1
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Kabasakal BV, McFarlane CR, Cotton CAR, Schmidt A, Kung A, Lieber L, Murray JW. The crystal structure of Shethna protein II (FeSII) from Azotobacter vinelandii suggests a domain swap. Acta Crystallogr D Struct Biol 2024; 80:599-604. [PMID: 38984904 PMCID: PMC11301756 DOI: 10.1107/s2059798324005928] [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: 02/07/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239-247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe-2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe-2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.
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Affiliation(s)
- Burak V. Kabasakal
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
- Turkish Accelerator and Radiation Laboratory, Gőlbaşı, 06830Ankara, Türkiye
| | - Ciaran R. McFarlane
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Charles A. R. Cotton
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
- Cambrium GmbH, Max-Urich-Strasse 3, 13355Berlin, Germany
| | - Anna Schmidt
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Andrea Kung
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Lucas Lieber
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
- Bioheuris Inc., 1100 Corporate Square Drive, St Louis, MO63132, USA
| | - James W. Murray
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
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2
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Badonyi M, Marsh JA. Hallmarks and evolutionary drivers of cotranslational protein complex assembly. FEBS J 2024; 291:3557-3567. [PMID: 37202910 DOI: 10.1111/febs.16869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 05/20/2023]
Abstract
Recent discoveries have highlighted the prevalence of cotranslational assembly in proteomes, revealing a range of mechanisms that enables the assembly of protein complex subunits on the ribosome. Structural analyses have uncovered emergent properties that may inherently control whether a subunit undergoes cotranslational assembly. However, the evolutionary paths that have yielded such complexes over an extended timescale remain largely unclear. In this review, we reflect on historical experiments that contributed to the field, including breakthroughs that have made possible the proteome-wide detection of cotranslational assembly, and the technical challenges yet to be overcome. We introduce a simple framework that encapsulates the hallmarks of cotranslational assembly and discuss how results from new experiments are shaping our view of the mechanistic, structural and evolutionary factors driving the phenomenon.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
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3
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Shor B, Schneidman-Duhovny D. CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2. Nat Methods 2024; 21:477-487. [PMID: 38326495 PMCID: PMC10927564 DOI: 10.1038/s41592-024-02174-0] [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: 05/17/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score >0.7) 72% of the complexes among the top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding Protein Data Bank entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold's high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
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Affiliation(s)
- Ben Shor
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Shor B, Schneidman-Duhovny D. Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541003. [PMID: 37293053 PMCID: PMC10245790 DOI: 10.1101/2023.05.16.541003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score > 0.7) 72% of the complexes among the Top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding PDB entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold's high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
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Affiliation(s)
- Ben Shor
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Natale AM, Deal PE, Minor DL. Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels. J Mol Biol 2021; 433:166995. [PMID: 33887333 PMCID: PMC8436263 DOI: 10.1016/j.jmb.2021.166995] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 01/10/2023]
Abstract
Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K2Ps contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K2Ps have established the basic architecture of this channel family, revealed key moving parts involved in K2P function, uncovered the importance of asymmetric pinching and dilation motions in the K2P selectivity filter (SF) C-type gate, and defined two K2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K2P:modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K2P activity. Such knowledge should catalyze development of new K2P modulators to probe function and treat a wide range of disorders.
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Affiliation(s)
- Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Parker E Deal
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience University of California, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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6
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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: 1.0] [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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7
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Kimberlin CR, Meshcheriakova A, Palty R, Raveh A, Karbat I, Reuveny E, Minor DL. SARAF Luminal Domain Structure Reveals a Novel Domain-Swapped β-Sandwich Fold Important for SOCE Modulation. J Mol Biol 2019; 431:2869-2883. [PMID: 31082439 DOI: 10.1016/j.jmb.2019.05.008] [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] [Received: 02/26/2019] [Revised: 04/29/2019] [Accepted: 05/05/2019] [Indexed: 02/02/2023]
Abstract
Store-Operated Calcium Entry (SOCE) plays key roles in cell proliferation, muscle contraction, immune responses, and memory formation. The coordinated interactions of a number of proteins from the plasma and endoplasmic reticulum membranes control SOCE to replenish internal Ca2+ stores and generate intracellular Ca2+ signals. SARAF, an endoplasmic reticulum resident component of the SOCE pathway having no homology to any characterized protein, serves as an important brake on SOCE. Here, we describe the X-ray crystal structure of the SARAF luminal domain, SARAFL. This domain forms a novel 10-stranded β-sandwich fold that includes a set of three conserved disulfide bonds, denoted the "SARAF-fold." The structure reveals a domain-swapped dimer in which the last two β-strands (β9 and β10) are exchanged forming a region denoted the "SARAF luminal switch" that is essential for dimerization. Sequence comparisons reveal that the SARAF-fold is highly conserved in vertebrates and in a variety of pathologic fungi. Förster resonance energy transfer experiments using full-length SARAF validate the formation of the domain-swapped dimer in cells and demonstrate that dimerization is reversible. A designed variant lacking the SARAF luminal switch shows that the domain swapping is essential to function and indicates that the SARAF dimer accelerates SOCE inactivation.
