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. 1999 Mar;76(3):1537–1551. doi: 10.1016/S0006-3495(99)77313-3

The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.

T C Mou 1, C W Gray 1, D M Gray 1
PMCID: PMC1300130  PMID: 10049334

Abstract

The Ff gene 5 protein (g5p) is considered to be a nonspecific single-stranded DNA binding protein, because it binds cooperatively to and saturates the Ff bacteriophage single-stranded DNA genome and other single-stranded polynucleotides. However, the binding affinity Komega (the intrinsic binding constant times a cooperativity factor) differs by over an order of magnitude for binding to single-stranded polynucleotides such as poly[d(A)] and poly[d(C)]. A polynucleotide that is more stacked, like poly[d(A)], binds more weakly than one that is less stacked, like poly[d(C)]. To test the hypothesis that DNA base stacking, a nearest-neighbor property, is involved in the binding affinity of the Ff g5p for different DNA sequences, Komega values were determined as a function of NaCl concentration for binding to six synthetic sequences 48 nucleotides in length: dA48, dC48, d(AAC)16, d(ACC)16, d(AACC)12, and d(AAACC)9A3. The binding affinities of the protein for these sequences were indeed found to be related to the nearest-neighbor compositions of the sequences, rather than to simple base compositions. That is, the g5p binding site, which is spanned by four nucleotides, discriminates among these sequences on the basis of the relative numbers of nearest neighbors (AA, CC, and AC plus CA) in the sequence. The results support the hypothesis that the extent of base stacking/unstacking of the free, nonbound ssDNA plays an important role in the binding affinity of the Ff gene 5 protein.

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Selected References

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  1. Alberts B., Frey L., Delius H. Isolation and characterization of gene 5 protein of filamentous bacterial viruses. J Mol Biol. 1972 Jul 14;68(1):139–152. doi: 10.1016/0022-2836(72)90269-0. [DOI] [PubMed] [Google Scholar]
  2. Allison T. J., Wood T. C., Briercheck D. M., Rastinejad F., Richardson J. P., Rule G. S. Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat Struct Biol. 1998 May;5(5):352–356. doi: 10.1038/nsb0598-352. [DOI] [PubMed] [Google Scholar]
  3. Alma N. C., Harmsen B. J., de Jong E. A., Ven J., Hilbers C. W. Fluorescence studies of the complex formation between the gene 5 protein of bacteriophage M13 and polynucleotides. J Mol Biol. 1983 Jan 5;163(1):47–62. doi: 10.1016/0022-2836(83)90029-3. [DOI] [PubMed] [Google Scholar]
  4. Alma N. C., Harmsen B. J., van Boom J. H., van der Marel G., Hilbers C. W. A 500-MHz proton nuclear magnetic resonance study of the structure and structural alterations of gene-5 protein-oligo(deoxyadenylic acid) complexes. Biochemistry. 1983 Apr 26;22(9):2104–2115. doi: 10.1021/bi00278a010. [DOI] [PubMed] [Google Scholar]
  5. Antao V. P., Gray D. M. CD spectral comparisons of the acid-induced structures of poly[d(A)], poly[r(A)], poly[d(C)], and poly[r(C)]. J Biomol Struct Dyn. 1993 Apr;10(5):819–839. doi: 10.1080/07391102.1993.10508677. [DOI] [PubMed] [Google Scholar]
  6. Bauer M., Smith G. P. Filamentous phage morphogenetic signal sequence and orientation of DNA in the virion and gene-V protein complex. Virology. 1988 Nov;167(1):166–175. doi: 10.1016/0042-6822(88)90066-9. [DOI] [PubMed] [Google Scholar]
  7. Bochkarev A., Pfuetzner R. A., Edwards A. M., Frappier L. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature. 1997 Jan 9;385(6612):176–181. doi: 10.1038/385176a0. [DOI] [PubMed] [Google Scholar]
