble into multisubunit complexes1. The persistence of these complexes across evolutionary time is usually explained as the result of natural selection for functional properties that depend on multimerization, such as intersubunit allostery or the capacity to do mechanical work2. In many complexes, however, multimerization does not enable any known function3. An alternative explanation is that multimers could become entrenched if substitutions accumulate that are neutral in multimers but deleterious in monomers; purifying selection would then prevent reversion to the unassembled form, even if assembly per se does not enhance biological function3-7. Here we show that a hydrophobic mutational ratchet systematically entrenches molecular complexes. By applying ancestral protein reconstruction and biochemical assays to the evolution of steroid hormone receptors, we show that an ancient hydrophobic interface, conserved for hundreds of millions of years, is entrenched because exposure of this interface to solvent reduces protein stability and causes aggregation, even though the interface makes no detectable contribution to function. Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers. In a database of hundreds of families of multimers, most show signatures of long-term hydrophobic entrenchment. It is therefore likely that many protein complexes persist because a simple ratchet-like mechanism entrenches them across evolutionary time, even when they are functionally gratuitous.
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Affiliation(s)
- Georg K A Hochberg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Brian P H Metzger
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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162
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Vrancken JPM, Tame JRH, Voet ARD. Development and applications of artificial symmetrical proteins. Comput Struct Biotechnol J 2020; 18:3959-3968. [PMID: 33335692 PMCID: PMC7734218 DOI: 10.1016/j.csbj.2020.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 12/28/2022] Open
Abstract
Since the determination of the first molecular models of proteins there has been interest in creating proteins artificially, but such methods have only become widely successful in the last decade. Gradual improvements over a long period of time have now yielded numerous examples of non-natural proteins, many of which are built from repeated elements. In this review we discuss the design of such symmetrical proteins and their various applications in chemistry and medicine.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
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163
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
| | - James B. Hilton
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
- School of BioSciences The University of Melbourne Parkville Victoria 3052 Australia
- Atomic Medicine Initiative The University of Technology Sydney Broadway New South Wales 2007 Australia
| | - Peter J. Crouch
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
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164
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Ghanbarpour A, Santos EM, Pinger C, Assar Z, Hossaini Nasr S, Vasileiou C, Spence D, Borhan B, Geiger JH. Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem 2020; 21:3192-3196. [PMID: 32608180 PMCID: PMC8220890 DOI: 10.1002/cbic.202000405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Yale University Medical School, Department of Cell Biology, 333 S. Cedar Street, New Haven, CT 06510, USA
| | - Elizabeth M Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Dow Performance Silicones, 2200W Salzburg Road, Midland, MI 48686, USA
| | - Cody Pinger
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
| | - Seyedmehdi Hossaini Nasr
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Dana Spence
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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165
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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166
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Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
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Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
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167
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Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. Sci Rep 2020; 10:17689. [PMID: 33077848 PMCID: PMC7573690 DOI: 10.1038/s41598-020-74811-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/29/2020] [Indexed: 11/08/2022] Open
Abstract
The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Protein homo-oligomerization, which is correlated with cooperativity in biology, is one means of scaling the complexity of protein networks. It can play critical roles in determining the sensitivity of genetic regulatory circuits and metabolic pathways. Therefore, understanding the roles of oligomerization may lead to new approaches of probing biological functions. Here, we analyzed the frequency of protein oligomerization degree in the cell proteome of nine different organisms, and then, we asked whether there are design trade-offs between protein oligomerization, information precision and energy costs of protein synthesis. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks. These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems.
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168
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Reboul CF, Kiesewetter S, Elmlund D, Elmlund H. Point-group symmetry detection in three-dimensional charge density of biomolecules. Bioinformatics 2020; 36:2237-2243. [PMID: 31790146 DOI: 10.1093/bioinformatics/btz904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/31/2019] [Accepted: 11/28/2019] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION No rigorous statistical tests for detecting point-group symmetry in three-dimensional (3D) charge density maps obtained by electron microscopy (EM) and related techniques have been developed. RESULTS We propose a method for determining the point-group symmetry of 3D charge density maps obtained by EM and related techniques. Our ab initio algorithm does not depend on atomic coordinates but utilizes the density map directly. We validate the approach for a range of publicly available single-particle cryo-EM datasets. In straightforward cases, our method enables fully automated single-particle 3D reconstruction without having to input an arbitrarily selected point-group symmetry. When pseudo-symmetry is present, our method provides statistics quantifying the degree to which the 3D density agrees with the different point-groups tested. AVAILABILITY AND IMPLEMENTATION The software is freely available at https://github.com/hael/SIMPLE3.0.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
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169
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Cai Y, Yu Q, Zhao H. Electrostatic assisted fabrication and dissociation of multi-component proteinosomes. J Colloid Interface Sci 2020; 576:90-98. [PMID: 32408164 DOI: 10.1016/j.jcis.2020.05.013] [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: 03/16/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/17/2023]
Abstract
Self-assembly of proteins into well-organized proteinosomes has attracted great interest due to the potential medical and biological applications of the structures. Herein, a new concept of electrostatic assisted fabrication of proteinosomes is proposed. The self-assembly is performed by using multi-step dialysis approach, where negatively charged bovine serum albumin-poly(N-isopropylacrylamide) (BSA-PNIPAM) bioconjugate and positively charged enzyme (lysozyme or trypsin) are initially dissolved in phosphate buffer (PB) solution at a high salt concentration, and subsequently the protein solution is dialyzed against PB solutions at low salt concentrations, resulting in the formation of biofunctional proteinosomes. Transmission electron microscopy (TEM), cryo-TEM and light scattering results all demonstrate the formation of hollow structures. The wall of a proteinosome is composed of BSA and enzyme (lysozyme or trypsin), and PNIPAM chains of the bioconjugate are in the corona stabilizing the structure. In comparison with the native enzymes, the enzyme molecules in the assemblies basically retain their bioactivities. The proteinosomes formed by BSA-PNIPAM and lysozyme can be dissociated in the presence of trypsin, and those self-assembled by BSA-PNIPAM and trypsin are able to be self-hydrolyzed, resulting in the dissociation of the structures in aqueous solution. The size and morphology changes of the proteinosomes in the hydrolysis are studied.