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Affiliation(s)
| | - Anna Meshcheriakova
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raz Palty
- Rappaport Family School of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Adi Raveh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 94148, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Fancisco, CA 94158, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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8
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Consta S, Malevanets A, Oh MI, Sharawy M. Role of a reaction coordinate in free energy calculations. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1445245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario , London, Canada
| | - Anatoly Malevanets
- Department of Electrical & Computer Engineering, The University of Western Ontario , London, Canada
| | - Myong In Oh
- Department of Chemistry, The University of Western Ontario , London, Canada
| | - Mahmoud Sharawy
- Department of Chemistry, The University of Western Ontario , London, Canada
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9
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Miller AF, Park JT, Ferguson KL, Pitsawong W, Bommarius AS. Informing Efforts to Develop Nitroreductase for Amine Production. Molecules 2018; 23:molecules23020211. [PMID: 29364838 PMCID: PMC6017928 DOI: 10.3390/molecules23020211] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
Nitroreductases (NRs) hold promise for converting nitroaromatics to aromatic amines. Nitroaromatic reduction rate increases with Hammett substituent constant for NRs from two different subgroups, confirming substrate identity as a key determinant of reactivity. Amine yields were low, but compounds yielding amines tend to have a large π system and electron withdrawing substituents. Therefore, we also assessed the prospects of varying the enzyme. Several different subgroups of NRs include members able to produce aromatic amines. Comparison of four NR subgroups shows that they provide contrasting substrate binding cavities with distinct constraints on substrate position relative to the flavin. The unique architecture of the NR dimer produces an enormous contact area which we propose provides the stabilization needed to offset the costs of insertion of the active sites between the monomers. Thus, we propose that the functional diversity included in the NR superfamily stems from the chemical versatility of the flavin cofactor in conjunction with a structure that permits tremendous active site variability. These complementary properties make NRs exceptionally promising enzymes for development for biocatalysis in prodrug activation and conversion of nitroaromatics to valuable aromatic amines. We provide a framework for identifying NRs and substrates with the greatest potential to advance.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Jonathan T Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Kyle L Ferguson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Warintra Pitsawong
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
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10
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Morreale FE, Testa A, Chaugule VK, Bortoluzzi A, Ciulli A, Walden H. Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements. J Med Chem 2017; 60:8183-8191. [PMID: 28933844 PMCID: PMC5663392 DOI: 10.1021/acs.jmedchem.7b01071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Efforts
to develop inhibitors, activators, and effectors of biological
reactions using small molecule libraries are often hampered by interference
compounds, artifacts, and false positives that permeate the pool of
initial hits. Here, we report the discovery of a promising initial
hit compound targeting the Fanconi anemia ubiquitin-conjugating enzyme
Ube2T and describe its biophysical and biochemical characterization.
Analysis of the co-crystal structure led to the identification of
a contaminating zinc ion as solely responsible for the observed effects.
Zinc binding to the active site cysteine induces a domain swap in
Ube2T that leads to cyclic trimerization organized in an open-ended
linear assembly. Our study serves as a cautionary tale for screening
small molecule libraries and provides insights into the structural
plasticity of ubiquitin-conjugating enzymes.
