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Mizrahi I, Bruinsma R, Rudnick J. Packaging contests between viral RNA molecules and kinetic selectivity. PLoS Comput Biol 2022; 18:e1009913. [PMID: 35363785 PMCID: PMC9022832 DOI: 10.1371/journal.pcbi.1009913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/21/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules by packaging signals during the nucleation stage of the assembly of small RNA viruses. The effects of the RNA secondary structure and folding geometry of the packaging signals on the assembly activation energy barrier are encoded by a pair of characteristics: the wrapping number and the maximum ladder distance. Kinetic selection is found to be optimal when assembly takes place under conditions of supersaturation and also when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. As a function of the height of the activation energy barrier, there is a form of order-disorder transition such that for sufficiently low activation energy barriers, kinetic selectivity is erased by entropic effects associated with the number of assembly pathways.
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Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- * E-mail:
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
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Peabody DS. Subunit fusion confers tolerance to peptide insertions in a virus coat protein. Arch Biochem Biophys 1997; 347:85-92. [PMID: 9344468 DOI: 10.1006/abbi.1997.0312] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An octapeptide sequence called Flag was inserted into the bacteriophage MS2 coat protein at two different locations and its effects on protein folding and virus assembly were determined. Assays of the translational repressor and capsid assembly functions of the recombinants show that when the peptide is inserted at its N-terminus coat protein folds properly into the form that binds RNA (i.e., the dimer), but is defective for capsid assembly. On the other hand, a recombinant protein which is expected to display the Flag insertion as a surface loop does not fold correctly and, as a consequence, is proteolytically degraded. Genetic fusion of the two subunits of the coat dimer results in a protein considerably more tolerant of these structural perturbations and mostly corrects the defects accompanying Flag peptide insertion. Increased resistance of the single-chain coat protein to urea denaturation indicates that the fused dimer is substantially more stable than wild type. Covalent joining of subunits of oligomers probably represents a general strategy for engineering increased protein stability.
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Affiliation(s)
- D S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine and, Albuquerque, New Mexico, 87131, USA
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Valegârd K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol 1997; 270:724-38. [PMID: 9245600 DOI: 10.1006/jmbi.1997.1144] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.
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Affiliation(s)
- K Valegârd
- Department of Molecular Biology, Uppsala University, Uppsala, Box 590, S-751 24, Sweden
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Stonehouse NJ, Stockley PG. Effects of amino acid substitution on the thermal stability of MS2 capsids lacking genomic RNA. FEBS Lett 1993; 334:355-9. [PMID: 8243647 DOI: 10.1016/0014-5793(93)80711-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The thermal stability of capsids of the bacteriophage MS2, lacking genomic RNA, has been investigated using electron microscopy. Coat protein mutants with amino acid substitutions at residues involved in making contracts at both inter-molecular interfaces and within the coat protein submit are also capable of forming 'empty' capsids of the same size and symmetry as the wild-type protein. Mutations have been characterised which are neutral, deleterious or advantageous in terms of thermal stability. In some cases, the results can be rationalised by reference to the recently refined X-ray crystal structure of the wild-type particle.
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Witherell GW, Gott JM, Uhlenbeck OC. Specific interaction between RNA phage coat proteins and RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1991; 40:185-220. [PMID: 2031083 DOI: 10.1016/s0079-6603(08)60842-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- G W Witherell
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309
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Valegård K, Liljas L, Fridborg K, Unge T. The three-dimensional structure of the bacterial virus MS2. Nature 1990; 345:36-41. [PMID: 2330049 DOI: 10.1038/345036a0] [Citation(s) in RCA: 293] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The structure of the icosahedral bacteriophage MS2 has been determined to 3.3 A resolution by X-ray crystallography. The phase determination involved both molecular replacement at low resolution using a known structure and heavy-atom substitution. The coat protein has no structural similarity to that of any other known RNA virus.