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Affiliation(s)
- Yaqian Cai
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Qianyu Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Hanying Zhao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China.
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170
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Ochoa JM, Nguyen VN, Nie M, Sawaya MR, Bobik TA, Yeates TO. Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization. Protein Sci 2020; 29:2201-2212. [PMID: 32885887 DOI: 10.1002/pro.3941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
Bacterial microcompartments are protein-based organelles that carry out specialized metabolic functions in diverse bacteria. Their outer shells are built from several thousand protein subunits. Some of the architectural principles of bacterial microcompartments have been articulated, with lateral packing of flat hexameric BMC proteins providing the basic foundation for assembly. Nonetheless, a complete understanding has been elusive, partly owing to polymorphic mechanisms of assembly exhibited by most microcompartment types. An earlier study of one homologous BMC shell protein subfamily, EutS/PduU, revealed a profoundly bent, rather than flat, hexameric structure. The possibility of a specialized architectural role was hypothesized, but artifactual effects of crystallization could not be ruled out. Here we report a series of crystal structures of an orthologous protein, CutR, from a glycyl-radical type choline-utilizing microcompartment from the bacterium Streptococcus intermedius. Depending on crystal form, expression construct, and minor mutations, a range of novel quaternary architectures was observed, including two spiral hexagonal assemblies. A new graphical approach helps illuminate the variations in BMC hexameric structure, with results substantiating the idea that the EutS/PduU/CutR subfamily of BMC proteins may endow microcompartment shells with flexible modes of assembly.
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Affiliation(s)
- Jessica M Ochoa
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Vy N Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Mengxiao Nie
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Michael R Sawaya
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Thomas A Bobik
- Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University, Ames, Iowa, USA
| | - Todd O Yeates
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
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171
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Yoo SH, Kim IR, Jung YJ. Novel functional characterization of the insecticidal protein Vip3Aa on DNA binding activity. Biochem Biophys Res Commun 2020; 530:322-328. [PMID: 32828306 DOI: 10.1016/j.bbrc.2020.07.019] [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: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 11/30/2022]
Abstract
The toxicity of Vip3Aa protein on insect pests is known, however, it remains unclear underlying the structure-dependent molecular function of the Vip3Aa protein. To investigate the novel function of the Vip3Aa protein, we isolated recombinant Vip3Aa protein. The recombinant Vip3Aa protein was mostly present as oligomeric form depending on the hydrophobic amino acid residue. We found that the oligomeric Vip3Aa protein specifically binds to nucleic acids, including single-stranded (ssDNA) and double-stranded DNA (dsDNA). The conformational and functional domains of the Vip3Aa protein were confirmed by separating the Vip3Aa full and Vip3Aa active (actVip3Aa) forms using size exclusion chromatography and nucleic acid binding activity. Interestingly, actVip3Aa protein had a conformational change and decreased DNA binding activity compared to that of the Vip3Aa full, suggesting that N-terminal part of the Vip3Aa play an important role in maintaining the conformation and nucleic acid binding activity. These studies highlight novel functional characterization of the insecticidal protein Vip3Aa on DNA binding activity and may be attributed to the protection of DNA from the damage caused by oxidative stress.
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Affiliation(s)
- Su-Hyang Yoo
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun, 33657, Republic of Korea
| | - Il Ryong Kim
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun, 33657, Republic of Korea
| | - Young Jun Jung
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun, 33657, Republic of Korea.
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172
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Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophys J 2020; 119:1525-1537. [PMID: 32946768 DOI: 10.1016/j.bpj.2020.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (Sconf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher-ordered oligomerization, and thereby affect crucial replication pathways.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Subhajit Roy
- Centre for Excellence in Basic Sciences (CBS), University of Mumbai, Vidyanagari, Mumbai, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
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173
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Harkness RW, Toyama Y, Kay LE. Analyzing multi-step ligand binding reactions for oligomeric proteins by NMR: Theoretical and computational considerations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106802. [PMID: 32818875 DOI: 10.1016/j.jmr.2020.106802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Solution NMR spectroscopy is widely used to investigate the thermodynamics and kinetics of the binding of ligands to their biological receptors, as it provides detailed, atomistic information, potentially leading to microscopic affinities for each binding event, and, to the development of allosteric pathways describing how the binding at one site affects distal sites in the molecule. Importantly, weak interactions that are often invisible to other biophysical methods can also be probed. Methodological advancements in NMR have enabled the investigation of high molecular weight, homo-oligomeric complexes that bind multiple ligand molecules, with increasing numbers of studies of the structural dynamics and binding properties of these systems. It therefore becomes of interest to consider how binding and kinetics parameters can be extracted from experiments on these more complicated molecules. Here we present the theoretical framework for analyzing binding reactions of homo-oligomeric complexes by NMR, taking into account all of the chemical species in solution and their corresponding NMR observables. A number of simulations are presented to illustrate the utility of the derived expressions.
