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Peabody DS, Peabody J, Bradfute SB, Chackerian B. RNA Phage VLP-Based Vaccine Platforms. Pharmaceuticals (Basel) 2021; 14:764. [PMID: 34451861 PMCID: PMC8401894 DOI: 10.3390/ph14080764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles from a variety of RNA bacteriophages have turned out to be useful platforms for delivery of vaccine antigens in a highly immunogenic format. Here we update the current state of development of RNA phage VLPs as platforms for presentation of diverse antigens by genetic, enzymatic, and chemical display methods.
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Affiliation(s)
- David S. Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
| | - Julianne Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
| | - Steven B. Bradfute
- Center for Global Health, Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 505, USA;
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
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2
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de Martín Garrido N, Crone MA, Ramlaul K, Simpson PA, Freemont PS, Aylett CHS. Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids. Mol Microbiol 2019; 113:143-152. [PMID: 31618483 PMCID: PMC7027807 DOI: 10.1111/mmi.14406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 Å and 6 Å respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
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Affiliation(s)
- Natàlia de Martín Garrido
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Michael A Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK.,UK DRI Care Research and Technology Centre, Imperial College London, London, UK
| | - Kailash Ramlaul
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Paul A Simpson
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK.,UK DRI Care Research and Technology Centre, Imperial College London, London, UK.,London BioFoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK
| | - Christopher H S Aylett
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
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Hartman EC, Jakobson CM, Favor AH, Lobba MJ, Álvarez-Benedicto E, Francis MB, Tullman-Ercek D. Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle. Nat Commun 2018; 9:1385. [PMID: 29643335 PMCID: PMC5895741 DOI: 10.1038/s41467-018-03783-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022] Open
Abstract
Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.
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Affiliation(s)
- Emily C Hartman
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Christopher M Jakobson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720-1460, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrew H Favor
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Marco J Lobba
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | | | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720-1460, USA.
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208-3120, USA.
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Lino CA, Caldeira JC, Peabody DS. Display of single-chain variable fragments on bacteriophage MS2 virus-like particles. J Nanobiotechnology 2017; 15:13. [PMID: 28193211 PMCID: PMC5307822 DOI: 10.1186/s12951-016-0240-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/03/2016] [Indexed: 11/11/2022] Open
Abstract
Background Virus-like particles (VLPs) of the RNA bacteriophage MS2 have many potential applications in biotechnology. MS2 VLPs provide a platform for peptide display and affinity selection (i.e. biopanning). They are also under investigation as vehicles for targeted drug delivery, using display of receptor-specific peptides or nucleic acid aptamers to direct their binding to specific cell-surface receptors. However, there are few molecules more suited to the precise targeting and binding of a cellular receptor than antibodies. Results Here we describe a strategy for display of four different functional single-chain variable fragments (scFvs) on the surface of the MS2 VLP. Each scFv is validated both for its presence on the surface of the VLP and for its ability to bind its cognate antigen. Conclusions This work demonstrates the suitability of the MS2 VLP platform to display genetically fused scFvs, allowing for many potential applications of these VLPs and paving the way for future work with libraries of scFvs displayed in a similar manner on the VLP surface. These libraries can then be biopanned and novel scFv binders to targets can be readily discovered.
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Affiliation(s)
- Christopher A Lino
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA.
| | - Jerri C Caldeira
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA
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ElSawy KM. The impact of viral RNA on the association free energies of capsid protein assembly: bacteriophage MS2 as a case study. J Mol Model 2017; 23:47. [DOI: 10.1007/s00894-017-3224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/11/2017] [Indexed: 11/24/2022]
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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Peabody DS, Manifold-Wheeler B, Medford A, Jordan SK, do Carmo Caldeira J, Chackerian B. Immunogenic display of diverse peptides on virus-like particles of RNA phage MS2. J Mol Biol 2008; 380:252-63. [PMID: 18508079 PMCID: PMC2481506 DOI: 10.1016/j.jmb.2008.04.049] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 04/16/2008] [Accepted: 04/22/2008] [Indexed: 11/21/2022]
Abstract
The high level of immunogenicity of peptides displayed in dense repetitive arrays on virus-like particles makes recombinant VLPs promising vaccine carriers. Here, we describe a platform for vaccine development based on the VLPs of RNA bacteriophage MS2. It serves for the engineered display of specific peptide sequences, but will also allow the construction of random peptide libraries from which specific binding activities can be recovered by affinity selection. Peptides representing the V3 loop of HIV gp120 and the ECL2 loop of the HIV coreceptor, CCR5, were inserted into a surface loop of MS2 coat protein. Both insertions disrupted coat VLP assembly, apparently by interfering with protein folding, but these defects were suppressed efficiently by genetically fusing coat protein's two identical polypeptides into a single-chain dimer. The resulting VLPs displayed the V3 and ECL2 peptides on their surfaces where they showed the potent immunogenicity that is the hallmark of VLP-displayed antigens. Experiments with random-sequence peptide libraries show the single-chain dimer to be highly tolerant of six, eight and ten amino acid insertions. MS2 VLPs support the display of a wide diversity of peptides in a highly immunogenic format, and they encapsidate the mRNAs that direct their synthesis, thus establishing the genotype/phenotype linkage necessary for recovery of affinity-selected sequences. The single-chain MS2 VLP therefore unites in a single structural platform the selective power of phage display with the high immunogenicity of VLPs.