  8. Briercheck D. M., Wood T. C., Allison T. J., Richardson J. P., Rule G. S. The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions. Nat Struct Biol. 1998 May;5(5):393–399. doi: 10.1038/nsb0598-393. [DOI] [PubMed] [Google Scholar]
  9. Bulsink H., Harmsen B. J., Hilbers C. W. Specificity of the binding of bacteriophage M13 encoded gene-5 protein to DNA and RNA studied by means of fluorescence titrations. J Biomol Struct Dyn. 1985 Oct;3(2):227–247. doi: 10.1080/07391102.1985.10508413. [DOI] [PubMed] [Google Scholar]
  10. Cheng X., Harms A. C., Goudreau P. N., Terwilliger T. C., Smith R. D. Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7022–7027. doi: 10.1073/pnas.93.14.7022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Compton L. A., Johnson W. C., Jr Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal Biochem. 1986 May 15;155(1):155–167. doi: 10.1016/0003-2697(86)90241-1. [DOI] [PubMed] [Google Scholar]
  12. Day L. A. Circular dichroism and ultraviolet absorption of a deoxyribonucleic acid binding protein of filamentous bacteriophage. Biochemistry. 1973 Dec 18;12(26):5329–5339. doi: 10.1021/bi00750a017. [DOI] [PubMed] [Google Scholar]
  13. Epstein I. R. Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys Chem. 1978 Sep;8(4):327–339. doi: 10.1016/0301-4622(78)80015-5. [DOI] [PubMed] [Google Scholar]
  14. Ferrari M. E., Lohman T. M. Apparent heat capacity change accompanying a nonspecific protein-DNA interaction. Escherichia coli SSB tetramer binding to oligodeoxyadenylates. Biochemistry. 1994 Nov 1;33(43):12896–12910. doi: 10.1021/bi00209a022. [DOI] [PubMed] [Google Scholar]
  15. Folkers P. J., van Duynhoven J. P., van Lieshout H. T., Harmsen B. J., van Boom J. H., Tesser G. I., Konings R. N., Hilbers C. W. Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR. Biochemistry. 1993 Sep 14;32(36):9407–9416. doi: 10.1021/bi00087a020. [DOI] [PubMed] [Google Scholar]
  16. Folmer R. H., Nilges M., Folkers P. J., Konings R. N., Hilbers C. W. A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13. J Mol Biol. 1994 Jul 22;240(4):341–357. doi: 10.1006/jmbi.1994.1449. [DOI] [PubMed] [Google Scholar]
  17. Folmer R. H., Nilges M., Konings R. N., Hilbers C. W. Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids. EMBO J. 1995 Sep 1;14(17):4132–4142. doi: 10.1002/j.1460-2075.1995.tb00087.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Folmer R. H., Nilges M., Papavoine C. H., Harmsen B. J., Konings R. N., Hilbers C. W. Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein. Biochemistry. 1997 Jul 29;36(30):9120–9135. doi: 10.1021/bi970251t. [DOI] [PubMed] [Google Scholar]
  19. Fulford W., Model P. Specificity of translational regulation by two DNA-binding proteins. J Mol Biol. 1984 Feb 25;173(2):211–226. doi: 10.1016/0022-2836(84)90190-6. [DOI] [PubMed] [Google Scholar]
  20. Gray C. W. Three-dimensional structure of complexes of single-stranded DNA-binding proteins with DNA. IKe and fd gene 5 proteins form left-handed helices with single-stranded DNA. J Mol Biol. 1989 Jul 5;208(1):57–64. doi: 10.1016/0022-2836(89)90087-9. [DOI] [PubMed] [Google Scholar]
  21. Gray D. M. Derivation of nearest-neighbor properties from data on nucleic acid oligomers. I. Simple sets of independent sequences and the influence of absent nearest neighbors. Biopolymers. 1997 Dec;42(7):783–793. doi: 10.1002/(sici)1097-0282(199712)42:7<783::aid-bip4>3.0.co;2-p. [DOI] [PubMed] [Google Scholar]