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Affiliation(s)
- Robert W Harkness
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Yuki Toyama
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada.
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174
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Müntener T, Böhm R, Atz K, Häussinger D, Hiller S. NMR pseudocontact shifts in a symmetric protein homotrimer. JOURNAL OF BIOMOLECULAR NMR 2020; 74:413-419. [PMID: 32621004 PMCID: PMC7508745 DOI: 10.1007/s10858-020-00329-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
NMR pseudocontact shifts are a valuable tool for structural and functional studies of proteins. Protein multimers mediate key functional roles in biology, but methods for their study by pseudocontact shifts are so far not available. Paramagnetic tags attached to identical subunits in multimeric proteins cause a combined pseudocontact shift that cannot be described by the standard single-point model. Here, we report pseudocontact shifts generated simultaneously by three paramagnetic Tm-M7PyThiazole-DOTA tags to the trimeric molecular chaperone Skp and provide an approach for the analysis of this and related symmetric systems. The pseudocontact shifts were described by a "three-point" model, in which positions and parameters of the three paramagnetic tags were fitted. A good correlation between experimental data and predicted values was found, validating the approach. The study establishes that pseudocontact shifts can readily be applied to multimeric proteins, offering new perspectives for studies of large protein complexes by paramagnetic NMR spectroscopy.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Raphael Böhm
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Kenneth Atz
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.
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175
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Yu L, Zhang W, Luo W, Dupont RL, Xu Y, Wang Y, Tu B, Xu H, Wang X, Fang Q, Yang Y, Wang C, Wang C. Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T. SCIENCE ADVANCES 2020; 6:eabc1449. [PMID: 32821844 PMCID: PMC7406363 DOI: 10.1126/sciadv.abc1449] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP8-37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 k B T, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 k B T). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.
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Affiliation(s)
- Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
| | - Wendi Luo
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Robert L. Dupont
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yang Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yibing Wang
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Bin Tu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Haiyan Xu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Xiaoguang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Qiaojun Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
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176
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Shalit Y, Tuvi-Arad I. Side chain flexibility and the symmetry of protein homodimers. PLoS One 2020; 15:e0235863. [PMID: 32706779 PMCID: PMC7380632 DOI: 10.1371/journal.pone.0235863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.
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Affiliation(s)
- Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
- * E-mail:
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177
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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178
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Holmquist ML, Ihms EC, Gollnick P, Wysocki VH, Foster MP. Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP. Biochemistry 2020; 59:2518-2527. [PMID: 32558551 PMCID: PMC8093080 DOI: 10.1021/acs.biochem.0c00352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding, it is necessary to define, at a microscopic level, the thermodynamic consequences of binding of each ligand to its energetically coupled site(s). However, extracting these microscopic constants is difficult for macromolecules with more than two binding sites, because the observable [e.g., nuclear magnetic resonance (NMR) chemical shift changes, fluorescence, and enthalpy] can be altered by allostery, thereby distorting its proportionality to site occupancy. Native mass spectrometry (MS) can directly quantify the populations of homo-oligomeric protein species with different numbers of bound ligands, provided the populations are proportional to ion counts and that MS-compatible electrolytes do not alter the overall thermodynamics. These measurements can help decipher allosteric mechanisms by providing unparalleled access to the statistical thermodynamic partition function. We used native MS (nMS) to study the cooperative binding of tryptophan (Trp) to Bacillus stearothermophilus trp RNA binding attenuation protein (TRAP), a ring-shaped homo-oligomeric protein complex with 11 identical binding sites. MS-compatible solutions did not significantly perturb protein structure or thermodynamics as assessed by isothermal titration calorimetry and NMR spectroscopy. Populations of Trpn-TRAP11 states were quantified as a function of Trp concentration by nMS. The population distributions could not be explained by a noncooperative binding model but were described well by a mechanistic nearest-neighbor cooperative model. Nonlinear least-squares fitting yielded microscopic thermodynamic constants that define the interactions between neighboring binding sites. This approach may be applied to quantify thermodynamic cooperativity in other ring-shaped proteins.
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Affiliation(s)
- Melody L Holmquist
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Elihu C Ihms
- VPPL, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 9W. Watkins Mill Road, Suite 250, Gaithersburg, Maryland 20878, United States
| | - Paul Gollnick
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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179
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Otsuka FAM, Chagas RS, Almeida VM, Marana SR. Homodimerization of a glycoside hydrolase family GH1 β-glucosidase suggests distinct activity of enzyme different states. Protein Sci 2020; 29:1879-1889. [PMID: 32597558 DOI: 10.1002/pro.3908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/06/2022]
Abstract
In this work, we investigated how activity and oligomeric state are related in a purified GH1 β-glucosidase from Spodoptera frugiperda (Sfβgly). Gel filtration chromatography coupled to a multiple angle light scattering detector allowed separation of the homodimer and monomer states and determination of the dimer dissociation constant (KD ), which was in the micromolar range. Enzyme kinetic parameters showed that the dimer is on average 2.5-fold more active. Later, we evaluated the kinetics of homodimerization, scanning the changes in the Sfβgly intrinsic fluorescence over time when the dimer dissociates into the monomer after a large dilution. We described how the rate constant of monomerization (koff ) is affected by temperature, revealing the enthalpic and entropic contributions to the process. We also evaluated how the rate constant (kobs ) by which equilibrium is reached after dimer dilution behaves when varying the initial Sfβgly concentration. These data indicated that Sfβgly dimerizes through the conformational selection mechanism, in which the monomer undergoes a conformational exchange and then binds to a similar monomer, forming a more active homodimer. Finally, we noted that conformational selection reports and experiments usually rely on a ligand whose concentration is in excess, but for homodimerization, this approach does not hold. Hence, since our approach overcomes this limitation, this study not only is a new contribution to the comprehension of GH1 β-glucosidases, but it can also help to elucidate protein interaction pathways.