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Affiliation(s)
- David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
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Caldeira JC, Peabody DS. Stability and assembly in vitro of bacteriophage PP7 virus-like particles. J Nanobiotechnology 2007; 5:10. [PMID: 18039380 PMCID: PMC2211308 DOI: 10.1186/1477-3155-5-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 11/26/2007] [Indexed: 11/10/2022] Open
Abstract
Background The stability of a virus-like particle (VLP) is an important consideration for its use in nanobiotechnology. The icosahedral capsid of the RNA bacteriophage PP7 is cross-linked by disulfide bonds between coat protein dimers at its 5-fold and quasi-6-fold symmetry axes. This work determined the effects of these disulfides on the VLP's thermal stability. Results Measurements of the thermal denaturation behavior of PP7 VLPs in the presence and absence of a reducing agent show that disulfide cross-links substantially stabilize them against thermal denaturation. Although dimers in the capsid are linked to one another by disulfides, the two subunits of dimers themselves are held together only by non-covalent interactions. In an effort to confer even greater stability a new cross-link was introduced by genetically fusing two coat protein monomers, thus producing a "single-chain dimer" that assembles normally into a completely cross-linked VLP. However, subunit fusion failed to increase the thermal stability of the particles, even though it stabilized the isolated dimer. As a step toward gaining control of the internal composition of the capsid, conditions that promote the assembly of PP7 coat protein dimers into virus-like particles in vitro were established. Conclusion The presence of inter-dimer disulfide bonds greatly stabilizes the PP7 virus-like particle against thermal denaturation. Covalently cross-linking the subunits of the dimers themselves by genetically fusing them through a dipeptide linker sequence, offers no further stabilization of the VLP, although it does stabilize the dimer. PP7 capsids readily assemble in vitro in a reaction that requires RNA.
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Affiliation(s)
- Jerri C Caldeira
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM87131, USA.
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Maier HJ, Kashiwagi T, Hara K, Brownlee GG. Differential role of the influenza A virus polymerase PA subunit for vRNA and cRNA promoter binding. Virology 2007; 370:194-204. [PMID: 17905403 DOI: 10.1016/j.virol.2007.08.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 08/20/2007] [Accepted: 08/27/2007] [Indexed: 11/16/2022]
Abstract
The RNA polymerase of influenza A virus is a heterotrimeric complex of PB1, PB2 and PA subunits that is required for transcription and replication of the viral genome. Here, we demonstrate a differential requirement of the PA subunit for binding to the vRNA and cRNA promoters--specifically, PA is more important for binding to the cRNA than the vRNA promoter. Furthermore, five point mutations were identified in the L163-I178 region of PA, which resulted in an inhibition of polymerase activity when provided with a cRNA compared to vRNA promoter. Cross-linking studies suggested that this inhibition was due to a reduction in promoter binding of the mutant polymerases to the cRNA promoter. We conclude that the L163-I178 region of PA is directly or indirectly involved in cRNA promoter binding and suggest a novel function for PA in modulating promoter binding.
