title: Unusually strong positive cooperativity in binding of peptides to latent membrane protein-1 DNA fragments of the Epstein-Barr viral gene.
abstract: The DNA-binding preferences of two oligopeptide amides, (His-Pro-Arg-Lys)(3)NH(2) (HR-12) and (Ser-Pro-Arg-Lys)(3)NH(2) (SP-12), have been examined by quantitative DNase I footprinting studies. Two different DNA fragments were investigated: a pair of 5'-(32)P-labeled duplexes from pBR322 with one or other of the complementary strands labeled and a corresponding pair of 5'-(32)P-labeled duplexes representing fragments of the latent membrane protein (LMP-1) gene from a pathogenic Epstein-Barr virus variant derived from nasopharyngeal carcinoma. The major objective was to examine molecular recognition and cooperative features associated with sequence-selective binding of synthetic peptides to the LMP-1 fragments. At various binding sites on the pBR322 fragments, Hill coefficients (n(H)) ranging from 1.9-2.2 were observed; these results indicate modest positive cooperativity between binding sites for both peptides. By contrast, unusually high values of n(H), ranging from 4.0-9.3, were observed at various binding sites on the LMP-1 fragments. Allosteric models can be constructed to interpret the observed cooperative interactions between different DNA recognition sites in the LMP-1 gene upon binding of the peptide ligands. It is noteworthy that these models feature a novel network of cooperativity interconnecting multiple DNA allosteric sites. The evidence of sequence selectivity and strong cooperativity discovered in this work may prove to be a general feature of peptide interactions with some nucleic acids.
authors.affiliation: Department of Chemistry, Tunghai Christian University, Taichung, Taiwan 407, R.O.C.
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Yang
authors.forename: Kee-Ching G
authors.initials: KC
authors.lastname: Jeng
authors.forename: Wan-Hsu
authors.initials: WH
authors.lastname: Yang
authors.forename: Yu-Ling
authors.initials: YL
authors.lastname: Chen
authors.forename: Chia-Chun
authors.initials: CC
authors.lastname: Hung
authors.forename: Juey-Wen
authors.initials: JW
authors.lastname: Lin
authors.forename: Shui-Tein
authors.initials: ST
authors.lastname: Chen
authors.forename: Simon
authors.initials: S
authors.lastname: Richardson
authors.forename: Christopher R H
authors.initials: CR
authors.lastname: Martin
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Waring
authors.forename: Leung
authors.initials: L
authors.lastname: Sheh
mesh_terms: D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D018983:DNA Footprinting; D004279:DNA, Viral / Q000235:genetics* / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D004854:Herpesvirus 4, Human / Q000235:genetics* / Q000378:metabolism*; D008969:Molecular Sequence Data; D010455:Peptides / Q000378:metabolism*; D014763:Viral Matrix Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004279:DNA, Viral; C037662:EBV-associated membrane antigen, Epstein-Barr virus; D010455:Peptides; D014763:Viral Matrix Proteins; D003850:Deoxyribonuclease I