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Affiliation(s)
- Francesca E Morreale
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Andrea Testa
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Alessio Bortoluzzi
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Alessio Ciulli
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
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11
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Murison DA, Timson RC, Koleva BN, Ordazzo M, Beuning PJ. Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD. Biochemistry 2017; 56:4773-4785. [DOI: 10.1021/acs.biochem.7b00560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David A. Murison
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rebecca C. Timson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Bilyana N. Koleva
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael Ordazzo
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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12
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Sala S, Catillon M, Hadzic E, Schaffner-Reckinger E, Van Troys M, Ampe C. The PET and LIM1-2 domains of testin contribute to intramolecular and homodimeric interactions. PLoS One 2017; 12:e0177879. [PMID: 28542564 PMCID: PMC5436826 DOI: 10.1371/journal.pone.0177879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/04/2017] [Indexed: 12/18/2022] Open
Abstract
The focal adhesion protein testin is a modular scaffold and tumour suppressor that consists of an N-terminal cysteine rich (CR) domain, a PET domain of unknown function and three C-terminal LIM domains. Testin has been proposed to have an open and a closed conformation based on the observation that its N-terminal half and C-terminal half directly interact. Here we extend the testin conformational model by demonstrating that testin can also form an antiparallel homodimer. In support of this extended model we determined that the testin region (amino acids 52–233) harbouring the PET domain interacts with the C-terminal LIM1-2 domains in vitro and in cells, and assign a critical role to tyrosine 288 in this interaction.
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Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Marie Catillon
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Ermin Hadzic
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | | | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
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13
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Mascarenhas NM, Gosavi S. Understanding protein domain-swapping using structure-based models of protein folding. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:113-120. [PMID: 27867057 PMCID: PMC7127520 DOI: 10.1016/j.pbiomolbio.2016.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/05/2016] [Accepted: 09/26/2016] [Indexed: 02/05/2023]
Abstract
In domain-swapping, two or more identical protein monomers exchange structural elements and fold into dimers or multimers whose units are structurally similar to the original monomer. Domain-swapping is of biotechnological interest because inhibiting domain-swapping can reduce disease-causing fibrillar protein aggregation. To achieve such inhibition, it is important to understand both the energetics that stabilize the domain-swapped structure and the protein dynamics that enable the swapping. Structure-based models (SBMs) encode the folded structure of the protein in their potential energy functions. SBMs have been successfully used to understand diverse aspects of monomer folding. Symmetrized SBMs model interactions between two identical protein chains using only intra-monomer interactions. Molecular dynamics simulations of such symmetrized SBMs have been used to correctly predict the domain-swapped structure and to understand the mechanism of domain-swapping. Here, we review such models and illustrate that monomer topology determines key aspects of domain-swapping. However, in some proteins, specifics of local energetic interactions modulate domain-swapping and these need to be added to the symmetrized SBMs. We then summarize some general principles of the mechanism of domain-swapping that emerge from the symmetrized SBM simulations. Finally, using our own results, we explore how symmetrized SBMs could be used to design domain-swapping in proteins.
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Affiliation(s)
- Nahren Manuel Mascarenhas
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
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14
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Woodard JC, Dunatunga S, Shakhnovich EI. A Simple Model of Protein Domain Swapping in Crowded Cellular Environments. Biophys J 2016; 110:2367-2376. [PMID: 27276255 DOI: 10.1016/j.bpj.2016.04.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/07/2016] [Accepted: 04/20/2016] [Indexed: 11/25/2022] Open
Abstract
Domain swapping in proteins is an important mechanism of functional and structural innovation. However, despite its ubiquity and importance, the physical mechanisms that lead to domain swapping are poorly understood. Here, we present a simple two-dimensional coarse-grained model of protein domain swapping in the cytoplasm. In our model, two-domain proteins partially unfold and diffuse in continuous space. Monte Carlo multiprotein simulations of the model reveal that domain swapping occurs at intermediate temperatures, whereas folded dimers and folded monomers prevail at low temperatures, and partially unfolded monomers predominate at high temperatures. We use a simplified amino acid alphabet consisting of four residue types, and find that the oligomeric state at a given temperature depends on the sequence of the protein. We also show that hinge strain between domains can promote domain swapping, consistent with experimental observations for real proteins. Domain swapping depends nonmonotonically on the protein concentration, with domain-swapped dimers occurring at intermediate concentrations and nonspecific interactions between partially unfolded proteins occurring at high concentrations. For folded proteins, we recover the result obtained in three-dimensional lattice simulations, i.e., that functional dimerization is most prevalent at intermediate temperatures and nonspecific interactions increase at low temperatures.