  22. Gray D. M. Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. Thermodynamic parameters of DNA.RNA hybrids and DNA duplexes. Biopolymers. 1997 Dec;42(7):795–810. doi: 10.1002/(sici)1097-0282(199712)42:7<795::aid-bip5>3.0.co;2-o. [DOI] [PubMed] [Google Scholar]
  23. Gray D. M., Gray C. W., Carlson R. D. Neutron scattering data on reconstituted complexes of fd deoxyribonucleic acid and gene 5 protein show that the deoxyribonucleic acid is near the center. Biochemistry. 1982 May 25;21(11):2702–2713. doi: 10.1021/bi00540a020. [DOI] [PubMed] [Google Scholar]
  24. Gray D. M., Hung S. H., Johnson K. H. Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 1995;246:19–34. doi: 10.1016/0076-6879(95)46005-5. [DOI] [PubMed] [Google Scholar]
  25. Gray D. M., Ratliff R. L., Vaughan M. R. Circular dichroism spectroscopy of DNA. Methods Enzymol. 1992;211:389–406. doi: 10.1016/0076-6879(92)11021-a. [DOI] [PubMed] [Google Scholar]
  26. Greve J., Maestre M. F., Moise H., Hosoda J. Circular dichroism studies of the interaction of a limited hydrolysate of T4 gene 32 protein with T4 DNA and poly[d(A-T)].poly[d(A-T)]. Biochemistry. 1978 Mar 7;17(5):893–898. doi: 10.1021/bi00598a023. [DOI] [PubMed] [Google Scholar]
  27. Greve J., Maestre M. F., Moise H., Hosoda J. Circular dichroism study of the interaction between T4 gene 32 protein and polynucleotides. Biochemistry. 1978 Mar 7;17(5):887–893. doi: 10.1021/bi00598a022. [DOI] [PubMed] [Google Scholar]
  28. Guan Y., Zhang H., Konings R. N., Hilbers C. W., Terwilliger T. C., Wang A. H. Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex. Biochemistry. 1994 Jun 28;33(25):7768–7778. [PubMed] [Google Scholar]
  29. Guan Y., Zhang H., Wang A. H. Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: a model of the GVP-ssDNA complex. Protein Sci. 1995 Feb;4(2):187–197. doi: 10.1002/pro.5560040206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Gupta G., Sasisekharan V. Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides. Nucleic Acids Res. 1978 May;5(5):1655–1673. doi: 10.1093/nar/5.5.1655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Heyer W. D., Kolodner R. D. Purification and characterization of a protein from Saccharomyces cerevisiae that binds tightly to single-stranded DNA and stimulates a cognate strand exchange protein. Biochemistry. 1989 Apr 4;28(7):2856–2862. doi: 10.1021/bi00433a017. [DOI] [PubMed] [Google Scholar]
  32. Heyer W. D., Rao M. R., Erdile L. F., Kelly T. J., Kolodner R. D. An essential Saccharomyces cerevisiae single-stranded DNA binding protein is homologous to the large subunit of human RP-A. EMBO J. 1990 Jul;9(7):2321–2329. doi: 10.1002/j.1460-2075.1990.tb07404.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ikoku A. S., Hearst J. E. Identification of a structural hairpin in the filamentous chimeric phage M13Gori1. J Mol Biol. 1981 Sep 15;151(2):245–259. doi: 10.1016/0022-2836(81)90514-3. [DOI] [PubMed] [Google Scholar]
  34. Jezewska M. J., Kim U. S., Bujalowski W. Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer. Biochemistry. 1996 Feb 20;35(7):2129–2145. doi: 10.1021/bi952345d. [DOI] [PubMed] [Google Scholar]
  35. Kansy J. W., Clack B. A., Gray D. M. The binding of fd gene 5 protein to polydeoxynucleotides: evidence from CD measurements for two binding modes. J Biomol Struct Dyn. 1986 Jun;3(6):1079–1110. doi: 10.1080/07391102.1986.10508487. [DOI] [PubMed] [Google Scholar]
  36. King G. C., Coleman J. E. The Ff gene 5 protein-d(pA)40-60 complex: 1H NMR supports a localized base-binding model. Biochemistry. 1988 Sep 6;27(18):6947–6953. doi: 10.1021/bi00418a041. [DOI] [PubMed] [Google Scholar]
