• Journal of the Korean Chemical Society
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• v.31 no.5
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• pp.471-475
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• 1987

Fe(II)-poly(D-glutamic acid) (PGA) complex in aqueous solution has been investigated as functions of pH and concentration of Fe(II) by using absorption and circular dichroism spectroscopies. The helix-breaking interaction occurred at pH 4.3 while the helix-directing one occurred at pH 5.7 after forming complex between PGA and Fe(II). The relationship between conformation change of PGA by forming complex with Fe(II) and complex constants for the above system was studied. As a result, stability constants in random coil structure of PGA are larger than those in ${\alpha}$-helix structure. This result indicates that the random coil structure of PGA-Fe(II) complex shows more stable complex than ${\alpha}$-helix one.

• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.817-819
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• 2003

현재 바이오인포매틱스(Bioinformatics) 분야에서 가장 중요한 부분 중의 하나는 유전자 및 단백질의 구조와 기능을 정확하게 예측하는 것이다. 이는 질병 치료 및 신약개발에 유용하여 이로부터 나온 결과로부터 경제적 산업적 효과를 기대할 수 있다. 이 논문에서는 기계학습(Machine Learning)의 한 분야인 SVM(Support Vector Machine)과 HMM(Hidden Markov Model)를 결합하여 단백질의 막횡단(Transmembrane) $\alpha$-Helix 단백질 지역을 예측하는 새로운 알고리즘을 개발, 구현 및 실험하였다. 그 결과 이 두 가지 알고리즘이 결합된 방식을 사용함으로써 성능을 향상 시킬 수 있음을 증명했다.

• Bulletin of the Korean Chemical Society
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• v.34 no.9
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• pp.2640-2644
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• 2013

The all-hydrocarbon i,i+4 stapling system using an oct-4-enyl crosslink is one of the most widely employed chemical tools to stabilize an ${\alpha}$-helical conformation of a short peptide. This crosslinking system has greatly extended our ability to modulate intracellular protein-macromolecule interactions. The helix-inducing property of the i,i+4 staple has shown to be highly dependent on the length and the stereochemistry of the oct-4-enyl crosslink. Here we show that changing the double bond position within the i,i+4 staple has a considerable impact not only on the formation of the crosslink but also on ${\alpha}$-helix induction. The data further increases the understanding of the structure-activity relationships of this valuable chemical tool.

• Journal of the Korean Chemical Society
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• v.39 no.10
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• pp.776-782
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• 1995

A theory of the helix/coil transition for $\alpha$ helical dimer such as $\alpha$ tropomycin and paramycin is developed. The treatment differs from those formulated previously for oligopeptide dimer which is explained by the matrix method using Zimm-Bragg parameter: In the present treatement, it is explained by the zipper model which can account for the dangling H-bond. We calculate the fractional helicity in $\alpha$ helical dimer as a function of helix initiation $constant(\sigma)$, helix stability constant(${\xi}$) and hydrophobic interaction parameter(w). For $\alpha$ tropomycin, the helix stability profile is also calculated. The transitions of this oligomer due to the change of temperature and the concentration of oligopeptide involve simultaneous dissociation of the dimer. The transitions of dimers which have cross-linked S-S bonds or have long chains don't occur, because they keep always helical structures. The transitons due to the concentration of the oligopeptides are steeper than those due to the chain length or temperature.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3627-3631
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• 2014

In this study we examined two ester-containing cross-links, hex-2-enyl acetate and hex-2-enyl propionate, as new cross-linking systems for helix stabilization of short peptides. We demonstrated that these hexenyl ester cross-links can be readily installed via a ruthenium-mediated ring-closing metathesis reaction of L-aspartic acid 4-allyl ester or L-glutamic acid 5-allyl ester at position i and (S)-2-(4'-pentenyl)alanine at position i+4 using second generation Hoveyda-Grubbs catalyst at $60^{\circ}C$. Between these two cross-links, we found that the hex-2-enyl propionate significantly stabilizes the ${\alpha}$-helical conformations of short model peptides. The helix-stabilizing effects of the hex-2-enyl propionate tether appear to be as powerful as Verdine's i,i+4 all-hydrocarbon stapling system, which is one of the most widely used and the most potent helix-stabilizing cross-linking systems. Furthermore, the hex-2-enyl propionate bridge is reasonably robust against non-enzymatic hydrolytic cleavage at a physiological pH. While extended studies for probing its chemical scopes and biological applications are needed, we believe that this new helix-stabilizing system could serve as a useful chemical tool for understanding protein folding and designing conformationally-constrained peptide drugs.

