Related ArticlesSolution structure of the conserved segment of the Myb cognate DNA sequence by 2D NMR, spectral simulation, restrained energy minimization, and distance geometry calculations.
Biochemistry. 1995 May 2;34(17):5913-22
Authors: Radha PK, Madan A, Nibedita R, Hosur RV
Solution structure of a self-complementary DNA duplex d-ACCGTTAACGGT containing the TAACGG recognition segment of Myb protein has been obtained by NMR spectroscopy. Complete resonance assignments of all the protons (except H5', H5" protons) have been obtained following standard procedures based on two-dimensional NMR techniques. Using a total of 72 coupling constants, and 95 NOE intensities, restrained energy minimization has been carried out, with the X-PLOR force field. The distance constraint set has been iteratively refined, for better fits with experimental NOE intensities. Using the final constraint set thus obtained, and explicit H-bond constraints for A.T, G.C base pairs in the duplex, distance geometry calculations have been carried in the torsion angle space with the program TANDY-2S to identify the family of structures consistent with the NMR data. We observe that the constraint set does indeed define a unique structure for the DNA segment. The structural details have been analyzed, and the sequence-dependent variations in torsion angles, base pair geometries, and helicoidal parameters have been documented. We observed that the helix axis displays a nonregular path, and three centered H-bonds have been seen at AA, AC, and CC steps in the major groove of the helix. Substantial variations have been observed for the helix axis and the groove widths at the recognition site. The base pairs exhibit high negative propeller twists. The structure is characterized by O4'-endo geometry for all the sugar rings (expect G10), and the other torsion angles belong to the B-DNA families.
[NMR paper] NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of
NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein.
Related Articles NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein.
Biochemistry. 2004 Nov 30;43(47):14940-7
Authors: Biverståhl H, Andersson A, Gräslund A, Mäler L
The structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein (bPrPp) has been investigated by NMR spectroscopy in phospholipid membrane mimetic systems. CD spectroscopy...
nmrlearner
Journal club
0
11-24-2010 10:03 PM
[NMR paper] NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-li
NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold.
Related Articles NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold.
Proteins. 2002 Sep 1;48(4):733-6
Authors: Cort JR, Chiang Y, Zheng D, Montelione GT, Kennedy MA
nmrlearner
Journal club
0
11-24-2010 08:58 PM
[NMR paper] NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
Related Articles NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
Nucleic Acids Res. 2001 Dec 15;29(24):5129-39
Authors: Nagaswamy U, Gao X, Martinis SA, Fox GE
The structure of a 23 nt RNA sequence, rGGACCCGGGCUCAACCUGGGUCC, was elucidated using homonuclear NMR, distance geometry and restrained molecular dynamics. This RNA is analogous to residues 612-628 of the Escherichia coli 16S rRNA. The structure of the RNA reveals the...
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] NMR-based structure of the conserved protein MTH865 from the archaeon Methanobacteriu
NMR-based structure of the conserved protein MTH865 from the archaeon Methanobacterium thermoautotrophicum.
Related Articles NMR-based structure of the conserved protein MTH865 from the archaeon Methanobacterium thermoautotrophicum.
J Biomol NMR. 2001 Sep;21(1):63-6
Authors: Lee GM, Edwards AM, Arrowsmith CH, McIntosh LP
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] NMR structure of the extended Myb cognate sequence and modeling studies on specific D
NMR structure of the extended Myb cognate sequence and modeling studies on specific DNA-Myb complexes.
Related Articles NMR structure of the extended Myb cognate sequence and modeling studies on specific DNA-Myb complexes.
Biochemistry. 1998 Jul 14;37(28):9952-63
Authors: Radha PK, Patel PK, Hosur RV
The recognition sequence of the Myb protein has been recently described to be pyAACKGHH (where py = T/C, K = G/T, and H = A/C/T), modifying the earlier identification as pyAACKG . We had earlier determined the solution structure of the minimal...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cry
Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography.
Related Articles Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography.
J Mol Biol. 2010 Oct 6;
Authors: Miyazaki Y, Irobalieva RN, Tolbert B, Smalls-Mantey A, Iyalla K, Loeliger K, D'Souza V, Khant H, Schmid MF, Garcia E, Telesnitsky A, Chiu W, Summers MF
The 5'-untranslated regions (5'-UTRs) of all gammaretroviruses contain a conserved "double hairpin motif" (?(CD)) that is required for...
nmrlearner
Journal club
0
10-12-2010 02:52 PM
[NMR paper] Sequence-specific 1H NMR assignments and secondary structure in solution of Escherich
Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor.
Related Articles Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor.
Biochemistry. 1990 Jul 10;29(27):6332-41
Authors: Arrowsmith CH, Pachter R, Altman RB, Iyer SB, Jardetzky O
Sequence-specific 1H NMR assignments are reported for the active L-tryptophan-bound form of Escherichia coli trp repressor. The repressor is a symmetric dimer of 107 residues per monomer; thus at 25 kDa, this...
nmrlearner
Journal club
0
08-21-2010 11:04 PM
[NMR paper] Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the exte
Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex.
Related Articles Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex.
J Biomol Struct Dyn. 1999 Jun;16(6):1145-57
Authors: Girard F, Barbault F, Gouyette C, Huynh-Dinh T, Paoletti J, Lancelot G
The genome of all retrovirus consists of two copies of genomic RNA which are noncovalently linked near their 5' end. A sequence localized immediately upstream from the splice donor site inside the HIV-1 psi-RNA...
Solution structure of the conserved segment of the Myb cognate DNA sequence by 2D NMR
Linear Mode
