A 500 MHz proton NMR study of interaction of tripeptides Lys-Tyr-Lys and Lys-Phe-Lys with deoxydinucleotide d-CpG.
The binding of di- and tetranucleotides with tri- and tetrapeptides containing Tyr, Trp, Phe having lysine on both ends has been studied using a 500 MHz proton NMR. The results show that d-CpG exists as a right-handed B-DNA structure with both sugars in 01'-endo sugar conformation and glycosidic bond angle as in anti domain. On binding to tripeptide Lys-Tyr-Lys, the Tyr ring protons shift upfield by 0.015 ppm at 285 degrees K, while the conformation of d-CpG remains unchanged. Change in chemical shift of Tyr and nucleotide protons decreases with temperature. This upfield shift is attributed to stacking with bases/base-pairs. The presence of intermolecular NOE's also supports this. Results of binding of d-CpG to Lys-Phe-Lys are similar to those with Lys-Tyr-Lys except that the chemical shift changes occur to a lesser extent. On comparing the results obtained with three different peptides, it is found that interaction decreases in the order Trp > Tyr > Phe which is similar to that found by theoretical energy calculations (reported elsewhere) and fluorescence measurements. The results also exhibit a specificity in recognition of these amino acid residues by dinucleotides.
Barthwal
R
R
Department of Biosciences and Biotechnology, University of Roorkee, India.
Kukreti
S
S
Mujeeb
A
A
D003845:Deoxycytosine Nucleotides / Q000737:chemistry*; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D003845:Deoxycytosine Nucleotides; D009842:Oligopeptides; C037781:deoxycytidylyl-(3'-5')-deoxyguanosine; C074312:lysyl-tyrosyl-lysine; C079731:lysyl-phenylalanyl-lysine; D003849:Deoxyguanosine