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Affiliation(s)
- K Valegård
- Department of Molecular Biology, Uppsala University, Sweden
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Beckett D, Uhlenbeck OC. Ribonucleoprotein complexes of R17 coat protein and a translational operator analog. J Mol Biol 1988; 204:927-38. [PMID: 3221400 DOI: 10.1016/0022-2836(88)90052-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The coat protein of the simple spherical (triangulation no. T = 3) RNA coliphage R17 protects the genomic RNA in the virus particle and acts as a translational repressor of the phage-encoded replicase gene. It has been suggested that these two functions are related and that the translational repression complex serves as a nucleation complex for subsequent assembly of the bacteriophage. We have used a translational operation fragment to examine the relationship between formation of the translational repression complex and the assembly of the protein into T = 3 capsids. In vitro analysis of the aggregation properties of R17 coat protein reveals that binding of the translational operator fragment to the protein dimer triggers polymerization of the protein into T = 3 capsids of well-defined composition. The data further implicate the translational operator in nucleation of assembly and suggest a possible physical-chemical basis of the nucleation step.
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Affiliation(s)
- D Beckett
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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Abstract
Novel capsomeric complexes, pentamers and hexamers were detected as chemical entities in phage Q beta. Both were composed of identical protein subunits and stabilized by intermolecular disulphide bonds. Their numbers per particle were about 12 for pentamers and about 20 for hexamers--consistent with theoretical expectation from the quasi-equivalent packing of 180 identical subunits in a coat protein shell.
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Berzin V, Borisova GP, Cielens I, Gribanov VA, Jansone I, Rosenthal G, Gren EJ. The regulatory region of MS2 phage RNA replicase cistron. Functional activity of individual MS2 RNA fragments. J Mol Biol 1978; 119:101-31. [PMID: 633365 DOI: 10.1016/0022-2836(78)90272-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Jamjoom GA, Naso RB, Arlinghaus RB. Selective decrease in the rate of cleavage of an intracellular precursor to Rauscher leukemia virus p30 by treatment of infected cells with actinomycin D. J Virol 1976; 19:1054-72. [PMID: 1085824 PMCID: PMC354946 DOI: 10.1128/jvi.19.3.1054-1072.1976] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cleavage of an intracellular 67,000- to 70,000-dalton precursor, termed Pr4 to Rauscher leukemia virus (RLV) p30 protein proceeded at a slower rate when virus-producing cells were treated with actinomycin D (AMD). Treatment with AMD also caused a slight accumulation of Pr4 in purified early virus particles produced by a cell line which usually produces virions that contain little Pr4. The cleavage of other intracellular viral precursor polypeptides was not affected by treatment with AMD. Treatment of infected cells with cycloheximide, on the other hand, allowed the cleavage of Pr4 to proceed at the usual rate for a short period of time before further cleavage was drastically slowed or prevented. The cleavage of several other viral precursor polypeptides was also inhibited by treatment with cycloheximide. Different lines of evidence suggest that the mechanism of action of AMD is not due to a possible indirect effect on protein synthesis. Thus, the rate of cleavage of Pr4 was not affected by the length of pretreatment with AMD between 1 to 8 h. In addition, the combined effect of AMD and cycloheximide, at their maximal inhibitory concentrations, was greater than the effect of either drug alone, indicating the involvement of two at least partially different mechanisms in the action of AMD and cycloheximide. Furthermore, AMD did not affect the pulse labeling of viral precursor polypeptides. These results suggest that the interaction with viral RNA, whose production is inhibited by AMD, accelerates the cleavage of Pr4 to p30 during virus assembly. A hypothetical model is presented to illustrate th possible advantages of having a step in virus assembly in which genomic RNA interacts with a precursor to capsid proteins before the cleavage of that precursor.