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Affiliation(s)
- Felipe A M Otsuka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael S Chagas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Vitor M Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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180
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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181
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Laville P, Fartek S, Cerisier N, Flatters D, Petitjean M, Regad L. Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease. BMC Mol Cell Biol 2020; 21:46. [PMID: 32576133 PMCID: PMC7310402 DOI: 10.1186/s12860-020-00290-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Drug resistance is a severe problem in HIV treatment. HIV protease is a common target for the design of new drugs for treating HIV infection. Previous studies have shown that the crystallographic structures of the HIV-2 protease (PR2) in bound and unbound forms exhibit structural asymmetry that is important for ligand recognition and binding. Here, we investigated the effects of resistance mutations on the structural asymmetry of PR2. Due to the lack of structural data on PR2 mutants, the 3D structures of 30 PR2 mutants of interest have been modeled using an in silico protocol. Structural asymmetry analysis was carried out with an in-house structural-alphabet-based approach. Results The systematic comparison of the asymmetry of the wild-type structure and a large number of mutants highlighted crucial residues for PR2 structure and function. In addition, our results revealed structural changes induced by PR2 flexibility or resistance mutations. The analysis of the highlighted structural changes showed that some mutations alter protein stability or inhibitor binding. Conclusions This work consists of a structural analysis of the impact of a large number of PR2 resistant mutants based on modeled structures. It suggests three possible resistance mechanisms of PR2, in which structural changes induced by resistance mutations lead to modifications in the dimerization interface, ligand recognition or inhibitor binding.
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Affiliation(s)
- Pierre Laville
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Sandrine Fartek
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Natacha Cerisier
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Delphine Flatters
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Michel Petitjean
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Leslie Regad
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France.
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182
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Crossing the Vacuolar Rubicon: Structural Insights into Effector Protein Trafficking in Apicomplexan Parasites. Microorganisms 2020; 8:microorganisms8060865. [PMID: 32521667 PMCID: PMC7355975 DOI: 10.3390/microorganisms8060865] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Apicomplexans form a large phylum of parasitic protozoa, including the genera Plasmodium, Toxoplasma, and Cryptosporidium, the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively. They cause diseases not only in humans but also in animals, with dramatic consequences in agriculture. Most apicomplexans are vacuole-dwelling and obligate intracellular parasites; as they invade the host cell, they become encased in a parasitophorous vacuole (PV) derived from the host cellular membrane. This creates a parasite-host interface that acts as a protective barrier but also constitutes an obstacle through which the pathogen must import nutrients, eliminate wastes, and eventually break free upon egress. Completion of the parasitic life cycle requires intense remodeling of the infected host cell. Host cell subversion is mediated by a subset of essential effector parasitic proteins and virulence factors actively trafficked across the PV membrane. In the malaria parasite Plasmodium, a unique and highly specialized ATP-driven vacuolar secretion system, the Plasmodium translocon of exported proteins (PTEX), transports effector proteins across the vacuolar membrane. Its core is composed of the three essential proteins EXP2, PTEX150, and HSP101, and is supplemented by the two auxiliary proteins TRX2 and PTEX88. Many but not all secreted malarial effector proteins contain a vacuolar trafficking signal or Plasmodium export element (PEXEL) that requires processing by an endoplasmic reticulum protease, plasmepsin V, for proper export. Because vacuolar parasitic protein export is essential to parasite survival and virulence, this pathway is a promising target for the development of novel antimalarial therapeutics. This review summarizes the current state of structural and mechanistic knowledge on the Plasmodium parasitic vacuolar secretion and effector trafficking pathway, describing its most salient features and discussing the existing differences and commonalities with the vacuolar effector translocation MYR machinery recently described in Toxoplasma and other apicomplexans of significance to medical and veterinary sciences.
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183
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Heckmeier PJ, Agam G, Teese MG, Hoyer M, Stehle R, Lamb DC, Langosch D. Determining the Stoichiometry of Small Protein Oligomers Using Steady-State Fluorescence Anisotropy. Biophys J 2020; 119:99-114. [PMID: 32553128 DOI: 10.1016/j.bpj.2020.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 11/19/2022] Open
Abstract
A large fraction of soluble and membrane-bound proteins exists as non-covalent dimers, trimers, and higher-order oligomers. The experimental determination of the oligomeric state or stoichiometry of proteins remains a nontrivial challenge. In one approach, the protein of interest is genetically fused to green fluorescent protein (GFP). If a fusion protein assembles into a non-covalent oligomeric complex, exciting their GFP moiety with polarized fluorescent light elicits homotypic Förster resonance energy transfer (homo-FRET), in which the emitted radiation is partially depolarized. Fluorescence depolarization is associated with a decrease in fluorescence anisotropy that can be exploited to calculate the oligomeric state. In a classical approach, several parameters obtained through time-resolved and steady-state anisotropy measurements are required for determining the stoichiometry of the oligomers. Here, we examined novel approaches in which time-resolved measurements of reference proteins provide the parameters that can be used to interpret the less expensive steady-state anisotropy data of candidates. In one approach, we find that using average homo-FRET rates (kFRET), average fluorescence lifetimes (τ), and average anisotropies of those fluorophores that are indirectly excited by homo-FRET (rET) do not compromise the accuracy of calculated stoichiometries. In the other approach, fractional photobleaching of reference oligomers provides a novel parameter a whose dependence on stoichiometry allows one to quantitatively interpret the increase of fluorescence anisotropy seen after photobleaching the candidates. These methods can at least reliably distinguish monomers from dimers and trimers.
