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Webby MN, Herr N, Bulloch EMM, Schmitz M, Keown JR, Goldstone DC, Kingston RL. Structural Analysis of the Menangle Virus P Protein Reveals a Soft Boundary between Ordered and Disordered Regions. Viruses 2021; 13:1737. [PMID: 34578318 DOI: 10.3390/v13091737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022] Open
Abstract
The paramyxoviral phosphoprotein (P protein) is the non-catalytic subunit of the viral RNA polymerase, and coordinates many of the molecular interactions required for RNA synthesis. All paramyxoviral P proteins oligomerize via a centrally located coiled-coil that is connected to a downstream binding domain by a dynamic linker. The C-terminal region of the P protein coordinates interactions between the catalytic subunit of the polymerase, and the viral nucleocapsid housing the genomic RNA. The inherent flexibility of the linker is believed to facilitate polymerase translocation. Here we report biophysical and structural characterization of the C-terminal region of the P protein from Menangle virus (MenV), a bat-borne paramyxovirus with zoonotic potential. The MenV P protein is tetrameric but can dissociate into dimers at sub-micromolar protein concentrations. The linker is globally disordered and can be modeled effectively as a worm-like chain. However, NMR analysis suggests very weak local preferences for alpha-helical and extended beta conformation exist within the linker. At the interface between the disordered linker and the structured C-terminal binding domain, a gradual disorder-to-order transition occurs, with X-ray crystallographic analysis revealing a dynamic interfacial structure that wraps the surface of the binding domain.
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Ding F, Hsu SH, Wu DH, Chiang WY. Drug Release from Interpenetrating Polymer Networks Based on Poly(ethylene glycol) Methyl Ether Acrylate and Gelatin. Journal of Biomaterials Science, Polymer Edition 2012; 20:605-18. [DOI: 10.1163/156856209x426420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Frank Ding
- a Department of Chemical Engineering, Tatung University, No. 40 Chunshan N. Road, Taipei, Taiwan
| | - S.-H. Hsu
- b Department of Chemical Engineering, Tatung University, No. 40 Chunshan N. Road, Taipei, Taiwan
| | - D.-H. Wu
- c Department of Chemical Engineering, Tatung University, No. 40 Chunshan N. Road, Taipei, Taiwan
| | - W.-Y. Chiang
- d Department of Chemical Engineering, Tatung University, No. 40 Chunshan N. Road, Taipei, Taiwan
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Bailey GD, Hyun JK, Mitra AK, Kingston RL. Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly. Structure 2009; 17:737-48. [PMID: 19446529 DOI: 10.1016/j.str.2009.03.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/07/2009] [Indexed: 11/19/2022]
Abstract
In mature retroviral particles, the capsid protein (CA) forms a shell encasing the viral replication complex. Human immunodeficiency virus (HIV) CA dimerizes in solution, through its C-terminal domain (CTD), and this interaction is important for capsid assembly. In contrast, other retroviral capsid proteins, including that of Rous sarcoma virus (RSV), do not dimerize with measurable affinity. Here we show, using X-ray crystallography and other biophysical methods, that acidification causes RSV CA to dimerize in a fashion analogous to HIV CA, and that this drives capsid assembly in vitro. A pair of aspartic acid residues, located within the CTD dimer interface, explains why dimerization is linked to proton binding. Our results show that despite overarching structural similarities, the intermolecular forces responsible for forming and stabilizing the retroviral capsid differ markedly across retroviral genera. Our data further suggest that proton binding may regulate RSV capsid assembly, or modulate stability of the assembled capsid.
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Affiliation(s)
- Graham D Bailey
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Abstract
The biological function of many proteins involves reversible interactions with other proteins, nucleic acids, or other non-protein ligands. Such interactions play many different roles in a wide range of cellular processes. A few examples are: (1) storing or transporting key metabolites (e.g., O(2) storage by myoglobin); (2) forming and maintaining the quaternary structure of multi-subunit enzymes; (3) specific binding and recognition events (antigen-antibody, hormone-receptor, transcription factor-promoter); and (4) self-assembly of large structures (microtubules, chromatin). Thus, the quantitative characterization of such interactions represents an important part of understanding the function of such proteins and their role in these cellular events. This unit sets the tone for the rest of the chapter, and gives important information necessary to understand some of the topics that will be covered in future supplements, such as sedimentation equilibrium (analytical and micro-preparative), surface plasmon resonance (SPR), size-exclusion chromatography (SEC) with on-line light scattering, and chemical cross-linking.