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Affiliation(s)
- Helena J Maier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Lima SMB, Vaz ACQ, Souza TLF, Peabody DS, Silva JL, Oliveira AC. Dissecting the role of protein-protein and protein-nucleic acid interactions in MS2 bacteriophage stability. FEBS J 2006; 273:1463-75. [PMID: 16689932 DOI: 10.1111/j.1742-4658.2006.05167.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate the role of protein-protein and protein-nucleic acid interactions in virus assembly, we compared the stabilities of native bacteriophage MS2, virus-like particles (VLPs) containing nonviral RNAs, and an assembly-defective coat protein mutant (dlFG) and its single-chain variant (sc-dlFG). Physical (high pressure) and chemical (urea and guanidine hydrochloride) agents were used to promote virus disassembly and protein denaturation, and the changes in virus and protein structure were monitored by measuring tryptophan intrinsic fluorescence, bis-ANS probe fluorescence, and light scattering. We found that VLPs dissociate into capsid proteins that remain folded and more stable than the proteins dissociated from authentic particles. The proposed model is that the capsid disassembles but the protein remains bound to the heterologous RNA encased by VLPs. The dlFG dimerizes correctly, but fails to assemble into capsids, because it lacks the 15-amino acid FG loop involved in inter-dimer interactions at the viral fivefold and quasi-sixfold axes. This protein was very unstable and, when compared with the dissociation/denaturation of the VLPs and the wild-type virus, it was much more susceptible to chemical and physical perturbation. Genetic fusion of the two subunits of the dimer in the single-chain dimer sc-dlFG stabilized the protein, as did the presence of 34-bp poly(GC) DNA. These studies reveal mechanisms by which interactions in the capsid lattice can be sufficiently stable and specific to ensure assembly, and they shed light on the processes that lead to the formation of infectious viral particles.
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Affiliation(s)
- Sheila M B Lima
- Programa de Biologia Estrutural and Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Brazil
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Hobson D, Uhlenbeck OC. Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots. J Mol Biol 2005; 356:613-24. [PMID: 16380130 DOI: 10.1016/j.jmb.2005.11.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 11/10/2005] [Accepted: 11/14/2005] [Indexed: 10/25/2022]
Abstract
The co-crystal structure of the MS2 coat protein dimer with its RNA operator reveals eight amino acid side-chains contacting seven of the RNA phosphates. These eight amino acids and five nearby control positions were individually changed to an alanine residue and the binding affinities of the mutant proteins to the RNA were determined. In general, the data agreed well with the crystal structure and previous RNA modification data. Interestingly, amino acid residues that are energetically most important for complex formation cluster in the middle of the RNA binding interface, forming thermodynamic hot spots, and are surrounded by energetically less relevant amino acids. In order to evaluate whether or not a given alanine mutation causes a global change in the RNA-protein interface, the affinities of the mutant proteins to RNAs containing one of 14 backbone modifications spanning the entire interface were determined. In three of six protein mutations tested, thermodynamic coupling between the site of the mutation and RNA groups that can be even more than 16 A away was detected. This suggests that, in some cases, the mutation may subtly alter the entire protein-RNA interface.
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Affiliation(s)
- Dagmar Hobson
- Department of Biochemistry, Molecular Biology, Cell Biology, Northwestern University 2205 Tech Drive, Hogan 2-100, Evanston, IL 60208, USA
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Lima SMB, Peabody DS, Silva JL, De Oliveira AC. Mutations in the hydrophobic core and in the protein-RNA interface affect the packing and stability of icosahedral viruses. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1432-1033.2003.03911.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Peabody DS. A Viral Platform for Chemical Modification and Multivalent Display. J Nanobiotechnology 2003; 1:5. [PMID: 12890286 PMCID: PMC169181 DOI: 10.1186/1477-3155-1-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 07/15/2003] [Indexed: 11/10/2022] Open
Abstract
The ability to chemically modify the surfaces of viruses and virus-like particles makes it possible to confer properties that make them potentially useful in biotechnology, nanotechnology and molecular electronics applications. RNA phages (e.g. MS2) have characteristics that make them suitable scaffolds to which a variety of substances could be chemically attached in definite geometric patterns. To provide for specific chemical modification of MS2's outer surface, cysteine residues were substituted for several amino acids present on the surface of the wild-type virus particle. Some substitutions resulted in coat protein folding or stability defects, but one allowed the production of an otherwise normal virus-like particle with an accessible sulfhydryl on its surface.
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Affiliation(s)
- David S Peabody
- Department of Molecular Genetics and Microbiology and the Cancer Research and Treatment Center University of New Mexico School of Medicine Albuquerque, New Mexico, USA 87131.