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Affiliation(s)
- Philipp J Heckmeier
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Ganesh Agam
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Mark G Teese
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Maria Hoyer
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM), Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany.
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184
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Zottig X, Côté-Cyr M, Arpin D, Archambault D, Bourgault S. Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1008. [PMID: 32466176 PMCID: PMC7281494 DOI: 10.3390/nano10051008] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022]
Abstract
Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.
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Affiliation(s)
- Ximena Zottig
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mélanie Côté-Cyr
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Dominic Arpin
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Denis Archambault
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
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185
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Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Sci Rep 2020; 10:8367. [PMID: 32433550 PMCID: PMC7239866 DOI: 10.1038/s41598-020-65097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.
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Affiliation(s)
- Maayan Bonjack
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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186
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Altobelli GG, Van Noorden S, Balato A, Cimini V. Copper/Zinc Superoxide Dismutase in Human Skin: Current Knowledge. Front Med (Lausanne) 2020; 7:183. [PMID: 32478084 PMCID: PMC7235401 DOI: 10.3389/fmed.2020.00183] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Superoxide dismutase is widespread in the human body, including skin and its appendages. Here, we focus on human skin copper/zinc superoxide dismutase, the enzyme that protects skin and its appendages against reactive oxygen species. Human skin copper/zinc superoxide dismutase resides in the cytoplasm of keratinocytes, where up to 90% of cellular reactive oxygen species is produced. Factors other than cell type, such as gender, age and diseased state influence its location in skin tissues. We review current knowledge of skin copper/zinc superoxide dismutase including recent studies in an attempt to contribute to solving the question of its remaining unexplained functions. The research described here may be applicable to pathologies associated with oxidative stress. However, recent studies on copper/zinc superoxide dismutase in yeast reveal that its predominant function may be in signaling pathways rather than in scavenging superoxide ions. If confirmed in the skin, novel approaches might be developed to unravel the enzyme's remaining mysteries.
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Affiliation(s)
- Giovanna G Altobelli
- Department of Advanced Biomedical Sciences, Medical School, "Federico II" University of Naples, Naples, Italy
| | - Susan Van Noorden
- Department of Histopathology, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Anna Balato
- Department of Advanced Biomedical Sciences, Medical School, "Federico II" University of Naples, Naples, Italy
| | - Vincenzo Cimini
- Department of Advanced Biomedical Sciences, Medical School, "Federico II" University of Naples, Naples, Italy
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187
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Abelmann L, Hageman TAG, Löthman PA, Mastrangeli M, Elwenspoek MC. Three-dimensional self-assembly using dipolar interaction. SCIENCE ADVANCES 2020; 6:eaba2007. [PMID: 32494725 PMCID: PMC7209989 DOI: 10.1126/sciadv.aba2007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/24/2020] [Indexed: 06/11/2023]
Abstract
Interaction between dipolar forces, such as permanent magnets, generally leads to the formation of one-dimensional chains and rings. We investigated whether it was possible to let dipoles self-assemble into three-dimensional structures by encapsulating them in a shell with a specific shape. We found that the condition for self-assembly of a three-dimensional crystal is satisfied when the energies of dipoles in the parallel and antiparallel states are equal. Our experiments show that the most regular structures are formed using cylinders and cuboids and not by spheroids. This simple design rule will help the self-assembly community to realize three-dimensional crystals from objects in the micrometer range, which opens up the way toward previously unknown metamaterials.
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Affiliation(s)
- Leon Abelmann
- KIST Europe, Saarland University, Saarbrücken, Germany
- University of Twente, Enschede, Netherlands
| | - Tijmen A. G. Hageman
- KIST Europe, Saarland University, Saarbrücken, Germany
- University of Twente, Enschede, Netherlands
| | - Per A. Löthman
- KIST Europe, Saarland University, Saarbrücken, Germany
- University of Twente, Enschede, Netherlands
| | - Massimo Mastrangeli
- Electronic Components, Technology and Materials, Department of Microelectronics, Delft University of Technology, Delft, Netherlands
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188
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Pillai AS, Chandler SA, Liu Y, Signore AV, Cortez-Romero CR, Benesch JLP, Laganowsky A, Storz JF, Hochberg GKA, Thornton JW. Origin of complexity in haemoglobin evolution. Nature 2020; 581:480-485. [PMID: 32461643 PMCID: PMC8259614 DOI: 10.1038/s41586-020-2292-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 04/07/2020] [Indexed: 02/02/2023]
Abstract
Most proteins associate into multimeric complexes with specific architectures1,2, which often have functional properties such as cooperative ligand binding or allosteric regulation3. No detailed knowledge is available about how any multimer and its functions arose during evolution. Here we use ancestral protein reconstruction and biophysical assays to elucidate the origins of vertebrate haemoglobin, a heterotetramer of paralogous α- and β-subunits that mediates respiratory oxygen transport and exchange by cooperatively binding oxygen with moderate affinity. We show that modern haemoglobin evolved from an ancient monomer and characterize the historical 'missing link' through which the modern tetramer evolved-a noncooperative homodimer with high oxygen affinity that existed before the gene duplication that generated distinct α- and β-subunits. Reintroducing just two post-duplication historical substitutions into the ancestral protein is sufficient to cause strong tetramerization by creating favourable contacts with more ancient residues on the opposing subunit. These surface substitutions markedly reduce oxygen affinity and even confer cooperativity, because an ancient linkage between the oxygen binding site and the multimerization interface was already an intrinsic feature of the protein's structure. Our findings establish that evolution can produce new complex molecular structures and functions via simple genetic mechanisms that recruit existing biophysical features into higher-level architectures.