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Affiliation(s)
- Jaie C Woodard
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Sachith Dunatunga
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
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15
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Smaldone G, Vigorita M, Ruggiero A, Balasco N, Dattelbaum JD, D'Auria S, Del Vecchio P, Graziano G, Vitagliano L. Proline 235 plays a key role in the regulation of the oligomeric states of Thermotoga maritima Arginine Binding Protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:814-24. [PMID: 27087545 DOI: 10.1016/j.bbapap.2016.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 10/22/2022]
Abstract
The Arginine Binding Protein isolated from Thermotoga maritima (TmArgBP) is a protein endowed with several peculiar properties. We have previously shown that TmArgBP dimerization is a consequence of the swapping of the C-terminal helix. Here we explored the structural determinants of TmArgBP domain swapping and oligomerization. In particular, we report a mutational analysis of the residue Pro235, which is located in the hinge region of the swapping dimer. This residue was either replaced with a Gly-Lys dipeptide (TmArgBP(P235GK)) or a Gly residue (TmArgBP(P235G)). Different forms of these mutants were generated and extensively characterized using biophysical techniques. For both TmArgBP(P235GK) and TmArgBP(P235G) mutants, the occurrence of multiple oligomerization states (monomers, dimers and trimers) was detected. The formation of well-folded monomeric forms for these mutants indicates that the dimerization through C-terminal domain swapping observed in wild-type TmArgBP is driven by conformational restraints imposed by the presence of Pro235 in the hinge region. Molecular dynamics studies corroborate this observation by showing that Gly235 assumes conformational states forbidden for Pro residues in the TmArgBP(P235G) monomer. Unexpectedly, the trimeric forms present: (a) peculiar circular dichroism spectra, (b) a great susceptibility to heating, and (c) the ability to bind the Thioflavin T dye. The present findings clearly demonstrate that single-point mutations have an important impact on the TmArgBP oligomerization process. In a wider context, they also indicate that proteins endowed with an intrinsic propensity to swap have an easy access to states with altered structural and, possibly, functional properties.
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Affiliation(s)
| | - Marilisa Vigorita
- Department of Sciences and Technologies, Università del Sannio, Via Port'arsa 11, Benevento 82100, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy; DiSTABiF, Second University of Naples, Caserta 81100, Italy
| | | | - Sabato D'Auria
- Institute of Food Science, CNR, Via Roma, 64, Avellino, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Department of Sciences and Technologies, Università del Sannio, Via Port'arsa 11, Benevento 82100, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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16
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Cox KS, Tang A, Chen Z, Horton MS, Yan H, Wang XM, Dubey SA, DiStefano DJ, Ettenger A, Fong RH, Doranz BJ, Casimiro DR, Vora KA. Rapid isolation of dengue-neutralizing antibodies from single cell-sorted human antigen-specific memory B-cell cultures. MAbs 2015; 8:129-40. [PMID: 26491897 PMCID: PMC4966506 DOI: 10.1080/19420862.2015.1109757] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Monitoring antigen-specific memory B cells and the antibodies they encode is important for understanding the specificity, breadth and duration of immune response to an infection or vaccination. The antibodies isolated could further help design vaccine antigens for raising relevant protective immune responses. However, developing assays to measure and isolate antigen-specific memory B cells is technically challenging due to the low frequencies of these cells that exist in the circulating blood. Here, we describe a flow cytometry method to identify and isolate dengue envelope-specific memory B cells using a labeled dengue envelope protein. We enumerated dengue-envelope specific memory B cells from a cohort of dengue seropositive donors using this direct flow cytometry assay. A more established and conventional assay, the cultured B ELISPOT, was used as a benchmark comparator. Furthermore, we were able to confirm the single-sorted memory B-cell specificity by culturing B cells and differentiating them into plasma cells using cell lines expressing CD40L. The culture supernatants were assayed for antigen binding and the ability of the antibodies to neutralize the cognate dengue virus. Moreover, we successfully isolated the heavy and light Ig sequences and expressed them as full-length recombinant antibodies to reproduce the activity seen in culture supernatants. Mapping of these antibodies revealed a novel epitope for dengue 2 virus serotype. In conclusion, we established a reproducible methodology to enumerate antigen-specific memory B cells and assay their encoded antibodies for functional characterization.
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Affiliation(s)
- Kara S Cox
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Aimin Tang
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Zhifeng Chen
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Melanie S Horton
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Hao Yan
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Xin-Min Wang
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Sheri A Dubey
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Daniel J DiStefano
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | | | | | | | - Danilo R Casimiro
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
| | - Kalpit A Vora
- a Department of Infectious Diseases and Vaccines-West Point ; PA; Merck Research Laboratories; Merck & Co.; Inc. Kenilworth ; NJ ; USA
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