Ning Zhou

I. 1H-NMR studies of [Sar1]angiotensin II conformation by nuclear Overhauser effect spectroscopy in the rotating frame (ROESY): Clustering of the aromatic rings in dimethylsulfoxide

The conformational properties of the octapeptide [Sar1]ANG II in dimethylsulfoxide-d6 were investigated by rotating frame nuclear Overhauser effect spectroscopy (ROESY). Interresidue ROESY interactions were observed between Tyr ortho and Phe ring protons, between Phe ring and Pro C gamma protons, and also between His C alpha and Pro C delta protons. A weak connectivity was also observed between the Sar N-CH3 protons and a Tyr ortho proton. Intraresidue interactions between alpha and beta protons in Tyr, His and Phe indicated restricted rotation for the side-chains of the three aromatic residues. These findings suggest that [Sar1]ANG II takes up a folded conformation in DMSO in which the three aromatic rings form a cluster. Connectivities between the His C alpha proton and the two Pro C delta protons illustrated a preferred conformation for angiotensin II in DMSO in which the His-Pro bond exists as the trans isomer. The NMR spectroscopic evidence is consistent with the presence of a Tyr charge relay system in the biologically active conformation of angiotensin II and with the postulated role of the Tyr hydroxyl group in angiotensin II for receptor activation.

Molecular dynamics simulations of bovine lactoferricin: turning a helix into a sheet

Bovine lactoferricin is a 25-residue peptide that is excised through pepsin cleavage in the stomach from the intact 80 kDa bovine milk protein lactoferrin. This basic peptide contains a single disulfide crosslink and is considerably more active as an antimicrobial peptide than the intact protein. It has been suggested that the dramatic difference in potency is related to a change in the secondary and tertiary structure of this peptide, moving from a mixed α-helical β-strand region in the protein to an amphipathic twisted antiparallel β-sheet in the peptide. Here we have used equilibrium and restrained molecular dynamics calculations to compare the stability of the solution structure of the isolated peptide with that excised from the intact protein. Simulations were performed for fully solvated peptides in the absence and presence of 250 mM salt. Our results show that the peptide as released from the protein is relatively unstable, particularly in the absence of salt. However, even though the simulations extended over 60 nsecs, no interconversion could be observed between the crystal and solution structures, unless a relatively small directional force was exerted on the peptide. A pathway for the structural transition from a helical to a sheet structure was identified in this fashion.

Proton NMR studies of angiotensin II and its analogs in aqueous solution

The1H nuclear magnetic resonance (NMR) spectra of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) and five of its octapeptide analogs as well as angiotensin I (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu) and angiotensin III (Arg-Val-Tyr-Ile-His-Pro-Phe) in aqueous solutions (90% H2O/10% D2O) were completely assigned by two-dimensional COSY and ROESY experiments. All of the peptides give rise to two distinct sets of signals. The minor set accounts for about 5% of the total population belowpH 5.5 and increases to 12–20% aroundpH 7.0. The two sets of signals result from acis-trans isomerization of the His-Pro peptide bond with the major resonances arising from thetrans isomer. One analog in which the Pro is replaced with a D-Pro displays a very different isomerization behavior. The measured coupling constants JNH-αCH, the temperature dependence of the amide proton shifts and the relative intensities of the intraresidue and sequential NH-αCH ROEs, are all indicative of an extended backbone conformation for ANGII. However, some evidence for the existence of conformers with local structure involving preferred sidechain positions for the Tyr, His, Phe, and the carboxyl group of the Phe was found, particularly in the ROESY andpH-titration experiments. Moreover,pH effects and the unusual amide exchange behavior of the Arg εNH suggests the presence of interactions between the Asp and Arg sidechains of ANGII. At low temperatures the Arg guanidinium NH2 protons were detected as two broad peaks which are related by sizeable exchange peaks in ROESY experiments. This behavior could be useful as a general probe for the study of Arg sidechain mobility and accessibility in other peptides and proteins

[9] Parallel-stranded duplex DNA: An NMR perspective

Publisher Summary This chapter describes the various forms of parallel-stranded duplex DNA that have been encountered and pays attention to the base pairing that defines the structures. The base pairing schemes that have been reported to date for homo and hetero base pairs are discussed in the chapter. The formation of parallel-stranded structures is not restricted to RNA, but has also been observed for oligodeoxy- and polydeoxyribonucleotides. Based on the spectroscopic and model-building studies, Brown et al. proposed a parallel-stranded double helical model for poly[d(CT)] at low pH 5 . A parallel-stranded double helical structure was found for the duplex formed from [α] anomeric deoxyoligonucleotides and the complementary natural [β] anomeric deoxyoligonucleotides. The structures of related sequences have been investigated by two-dimensional NMR. This study provided evidence for a right-handed double helical structure with parallel strand alignment. The bases of the [β] anomeric strand are in the anti-orientation and those of the [α] strand are in the syn orientation; the base pairing is of the Watson-Crick type. Parallel strand disposition can also be induced by ligands that bind to nucleic acids. The nonself-complementary dinucleoside monophosphate CpA forms a right-handed base-paired parallel-stranded structure, containing one intercalated proflavine.