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Affiliation(s)
- Arvind S Pillai
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Shane A Chandler
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Justin L P Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Georg K A Hochberg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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189
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Cifuente JO, Comino N, D'Angelo C, Marina A, Gil-Carton D, Albesa-Jové D, Guerin ME. The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM. Curr Res Struct Biol 2020; 2:89-103. [PMID: 34235472 PMCID: PMC8244506 DOI: 10.1016/j.crstbi.2020.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/10/2022] Open
Abstract
Glycogen and starch are the major carbon and energy reserve polysaccharides in nature, providing living organisms with a survival advantage. The evolution of the enzymatic machinery responsible for the biosynthesis and degradation of such polysaccharides, led the development of mechanisms to control the assembly and disassembly rate, to store and recover glucose according to cell energy demands. The tetrameric enzyme ADP-glucose pyrophosphorylase (AGPase) catalyzes and regulates the initial step in the biosynthesis of both α-polyglucans. AGPase displays cooperativity and allosteric regulation by sensing metabolites from the cell energy flux. The understanding of the allosteric signal transduction mechanisms in AGPase arises as a long-standing challenge. In this work, we disclose the cryoEM structures of the paradigmatic homotetrameric AGPase from Escherichia coli (EcAGPase), in complex with either positive or negative physiological allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP respectively, both at 3.0 Å resolution. Strikingly, the structures reveal that FBP binds deeply into the allosteric cleft and overlaps the AMP site. As a consequence, FBP promotes a concerted conformational switch of a regulatory loop, RL2, from a "locked" to a "free" state, modulating ATP binding and activating the enzyme. This notion is strongly supported by our complementary biophysical and bioinformatics evidence, and a careful analysis of vast enzyme kinetics data on single-point mutants of EcAGPase. The cryoEM structures uncover the residue interaction networks (RIN) between the allosteric and the catalytic components of the enzyme, providing unique details on how the signaling information is transmitted across the tetramer, from which cooperativity emerges. Altogether, the conformational states visualized by cryoEM reveal the regulatory mechanism of EcAGPase, laying the foundations to understand the allosteric control of bacterial glycogen biosynthesis at the molecular level of detail.
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Key Words
- AGPase, ADP-glucose pyrophosphorylase
- AMP, adenosine 5′-monophosphate
- ATP, adenosine 5′-triphosphate
- EcAGPase, AGPase from E. coli
- Enzyme allosterism
- FBP, fructose 1,6-bisphosphate
- G1P, α-d-glucose-1-phosphate
- GBE, glycogen branching enzyme
- GDE, glycogen debranching enzyme
- GP, glycogen phosphorylase
- GS, glycogen synthase
- GTA-like, glycosyltransferase-A like domain
- Glycogen biosynthesis
- Glycogen regulation
- LβH, left-handed β-helix domain
- Nucleotide sugar biosynthesis
- PPi, pyrophosphate
- RIN, residue interaction network
- SM, sensory motif
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Affiliation(s)
- Javier O. Cifuente
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Cecilia D'Angelo
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Alberto Marina
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Albesa-Jové
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Marcelo E. Guerin
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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190
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Jin Y, Manabe T. Simultaneous speculation of 401 monomeric or homo-oligomeric subunit structures of human cellular proteins, mining the information in 1901 native 2D protein maps reconstructed from one nondenaturing 2DE gel. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1144:122104. [PMID: 32278290 DOI: 10.1016/j.jchromb.2020.122104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 11/29/2022]
Abstract
Subunit structures of proteins are essential for their properties and functions, but there is a lack of method for global detection of the status of proteins being monomers or homo-oligomers. In this work, we report on a new method to simultaneously speculate hundreds of monomeric or homo-oligomeric subunit structures of cellular proteins, based on in-depth analysis of native 2D protein maps. Previously we have reported on the analysis of soluble proteins of human bronchial muscle cells (HBSMC) by combining nondenaturing 2DE, grid gel-cutting and quantitative LC-MS/MS. Totally 4323 proteins were detected and for each protein the quantity distribution on the gel was reconstructed as a native 2D map. In this work, this large dataset of maps were further mined with bioinformatic analysis. The native 2D maps of 1901 HBSMC proteins that were detected in at least five out of the grid-cut 972 gel squares were examined and 658 proteins that showed one major quantity-peak distribution were subjected to further analysis. After excluding those that mainly formed hetero-oligomeric structures, the monomeric or homo-oligomeric subunit structures of 505 proteins were speculated. The quotient of the apparent molecular mass of the quantity-peak position on the native 2D map divided by the theoretical molecular mass was calculated for each protein, to speculate the number of monomers which constituted its subunit structure. The suggested composition was then compared with the "Subunit structure" record of the protein in UniProtKB. When the database record included possible interactions with other proteins, their native 2D maps were extracted from the native map dataset, presented together and compared to confirm the prominent subunit structure. With this new approach, the monomeric or homo-oligomeric subunit structures of 401 proteins were speculated. Among them, 162 proteins had the speculated subunit structures coinciding with their database records, and 91 proteins with matched database records as being monomers or homo-oligomers but mismatched at the numbers of the composing monomers. For 148 proteins that did not have database record, their subunit structures were newly speculated. We expect this method, combining nondenaturing 2DE separation with in-depth proteomic and bioinformatic analysis, would suggest a means to achieve large-scale information on monomeric and homo-oligomeric subunit structures of cellular proteins.