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Affiliation(s)
- J S Philo
- Alliance Protein Laboratories, Thousand Oaks, California, USA
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Beckett D. Reduced-scale large-zone analytical gel-filtration chromatography for measurement of protein association equilibria. Curr Protoc Protein Sci 2008; Chapter 20:Unit20.5. [PMID: 18429160 DOI: 10.1002/0471140864.ps2005s18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The proteasome plays a central role in eukaryotic cells since it is responsible for the degradation of specific proteins involved in a large range of cellular processes. Analysis of proteasome mechanisms of action, or in vitro reconstitution, or dissection of the complex biological pathways in which it partakes, requires a reliable source of pure active proteasome. Although the biologically relevant form of the proteasome is usually considered to be the 26S proteasome, this unit describes different methods for purification and study of both 26S and 20S proteasomes from Saccharomyces cerevisiae cells.
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Affiliation(s)
- D Beckett
- University of Maryland, College Park, USA
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Pazehoski KO, Collins TC, Boyle RJ, Jensen-Seaman MI, Dameron CT. Stalking metal-linked dimers. J Inorg Biochem 2008; 102:522-31. [DOI: 10.1016/j.jinorgbio.2007.10.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/02/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
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Chen B, Doucleff M, Wemmer DE, De Carlo S, Huang HH, Nogales E, Hoover TR, Kondrashkina E, Guo L, Nixon BT. ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54. Structure 2007; 15:429-40. [PMID: 17437715 PMCID: PMC2680074 DOI: 10.1016/j.str.2007.02.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 11/01/2006] [Accepted: 02/22/2007] [Indexed: 11/28/2022]
Abstract
Transcription initiation by the sigma54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeF(x) (ground-state mimics), ADP-AlF(x) (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeF(x) state, and from the ADP-AlF(x) state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to sigma54, with ADP-AlF(x) having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and sigma54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.
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Affiliation(s)
- Baoyu Chen
- Integrative Biosciences Graduate Degree Program – Chemical Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michaeleen Doucleff
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sacha De Carlo
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hector H. Huang
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Elena Kondrashkina
- BioCAT at APS/Argonne National Lab, Illinois Institute of Technology, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Liang Guo
- BioCAT at APS/Argonne National Lab, Illinois Institute of Technology, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Affiliation(s)
- Gary K Ackers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Abstract
Small zone gel filtration chromatography can be used for qualitative and quantitative analysis of protein interactions and aggregation phenomena. The technique is fast, accessible to most laboratories, and can be combined with computer simulation to extract quantitative information from experimental data. The programs KRUNCH and SCIMZ will be furnished on written request to the authors.
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Affiliation(s)
- R Raffen
- Biosciences Division, Argonne National Laboratory, Illinois 60439, USA
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Drohat AC, Nenortas E, Beckett D, Weber DJ. Oligomerization state of S100B at nanomolar concentration determined by large-zone analytical gel filtration chromatography. Protein Sci 1997; 6:1577-82. [PMID: 9232658 PMCID: PMC2143756 DOI: 10.1002/pro.5560060721] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
S100B is a Ca(2+)-binding protein known to be a non-covalently associated dimer, S100B(beta beta), at high concentrations (0.2-3.0 mM) under reducing conditions. The solution structure of apo-S100B (beta beta) shows that the subunits associate in an antiparallel manner to form a tightly packed hydrophobic core at the dimer interface involving six of eight helices and the C-terminal loop (Drohat AC, Amburgey JC, Abildgaard F, Starich MR, Baldisseri D, Weber DJ. 1996. Solution structure of rat apo-S100B (beta beta) as determined by NMR spectroscopy. Biochemistry 35:11577-11588). The C-terminal loop, however, is also known to participate in the binding of S100B to target proteins, so its participation in the dimer interface raises questions as to the physiological relevance of dimeric S100B (beta beta). Therefore, we investigated the oligomerization state of S100B at low concentrations (1-10,000 nM) using large-zone analytical gel filtration chromatography with 35S-labeled S100B. We found that S100B exists (> 99%) as a non-covalently associated dimer, S100B (beta beta), at 1 nM subunit concentration (500 pM dimer) in the presence or absence of saturating levels of Ca2+, which implies a dissociation constant in the picomolar range or lower. These results demonstrate for the first time that in reducing environments and at physiological concentrations, S100B exists as dimeric S100B (beta beta) in the presence or absence of Ca2+, and that the non-covalent dimer is most likely the form of S100B presented to target proteins.
