• Journal of the Korean Magnetic Resonance Society
• /
• v.2 no.1
• /
• pp.41-49
• /
• 1998

A linear undecapeptide, Substance P (SP) is involved in a wide variety of physiological processes such as pain, inflammation, salivation, and hypertension. Tertiary structure of SP in dodecylphosphocholine (DPC) micelles has been investigated by CD, NMR spectroscopy, and DGII calculation. CD spectrum of SP in the presence of 7.5 mM DPC micelles does not show any favorable secondary structure. The tertiary structure determined by NMR spectroscopy and DGII calculation shows that the Phe7-Phr8-Gly9-Leu10 region adopts a turn structure, while the N-terminal region is quite flexible. Both prolines in SP exist preferentially as the trans isoforms and the aromatic ring of Phe7 protrudes outward. Conformation of SP may be restrained by the contact of the Phe7 aromatic ring with the hydrophobic side chains of the DPC micelles and this interaction induces a turn structure. Structure of SP in aqueous solution in the presence of DPC micelles can represent a good model to study the conformation recognized by the receptor near neutral membrane.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.2
• /
• pp.327-330
• /
• 2005

• Proceedings of the Korean Biophysical Society Conference
• /
• 1996.07a
• /
• pp.28-28
• /
• 1996

NMR studies on the structure of the luteinizing hormone releasing hormone (LHRH) in aqueous buffer and trifluoroethanol (TFE)/aqueous buffer (1:1, v/v) solution were performed. The NMR data under these conditions suggested a unique conformation which includes a ${\beta}$-1 turn of the Tyr5-Arg8 segment and an unusual turn of Ser4-Gly6 segment staggered with the ${\beta}$-I turn. (omitted)

• Proceedings of the PSK Conference
• /
• 2003.10a
• /
• pp.91-91
• /
• 2003

The beta-turn has been implicated as an important conformation for biological recognition of peptides or proteins. We adapted the concept of general Ca atom positioning from the cluster analysis and recombination of each ideal beta-turn conformation pattern by Garland and Dean (1. Computer-Aided Molecular Design, 1999, 13, 469) as one strategy of designing non-peptide beta-turn scaffolds. (omitted)

• Journal of the Korean Chemical Society
• /
• v.43 no.5
• /
• pp.540-546
• /
• 1999

Solution conformation of cyclo-($Gln^1-Trp^2-Phe^3-{\beta}Ala^4-Leu^5-Met^6$), new NK-2 antagonist in dimethyl sulfoxide solution, has been determined by the use of two-dimensional nuclear magnetic resonance spectroscopy combined with simulated annealing calculations. The peptide exhibited converged structures with the atomic root-mean-square difference for the backbone atoms ($N,\;C^{\alpha},\;C'$) of all residues being 0.02${\AA}$ in the 25 annealed structures. The analysis of the structures indicated that the cyclic peptide has three intramolecular hydrogen bonds between $Met^6NH$ and ${\beta}Ala^4CO$, ${\beta}Ala^4NH$ and $Met^6CO$, $Phe^3NH$ and $Met^6CO$, and contain a type-I ${\beta}$-turn with Gln and Trp and ${\gamma}$-turn with Leu. The addition of an extra methylene group to Gly, i.e. P-Ala residue, may relax some unfavorable restraints in the cyclic backbone structure, hence enabling an additional hydrogen bond, which results in stabilizing one conformation.