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Affiliation(s)
- Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China.
| | - Takashi Manabe
- Faculty of Science, Ehime University, Matsuyama 790-0825, Japan
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191
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Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin. Nat Commun 2020; 11:1916. [PMID: 32317635 PMCID: PMC7174398 DOI: 10.1038/s41467-020-15698-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF3-bound) ground-state mimic double-ring mHsp6014-(mHsp107)2 football complex, and the cryo-EM structures of the ADP-bound successor mHsp6014-(mHsp107)2 complex, and a single-ring mHsp607-mHsp107 half-football. The structures explain the nucleotide dependence of mHsp60 ring formation, and reveal an inter-ring nucleotide symmetry consistent with the absence of negative cooperativity. In the ground-state a two-fold symmetric H-bond and a salt bridge stitch the double-rings together, whereas only the H-bond remains as the equatorial gap increases in an ADP football poised to split into half-footballs. Refolding assays demonstrate obligate single- and double-ring mHsp60 variants are active, and complementation analysis in bacteria shows the single-ring variant is as efficient as wild-type mHsp60. Our work provides a structural basis for active single- and double-ring complexes coexisting in the mHsp60-mHsp10 chaperonin reaction cycle.
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192
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Dadinova LA, Soshinskaia EY, Jeffries CM, Svergun DI, Shtykova EV. Tetrameric Structures of Inorganic CBS-Pyrophosphatases from Various Bacterial Species Revealed by Small-Angle X-ray Scattering in Solution. Biomolecules 2020; 10:E564. [PMID: 32272694 PMCID: PMC7226116 DOI: 10.3390/biom10040564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/29/2022] Open
Abstract
Quaternary structure of CBS-pyrophosphatases (CBS-PPases), which belong to the PPases of family II, plays an important role in their function ensuring cooperative behavior of the enzymes. Despite an intensive research, high resolution structures of the full-length CBS-PPases are not yet available making it difficult to determine the signal transmission path from the regulatory to the active center. In the present work, small-angle X-ray scattering (SAXS) combined with size-exclusion chromatography was applied to determine the solution structures of the full-length wild-type CBS-PPases from three different bacterial species. Previously, in the absence of an experimentally determined full-length CBS-PPase structure, a homodimeric model of the enzyme based on known crystal structures of the CBS domain and family II PPase without this domain has been proposed. Our SAXS analyses demonstrate, for the first time, the existence of stable tetramers in solution for all studied CBS-PPases from different sources. Our findings show that further studies are required to establish the functional properties of these enzymes. This is important not only to enhance our understanding of the relation between CBS-PPases structure and function under normal conditions but also because some human pathogens harbor this class of enzymes.
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Affiliation(s)
- Liubov A. Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (E.Y.S.); (E.V.S.)
| | - Ekaterina Yu. Soshinskaia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (E.Y.S.); (E.V.S.)
| | - Cy M. Jeffries
- EMBL, Hamburg Unit, c/o DESY, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany; (C.M.J.); (D.I.S.)
| | - Dmitri I. Svergun
- EMBL, Hamburg Unit, c/o DESY, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany; (C.M.J.); (D.I.S.)
| | - Eleonora V. Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (E.Y.S.); (E.V.S.)
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193
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Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. J Mol Evol 2020; 88:319-344. [PMID: 32189026 PMCID: PMC7162841 DOI: 10.1007/s00239-020-09934-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/16/2020] [Indexed: 11/05/2022]
Abstract
The polytopic helical membrane proteome is dominated by proteins containing seven transmembrane helices (7TMHs). They cannot be grouped under a monolithic fold or superfold. However, a parallel structural analysis of folds around that magic number of seven in distinct protein superfamilies (SWEET, PnuC, TRIC, FocA, Aquaporin, GPCRs) reveals a common homology, not in their structural fold, but in their systematic pseudo-symmetric construction during their evolution. Our analysis leads to guiding principles of intragenic duplication and pseudo-symmetric assembly of ancestral transmembrane helical protodomains, consisting of 3 (or 4) helices. A parallel deconstruction and reconstruction of these domains provides a structural and mechanistic framework for their evolutionary paths. It highlights the conformational plasticity inherent to fold formation itself, the role of structural as well as functional constraints in shaping that fold, and the usefulness of protodomains as a tool to probe convergent vs divergent evolution. In the case of FocA vs. Aquaporin, this protodomain analysis sheds new light on their potential divergent evolution at the protodomain level followed by duplication and parallel evolution of the two folds. GPCR domains, whose function does not seem to require symmetry, nevertheless exhibit structural pseudo-symmetry. Their construction follows the same protodomain assembly as any other pseudo-symmetric protein suggesting their potential evolutionary origins. Interestingly, all the 6/7/8TMH pseudo-symmetric folds in this study also assemble as oligomeric forms in the membrane, emphasizing the role of symmetry in evolution, revealing self-assembly and co-evolution not only at the protodomain level but also at the domain level.