  37. Kozlov A. G., Lohman T. M. Calorimetric studies of E. coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy. J Mol Biol. 1998 May 22;278(5):999–1014. doi: 10.1006/jmbi.1998.1738. [DOI] [PubMed] [Google Scholar]
  38. Lohman T. M., Overman L. B., Ferrari M. E., Kozlov A. G. A highly salt-dependent enthalpy change for Escherichia coli SSB protein-nucleic acid binding due to ion-protein interactions. Biochemistry. 1996 Apr 23;35(16):5272–5279. doi: 10.1021/bi9527606. [DOI] [PubMed] [Google Scholar]
  39. Mark B. L., Gray D. M. Tyrosine mutant helps define overlapping CD bands from fd gene 5 protein.nucleic acid complexes. Biopolymers. 1997 Sep;42(3):337–348. doi: 10.1002/(SICI)1097-0282(199709)42:3<337::AID-BIP6>3.0.CO;2-N. [DOI] [PubMed] [Google Scholar]
  40. Mark B. L., Terwilliger T. C., Vaughan M. R., Gray D. M. Circular dichroism spectroscopy of three tyrosine-to-phenylalanine substitutions of fd gene 5 protein. Biochemistry. 1995 Oct 3;34(39):12854–12865. doi: 10.1021/bi00039a047. [DOI] [PubMed] [Google Scholar]
  41. Mascotti D. P., Lohman T. M. Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry. 1997 Jun 10;36(23):7272–7279. doi: 10.1021/bi970272n. [DOI] [PubMed] [Google Scholar]
  42. McGhee J. D., von Hippel P. H. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974 Jun 25;86(2):469–489. doi: 10.1016/0022-2836(74)90031-x. [DOI] [PubMed] [Google Scholar]
  43. Michel B., Zinder N. D. In vitro binding of the bacteriophage f1 gene V protein to the gene II RNA-operator and its DNA analog. Nucleic Acids Res. 1989 Sep 25;17(18):7333–7344. doi: 10.1093/nar/17.18.7333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Newport J. W., Lonberg N., Kowalczykowski S. C., von Hippel P. H. Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. II. Specificity of binding to DNA and RNA. J Mol Biol. 1981 Jan 5;145(1):105–121. doi: 10.1016/0022-2836(81)90336-3. [DOI] [PubMed] [Google Scholar]
  45. Olah G. A., Gray D. M., Gray C. W., Kergil D. L., Sosnick T. R., Mark B. L., Vaughan M. R., Trewhella J. Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study. J Mol Biol. 1995 Jun 9;249(3):576–594. doi: 10.1006/jmbi.1995.0320. [DOI] [PubMed] [Google Scholar]
  46. Overman L. B., Bujalowski W., Lohman T. M. Equilibrium binding of Escherichia coli single-strand binding protein to single-stranded nucleic acids in the (SSB)65 binding mode. Cation and anion effects and polynucleotide specificity. Biochemistry. 1988 Jan 12;27(1):456–471. doi: 10.1021/bi00401a067. [DOI] [PubMed] [Google Scholar]
  47. Pörschke D., Rauh H. Cooperative, excluded-site binding and its dynamics for the interaction of gene 5 protein with polynucleotides. Biochemistry. 1983 Sep 27;22(20):4737–4745. doi: 10.1021/bi00289a019. [DOI] [PubMed] [Google Scholar]
  48. Raghunathan S., Ricard C. S., Lohman T. M., Waksman G. Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6652–6657. doi: 10.1073/pnas.94.13.6652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Record M. T., Jr, Anderson C. F., Lohman T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys. 1978 May;11(2):103–178. doi: 10.1017/s003358350000202x. [DOI] [PubMed] [Google Scholar]
  50. Sang B. C., Gray D. M. CD measurements show that fd and IKe gene 5 proteins undergo minimal conformational changes upon binding to poly(rA). Biochemistry. 1989 Nov 28;28(24):9502–9507. doi: 10.1021/bi00450a038. [DOI] [PubMed] [Google Scholar]
  51. Sang B. C., Gray D. M. Specificity of the binding of fd gene 5 protein to polydeoxyribonucleotides. J Biomol Struct Dyn. 1989 Dec;7(3):693–706. doi: 10.1080/07391102.1989.10508514. [DOI] [PubMed] [Google Scholar]