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Affiliation(s)
- A C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore 21201, USA
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Doyle ML, Hensley P. Experimental Dissection of Protein-Protein Interactions in Solution. Elsevier; 1997. pp. 279-337. [DOI: 10.1016/s1569-2558(08)60112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Affiliation(s)
- Howard G. Barth
- DuPont Company, Central Research and Development, Experimental Station, P.O. Box 80228, Wilmington, Delaware 19880-0228, and Rockland Technologies, Inc., 538 First State Boulevard, Newport, Delaware 19804
| | - Barry E. Boyes
- DuPont Company, Central Research and Development, Experimental Station, P.O. Box 80228, Wilmington, Delaware 19880-0228, and Rockland Technologies, Inc., 538 First State Boulevard, Newport, Delaware 19804
| | - Christian Jackson
- DuPont Company, Central Research and Development, Experimental Station, P.O. Box 80228, Wilmington, Delaware 19880-0228, and Rockland Technologies, Inc., 538 First State Boulevard, Newport, Delaware 19804
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Steiner RF, Juminaga D, Albaugh S, Washington H. A comparison of the properties of the binary and ternary complexes formed by calmodulin and troponin C with two regulatory peptides of phosphorylase kinase. Biophys Chem 1996; 59:277-88. [PMID: 8672716 DOI: 10.1016/0301-4622(95)00125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulatory peptides Phk13 (301-327) and a modified form of Phk5 (342-367) from the gamma-subunit of glycogen phosphorylase kinase form binary and ternary complexes with both calmodulin and the related muscle protein troponin C. Neither peptide appears to affect to a major extent a fluorescent probe linked to Cys-27 of wheat germ calmodulin. Phk13, but not Phk5, significantly modifies the properties of a probe joined to Cys-98 of troponin C. A comparison by means of radiationless energy transfer of the average separations of Trp-16 of Phk5 from specific groups in the N- and C-terminal halves of calmodulin and troponin C indicate significant changes upon going from the 1:1 binary complex to the 1:1:1 ternary complex with Phk13. A comparison of the effects of addition of Phk13 to calmodulin, troponin C, and their binary complexes with Phk5 suggests that the conformation of Phk13 is similar in the binary and ternary complexes.
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Affiliation(s)
- R F Steiner
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore 21228, USA
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Malhotra OP, Prabhakar P, Kayastha AM. Application of short column gel permeation in the study of protein-protein interactions. J Biochem Biophys Methods 1996; 31:23-30. [PMID: 8926335 DOI: 10.1016/0165-022x(95)00025-m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A simple and rapid procedure based on the gel filtration principle is described together with its applicability to the study of protein-protein interactions including subunit-subunit and enzyme-enzyme interactions. Using this procedure, it is shown that phosphoglycerate kinase (PGK) and glyceraldehyde-3-phosphate dehydrogenase (GPDH) interact with a stoichiometry of one PGK molecule combining with one monomeric subunit of GPDH. This interaction has been observed with both enzymes being from the same, as well as from different, species. The Kd values for rabbit muscle PGK and porcine muscle GPDH complex and that for the rabbit muscle PGK and yeast GPDH complex are found to be (4.5 +/- 2.0) x 10(-7) M and (6.5 +/- 1.7) x 10(-7) M, respectively. The specificity of bienzyme association is stronger when enzymes are from the same species than when they are from different species.
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Affiliation(s)
- O P Malhotra
- Department of Chemistry, Banaras Hindu University, Varanasi, India
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