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194
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Terashi G, Kagaya Y, Kihara D. MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. J Chem Inf Model 2020; 60:2634-2643. [PMID: 32197044 DOI: 10.1021/acs.jcim.9b01110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuki Kagaya
- Graduate School of Information Sciences, Tohoku University, Aramaki Aza, Aoba 6-3-09, Aoba-Ku, Sendai, Miyagi 980-8579, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States
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195
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Better together: building protein oligomers naturally and by design. Biochem Soc Trans 2020; 47:1773-1780. [PMID: 31803901 PMCID: PMC6925524 DOI: 10.1042/bst20190283] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.
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196
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Minicozzi V, Di Venere A, Nicolai E, Giuliani A, Caccuri AM, Di Paola L, Mei G. Non-symmetrical structural behavior of a symmetric protein: the case of homo-trimeric TRAF2 (tumor necrosis factor-receptor associated factor 2). J Biomol Struct Dyn 2020; 39:319-329. [PMID: 31980009 DOI: 10.1080/07391102.2020.1719202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The oligomeric state of TRAF2 (tumor necrosis factor-receptor associated factor 2), a TNF (tumor necrosis factor) receptor-associated factor, is crucial for membrane binding and probably plays a fundamental role in regulating the protein function in vivo. In this study we have combined molecular dynamics with the protein contact network approach to characterize the interaction of the three identical subunits of TRAF2. The average structure obtained after a 225 ns simulation reveals that two clusters of different size are formed, one of which includes almost completely two subunits, while the third monomer appears to be more independent. This picture is also confirmed by the estimated average number of inter-subunit contacts and by the comparison of side chains mobility in each monomer. The analysis of equilibrium pressure-induced dissociation measurements supports such findings, indicating that the dimeric-monomeric (2 + 1) might be prevalent with respect to the trimeric configuration, especially in the case of more diluted samples. These findings suggest that the formation of monomeric species, which is crucial for the formation of intra-luminal vesicles, might depend on preferential asymmetric interactions among the three subunits.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Velia Minicozzi
- INFN and Department of Physics, University of Rome Tor Vergata, Rome, Italy
| | - Almerinda Di Venere
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Eleonora Nicolai
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Luisa Di Paola
- Department of Engineering, Unit of Chemical-Physics Fundamentals in Chemical Engineering, Università Campus Bio-Medico of Rome, Rome, Italy
| | - Giampiero Mei
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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197
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Liu D, Geary CW, Chen G, Shao Y, Li M, Mao C, Andersen ES, Piccirilli JA, Rothemund PWK, Weizmann Y. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem 2020; 12:249-259. [PMID: 31959958 DOI: 10.1038/s41557-019-0406-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/06/2019] [Indexed: 01/31/2023]
Abstract
In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.
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Affiliation(s)
- Di Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cody W Geary
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA
| | - Gang Chen
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Ebbe S Andersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Paul W K Rothemund
- Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA.
| | - Yossi Weizmann
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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198
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Esch R, Merkl R. Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. BMC Bioinformatics 2020; 21:5. [PMID: 31900122 PMCID: PMC6941341 DOI: 10.1186/s12859-019-3200-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The order of genes in bacterial genomes is not random; for example, the products of genes belonging to an operon work together in the same pathway. The cotranslational assembly of protein complexes is deemed to conserve genomic neighborhoods even stronger than a common function. This is why a conserved genomic neighborhood can be utilized to predict, whether gene products form protein complexes. RESULTS We were interested to assess the performance of a neighborhood-based classifier that analyzes a large number of genomes. Thus, we determined for the genes encoding the subunits of 494 experimentally verified hetero-dimers their local genomic context. In order to generate phylogenetically comprehensive genomic neighborhoods, we utilized the tools offered by the Enzyme Function Initiative. For each subunit, a sequence similarity network was generated and the corresponding genome neighborhood network was analyzed to deduce the most frequent gene product. This was predicted as interaction partner, if its abundance exceeded a threshold, which was the frequency giving rise to the maximal Matthews correlation coefficient. For the threshold of 16%, the true positive rate was 45%, the false positive rate 0.06%, and the precision 55%. For approximately 20% of the subunits, the interaction partner was not found in a neighborhood of ± 10 genes. CONCLUSIONS Our phylogenetically comprehensive analysis confirmed that complex formation is a strong evolutionary factor that conserves genome neighborhoods. On the other hand, for 55% of the cases analyzed here, classification failed. Either, the interaction partner was not present in a ± 10 gene window or was not the most frequent gene product.
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Affiliation(s)
- Robert Esch
- Faculty of Mathematics and Computer Science, University of Hagen, D-58084, Hagen, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040, Regensburg, Germany.
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199
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Baek M, Park T, Heo L, Seok C. Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. Methods Mol Biol 2020; 2165:127-137. [PMID: 32621222 DOI: 10.1007/978-1-0716-0708-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cellular processes, such as metabolism, signal transduction, or immunity, often depend on the homo-oligomerization of proteins. Detailed structural knowledge of the homo-oligomer structure is therefore crucial for molecular-level understanding of protein functions and their regulation. In this chapter, we introduce the GalaxyHomomer server, which supports easy-to-use web interfaces for general users. It is freely accessible at http://galaxy.seoklab.org/homomer . GalaxyHomomer carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality by performing symmetric loop modeling and overall structure refinement. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state, and locations of unreliable/flexible loops or termini.
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Affiliation(s)
- Minkyung Baek
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Taeyong Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Lim Heo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
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200
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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