  52. Shamoo Y., Friedman A. M., Parsons M. R., Konigsberg W. H., Steitz T. A. Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature. 1995 Jul 27;376(6538):362–366. doi: 10.1038/376362a0. [DOI] [PubMed] [Google Scholar]
  53. Skinner M. M., Zhang H., Leschnitzer D. H., Guan Y., Bellamy H., Sweet R. M., Gray C. W., Konings R. N., Wang A. H., Terwilliger T. C. Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2071–2075. doi: 10.1073/pnas.91.6.2071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Stassen A. P., Zaman G. J., van Deursen J. M., Schoenmakers J. G., Konings R. N. Selection and characterization of randomly produced mutants of gene V protein of bacteriophage M13. Eur J Biochem. 1992 Mar 15;204(3):1003–1004. doi: 10.1111/j.1432-1033.1992.tb16722.x. [DOI] [PubMed] [Google Scholar]
  55. Terwilliger T. C. Gene V protein dimerization and cooperativity of binding of poly(dA). Biochemistry. 1996 Dec 24;35(51):16652–16664. doi: 10.1021/bi961050c. [DOI] [PubMed] [Google Scholar]
  56. Thompson T. M., Mark B. L., Gray C. W., Terwilliger T. C., Sreerama N., Woody R. W., Gray D. M. Circular dichroism and electron microscopy of a core Y61F mutant of the F1 gene 5 single-stranded DNA-binding protein and theoretical analysis of CD spectra of four Tyr --> Phe substitutions. Biochemistry. 1998 May 19;37(20):7463–7477. doi: 10.1021/bi972545k. [DOI] [PubMed] [Google Scholar]
  57. Walstrom K. M., Dozono J. M., von Hippel P. H. Effects of reaction conditions on RNA secondary structure and on the helicase activity of Escherichia coli transcription termination factor Rho. J Mol Biol. 1998 Jun 19;279(4):713–726. doi: 10.1006/jmbi.1998.1814. [DOI] [PubMed] [Google Scholar]
  58. Webster R. E., Grant R. A., Hamilton L. A. Orientation of the DNA in the filamentous bacteriophage f1. J Mol Biol. 1981 Oct 25;152(2):357–374. doi: 10.1016/0022-2836(81)90247-3. [DOI] [PubMed] [Google Scholar]
  59. Wold M. S., Kelly T. Purification and characterization of replication protein A, a cellular protein required for in vitro replication of simian virus 40 DNA. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2523–2527. doi: 10.1073/pnas.85.8.2523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Yu L., Zhu C. X., Tse-Dinh Y. C., Fesik S. W. Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Biochemistry. 1995 Jun 13;34(23):7622–7628. doi: 10.1021/bi00023a008. [DOI] [PubMed] [Google Scholar]
  61. Zaman G. J., Kaan A. M., Schoenmakers J. G., Konings R. N. Gene V protein-mediated translational regulation of the synthesis of gene II protein of the filamentous bacteriophage M13: a dispensable function of the filamentous-phage genome. J Bacteriol. 1992 Jan;174(2):595–600. doi: 10.1128/jb.174.2.595-600.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Zaman G., Smetsers A., Kaan A., Schoenmakers J., Konings R. Regulation of expression of the genome of bacteriophage M13. Gene V protein regulated translation of the mRNAs encoded by genes I, III, V and X. Biochim Biophys Acta. 1991 Jun 13;1089(2):183–192. doi: 10.1016/0167-4781(91)90006-8. [DOI] [PubMed] [Google Scholar]
  63. Zhang H., Skinner M. M., Sandberg W. S., Wang A. H., Terwilliger T. C. Context dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants. J Mol Biol. 1996 May 31;259(1):148–159. doi: 10.1006/jmbi.1996.0309. [DOI] [PubMed] [Google Scholar]
  64. von Hippel P. H., Kowalczykowski S. C., Lonberg N., Newport J. W., Paul L. S., Stormo G. D., Gold L. Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 (single-stranded DNA binding) protein system. J Mol Biol. 1982 Dec 25;162(4):795–818. doi: 10.1016/0022-2836(82)90548-4. [DOI] [PubMed] [Google Scholar]

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