• BMB Reports
• /
• v.36 no.6
• /
• pp.552-557
• /
• 2003

Oligomers with $\alpha$-aminooxy acids are reported to form very stable turn and helix structures, and they are supposed to be useful peptidomimetics for drug design. A recent report suggested that homochiral oxa-peptides form a strong eight-member-ring structure by a hydrogen bond between adjacent aminooxy-acid residues in a $CDCl_3$ solution. In order to design an $\alpha$-MSH analog with a stable turn conformation, we synthesized four tetramers and one pentamer, based on $\alpha$-MSH sequence, and determined the solution structures of the molecules by two-dimensional NMR spectroscopy and simulated annealing calculations. The solution conformations of the three peptidomimetic molecules (TLV, TDV, and TLL) in DMSO-$d_6$ contain a stable 7-membered-ring structure that is similar to a $\gamma$-turn in normal peptides. Newly-designed tetramer TDF and pentamer PDF have a ball-type rigid structure that is induced by strong hydrogen bonds between adjacent amide protons and carbonyl oxygens. In conclusion, the aminooxy acids, easily prepared from natural or unnatural amino acids, can be employed to prepare peptidomimetic analogues with well-defined turn structures for pharmaceutical interest.

• Proceedings of the PSK Conference
• /
• 2002.10a
• /
• pp.342.2-342.2
• /
• 2002

The ${\beta}$-turn has been implicated as an important conformation for biological recognition of peptides or proteins. Benzodiazepine classes have been known as one of the non peptide ${\beta}$-turn mimic scaffolds. We have developed an efficient approach for the synthesis and derivatization of a scaffold of hydroxytetrahydrodizepinone class in order to screen compound library in various protein targets for new lead generations as well as for structure activity relationships of the scaffold. (omitted)

• Proceedings of the Polymer Society of Korea Conference
• /
• 2006.10a
• /
• pp.19-20
• /
• 2006

We report the design of electroluminescent conjugated polymers for high efficiency, turn-on voltage, color Tuning, and easy processing. Three approaches for the design are reported, being: (1) single chain consideration, (2) supramolecular structure consideration, and (3) conformation manipulation. Two polymer systems are to be reported, being fluorene-based and carbazole-based conjugated polymers.

• Proceedings of the PSK Conference
• /
• 2002.10a
• /
• pp.330.2-330.2
• /
• 2002

The conformational study on cyclic Ac-Cys-Pro-Xaa-Cys-NHMe (Ac-CPXC-NHMe: X = Ala, Val. Leu. Aib. Gly. His. Phe, Tyr. Asn. and Ser) peptides has been carried out using the ECEPP/3 force field and the hydration shell model in the unhydrated and hydrated states. This work has been undertaken to investigate structural implications of the CPXC sequence as the chain reversal for the initiation of protein folding and as the motif for active site of disulfide oxidoreductases. The backbone conformation DAAA is in common the most feasible for cyclic CPXC peptides in the hydrated state. which has a type 1${\beta}$-turn at the Pro-Xaa sequence. The proline residue and the hydrogen bond between backbones of two cystines appear to play a role in stabilizing this preferred conformation of cycilc CPXC peptides. However. the distributions of backbone conformations and ${\beta}$-turns may indicate that the cyclic CPXC peptide seems to exist as an ensemble of ${\beta}$-turns and coiled conformations. The intirnsic stability of the cyclic CPXC motif itself the active conformation appears to play a role in determining electrochemical properties of disulfide oxidoreductases.

• Molecules and Cells
• /
• v.25 no.3
• /
• pp.352-357
• /
• 2008

Osteoprotegerin (OPG) is a soluble decoy receptor that inhibits osteoclastogenesis and is closely associated with bone resorption processes. We have designed and determined the solution structures of potent OPG analogue peptides, derived from sequences of the cysteine-rich domain of OPG. The inhibitory effects of the peptides on osteoclastogenesis are dose-dependent ($10^{-6}M-10^{-4}M$), and the activity of the linear peptide at $10^{-4}M$ is ten-fold higher than that of the cyclic OPG peptide. Both linear and cyclic peptides have a ${\beta}$-turn-like conformation and the cyclic peptide has a rigid conformation, suggesting that structural flexibility is an important factor for receptor binding. Based on structural and biochemical information about RANKL and the OPG peptides, we suggest that complex formation between the peptide and RANKL is mediated by both hydrophobic and hydrogen bonding interactions. These results provide structural insights that should aid in the design of peptidyl-mimetic inhibitors for treating metabolic bone diseases caused by abnormal osteoclast recruitment.