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Thomas GJ, Prescott B, McDonald-Ordzie PE, Hartman KA. Studies of virus structure by laser-Raman spectroscopy. II. MS2 phage, MS2 capsids and MS2 RNA in aqueous solutions. J Mol Biol 1976; 102:103-24. [PMID: 1271459 DOI: 10.1016/0022-2836(76)90076-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Hsu CH, Sehgal OP, Pickett EE. Stabilizing effect of divalent metal ions on virions of southern bean mosaic virus. Virology 1976; 69:587-95. [PMID: 3878 DOI: 10.1016/0042-6822(76)90487-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zagórska L, Chroboczek J, Zagórski W. Template activity of complexes formed between bacteriophage f2 RNA and coat protein. J Virol 1975; 15:509-14. [PMID: 1113377 PMCID: PMC354487 DOI: 10.1128/jvi.15.3.509-514.1975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Formation of complexes between f2 RNA polymerase cistron was partially inhibited, some RNA and coat protein was studied using salt conditions which are optimum for phage protein synthesis. In this ionic environment, coat protein precipitation can be prevented by sulfhydryl group-protecting agents. Complexes formed at different protein-RNA input molar ratios were isolated and tested for template activity in an in vitro protein synthesizing system. Simultaneously, the number of protein molecules bound per RNA strand in such complexes was measured by the membrane (Millipore) filtration technique. Under conditions in which translation of the RNA strands were complexed with six molecules of coat protein, whereas some remained unbound. Strong inhibition of the translation of the RNA polymerase cistron was observed when each of the RNA strands present in the mixture was associated with six molecules of coat protein.
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Korant BD, Lonberg-Holm K, Yin FH, Noble-Harvey J. Fractionation of biologically active and inactive populations of human rhinovirus type 2. Virology 1975; 63:384-94. [PMID: 163526 DOI: 10.1016/0042-6822(75)90311-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Adolph KW, Butler PJ. Studies on the assembly of a spherical plant virus. I. States of aggregation of the isolated protein. J Mol Biol 1974; 88:327-41. [PMID: 4452998 DOI: 10.1016/0022-2836(74)90485-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Kaper JM. Arrangement and identification of simple isometric viruses according to their dominating stabilizing interactions. Virology 1973; 55:299-304. [PMID: 4728830 DOI: 10.1016/s0042-6822(73)81035-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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O'Callaghan R, Bradley R, Paranchych W. Controlled alterations in the physical and biological properties of R17 bacteriophage induced by gunaidine hydrochloride. Virology 1973; 54:476-94. [PMID: 4125252 DOI: 10.1016/0042-6822(73)90158-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Chroboczek J, Pietrzak M, Zagórski W. Specificity of formation of complexes between coat protein and bacteriophage f2 RNA. J Virol 1973; 12:230-40. [PMID: 4201187 PMCID: PMC356617 DOI: 10.1128/jvi.12.2.230-240.1973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The specificity of formation of phage f2 RNA-protein complexes was studied. Complex I contains up to 8 mol of coat protein per 1 mol of RNA. Its formation proceeds equally well in medium (i) without magnesium ions, (ii) containing magnesium ions, (iii) containing 4 mM EDTA, and (iv) at temperatures from 0 to 45 C. Complex II contains up to 200 mol of coat protein per 1 mol of RNA. Its formation is inhibited by the presence of magnesium ions in medium. Formaldehyde- or methoxyamine-treated f2 RNA in which only exposed bases were modified showed a normal pattern of complex II formation, whereas formation of complex I was inhibited or abolished. We conclude that complex I formation involves the interaction between coat protein and specific region of exposed bases in RNA. A possible site of attachment of coat protein is discussed.
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Zipper P, Schubert D, Vogt J. Small-angle x-ray scattering studies on virus-like protein particles derived from bacteriophage fr. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 36:301-10. [PMID: 4730957 DOI: 10.1111/j.1432-1033.1973.tb02914.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Matthews KS, Cole RD. Effects of chemical modification of f2 viral coat protein on its shell-forming activity. J Mol Biol 1972; 65:17-23. [PMID: 4553256 DOI: 10.1016/0022-2836(72)90488-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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