• Kyungpook Mathematical Journal
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• v.56 no.3
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• pp.1003-1016
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• 2016

In this paper, we introduce a new kind of slant helix for null curves called null $W_n$-slant helix and we give a definition of new harmonic curvature functions of a null curve in terms of $W_n$ in (n + 2)-dimensional Lorentzian space $M^{n+2}_1$ (for n > 3). Also, we obtain a characterization such as: "The curve ${\alpha}$ s a null $W_n$-slant helix ${\Leftrightarrow}H^{\prime}_n-k_1H_{n-1}-k_2H_{n-3}=0$" where $H_n,H_{n-1}$ and $H_{n-3}$ are harmonic curvature functions and $k_1,k_2$ are the Cartan curvature functions of the null curve ${\alpha}$.

• Proceedings of the Korean Biophysical Society Conference
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• 1999.06a
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• pp.39-39
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• 1999

Single chain-monellin (SCM) was recently constructed by fusing the two chains of monellin. From the view of protein folding, SCM serves as an ideal model system especially in tackling ${\alpha}$-helix-${\beta}$-sheet interactions due to the following reasons： First, it consists of simple distinct structural elements (${\alpha}$-helix and ${\beta}$-sheet) which are assembled in a perpendicular manner.(omitted)

• Journal of the Korean Mathematical Society
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• v.48 no.1
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• pp.159-167
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• 2011

We consider a curve $\alpha$= $\alpha$(s) in Minkowski 3-space $E_1^3$ and denote by {T, N, B} the Frenet frame of $\alpha$. We say that $\alpha$ is a slant helix if there exists a fixed direction U of $E_1^3$ such that the function is constant. In this work we give characterizations of slant helices in terms of the curvature and torsion of $\alpha$. Finally, we discuss the tangent and binormal indicatrices of slant curves, proving that they are helices in $E_1^3$.

• KIPS Transactions on Software and Data Engineering
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• v.3 no.4
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• pp.163-168
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• 2014

In a protein molecule, ${\alpha}$-helices are important for protein structure, function, and binding to other proteins, so the analysis on the structure of helices has been researched. Since an interaction between two helices is evaluated based on their axes, massive errors in protein structure analysis would be caused if a curved or kinked long ${\alpha}$-helix is considered as a linear one. In this paper, we present an algorithm to reconstruct ${\alpha}$-helices in a protein molecule as a sequence of straight helices under given threshold.

• Bulletin of the Korean Chemical Society
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• v.19 no.1
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• pp.57-62
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• 1998

We have synthesized a 17-residue peptide with the amino acid sequence RQMKEDAKGKSEEELAD corresponding to residues 84-100 of chicken skeletal troponin C. This stretch of the protein sequence is in the middle one-third of the 32-residue 9-turn α-helix that connects the two globular domains of the dumbell-shaped molecule and includes the D/E linker helix. We describe here the solution conformation of the helix linker as studied by circular dichroism (CD) and two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy. The NOE connectivities together with the vicinal $^3J_{N{\alpha}}$ coupling constants suggest that the peptide exists in a fast conformational equilibrium among several secondary structure: a nascent helix near the N-terminus, a helix, and a substational population of extended and random coil forms. In addition, two interresidue α-α NOEs are observed suggesting a bent structure with a bend that includes the single glycine in position 92. These results are consistent with the ideas that in neutral solution the D/E linker region of the central helix in troponin C can adopt a helical conformation and the central helix may have a segmental flexibility around Gly 92.