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Yang Y, Declerck N, Manival X, Aymerich S, Kochoyan M. Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT. EMBO J 2002; 21:1987-97. [PMID: 11953318 PMCID: PMC125969 DOI: 10.1093/emboj/21.8.1987] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
LicT is a bacterial regulatory protein able to prevent the premature arrest of transcription. When activated, LicT binds to a 29 base RNA hairpin overlapping a terminator located in the 5' mRNA leader region of the target genes. We have determined the solution structure of the LicT RNA-binding domain (CAT) in complex with its ribonucleic antiterminator (RAT) target by NMR spectroscopy (PDB 1L1C). CAT is a beta-stranded homodimer that undergoes no important conformational changes upon complex formation. It interacts, through mostly hydrophobic and stacking interactions, with the distorted minor groove of the hairpin stem that is interrupted by two asymmetric internal loops. Although different in sequence, these loops share sufficient structural analogy to be recognized similarly by symmetry-related elements of the protein dimer, leading to a quasi- symmetric structure reminiscent of that observed with dimeric transcription regulators bound to palindromic DNA. Sequence analysis suggests that this RNA- binding mode, where the RAT strands are clamped by the CAT dimer, is conserved in homologous systems.
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Affiliation(s)
- Yinshan Yang
- Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U554, Université de Montpellier I, 29 rue de Navacelles, F-34090 Montpellier, France
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Abstract
The interaction between the MS2 bacteriophage coat protein homodimer and its cognate RNA hairpin is facilitated by 21 different RNA-protein contacts. In one of these contacts, the 2'-hydroxyl group at ribose -5 of the RNA acts as a hydrogen bond donor to Glu63 in one subunit of the protein. Previous experiments showed that substitution of ribose -5 with deoxyribose resulted in a 24-fold decrease in binding affinity between RNA and protein. Using a protein where the two MS2 monomers were fused to increase stability, the contribution of this contact to the overall binding affinity was investigated by site-directed mutagenesis. When Glu63 was substituted with glutamine, aspartate, or alanine, the binding affinity of the hairpin for the protein was weakened by 12 to 100-fold, similar to that observed with deoxyribose at position -5. However, the specificity of the three mutant proteins for RNAs with various modifications at the 2'-position of ribose -5 differed dramatically. While the Glu63Asp protein resembled the wild-type protein in preferring the 2'-hydroxyl group over a proton or a bulky 2'-substituent, both the Glu63Ala and Glu63Gln proteins preferred bulky 2'-substituents over the 2'-hydroxyl group by more than 100-fold. These experiments emphasize the ease with which the specificity of a protein-nucleic acid interaction can be changed at thermodynamically important sites.
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Affiliation(s)
- D Dertinger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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Powell AJ, Peabody DS. Asymmetric interactions in the adenosine-binding pockets of the MS2 coat protein dimer. BMC Mol Biol 2001; 2:6. [PMID: 11504563 PMCID: PMC37355 DOI: 10.1186/1471-2199-2-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2001] [Accepted: 07/25/2001] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The X-ray structure of the MS2 coat protein-operator RNA complex reveals the existence of quasi-synmetric interactions of adenosines -4 and -10 in pockets formed on different subunits of the coat protein dimer. Both pockets utilize the same five amino acid residues, namely Val29, Thr45, Ser47, Thr59, and Lys61. We call these sites the adenosine-binding pockets. RESULTS We present here a heterodimer complementation analysis of the contributions of individual A-pocket amino acids to the binding of A-4 and A-10 in different halves of the dimer. Various substitutions of A-pocket residues were introduced into one half of single-chain coat protein heterodimers where they were tested for their abilities to complement Y85H or T91I substitutions (defects in the A-4 and A-10 half-sites, respectively) present in the other dimer half. CONCLUSIONS These experiments provide functional tests of interactions predicted from structural analyses, demonstrating the importance of certain amino acid-nucleotide contacts observed in the crystal structure, and showing that others make little or no contribution to the stability of the complex. In summary, Val29 and Lys61 form important stabilizing interactions with both A-4 and A-10. Meanwhile, Ser47 and Thr59 interact primarily with A-10. The important interactions with Thr45 are restricted to A-4.
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Affiliation(s)
- Amy J Powell
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico, 87131, USA
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico, 87131, USA
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