• Bulletin of the Korean Chemical Society
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• v.4 no.1
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• pp.36-41
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• 1983

An equation is derived which correlates the unperturbed dimensions $_0$ of polypeptides with the helical contents in the helix-coil transition region by using a simple model of a polypeptide chain. The model is a chain of connected balls which represent the repeating units, -CO-NH-CHR-, based on the fact that the repeating unit has a plane structure. The changing trend of the expansion factor ${\alpha}_{\eta}$ in the transition region is connected with the helical content $f_H$. The intrinsic viscosities [${\eta}$] of polypeptides are calculated from the unperturbed dimensions and the ${\alpha}_{\eta}$ factors. The above calculated results concerning $_0$ and [${\eta}$] are compared with other authors' theoretical and experimental results. From the comparison, we concluded that our theory explains better the chain dimensional behavior of polypeptides in the helix-coil transition region than others.

• BMB Reports
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• v.44 no.2
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• BMB Reports
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• v.43 no.5
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• pp.362-368
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• 2010

Dermcidin is a human antibiotic peptide that is secreted by the sweat glands and has no homology to other known antimicrobial peptides. As an initial step toward understanding dermcidin's mode of action at bacterial membranes, we used homonuclear and heteronuclear NMR to determine the conformation of the peptide in 50% trifluoroethanol solution. We found that dermcidin adopts a flexible amphipathic $\alpha$-helical structure with a helix-hinge-helix motif, which is a common molecular fold among antimicrobial peptides. Spin-down assays of dermcidin and several related peptides revealed that the affinity with which dermcidin binds to bacterial-mimetic membranes is primarily dependent on its amphipathic $\alpha$-helical structure and its length (>30 residues); its negative net charge and acidic pI have little effect on binding. These findings suggest that the mode of action of dermcidin is similar to that of other membrane-targeting antimicrobial peptides, though the details of its antimicrobial action remain to be determined.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.62-66
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• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.16 no.2
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• pp.1563-1570
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• 2015

Conformational change during chain propagation of alanine oligomer was investigated by quantum chemical calculation(QCC) using 2~5mers(${\times}=2{\sim}5$) models. For estimation of the end group effects, two types of end group. "amide type" ($CH_3CONH-and-CONHCH_3$) and "methyl type" ($CH_3CONH-and-CONHCH_3$), were prepared as both ends(N-and-C). Conformers optimized for 5-mer converged to three types of ${\Phi}/{\Psi}$ : ${\alpha}$-helix(g+/g+, or g-/g-), PPII-like(extended helix-like, g+/g-, or g-/g+), and ${\beta}$-extended (t+/t-, or t-/t+), in the order of lower energy, and the energies of left- and right- handed conformers were the same (5-mer. amide type ${\Delta}E=-1.05$, right type ${\Delta}E=-1.62$). Energies of the monomer unit(${\Delta}E$) of ${\alpha}$-helix decreased with increases of monomer.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.63-63
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• 2003

$\alpha$$_1$-Antityrpsin is a member of the serine protease inhibitor (SERPIN) family that shares a common tertiary structure. The reactive site loop (RSL) of serpins is exposed at one end of the molecule for protease binding. Upon cleavage by a target protease, the RSL is inserted into the major $\beta$-sheet A, which is a necessary process for formation of a tight inhibitory complex. Various biochemical and structural studies suggest that the rate of the RSL insertion upon binding a target protease is critical for inhibitory activity, and it is thought that helix F region (thFs3A and helix F) located in front of $\beta$-sheet A, should be lifted for the loop insertion during complex formation.

• Proceedings of the Korean Biophysical Society Conference
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• 1997.07a
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• pp.42-42
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• 1997

Local conformation of helical peptides in TFE solution are studied by NMR spectroscopy. One is a helix containing proline and the other is its alanine derivative in which alanine is substituted for the proline. Chemical shift and temperature coefficient In NMR spectroscopy can be used preliminarily to determine secondary structure in proteins and peptides.(omitted)

• Proceedings of the Korean Biophysical Society Conference
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• 1997.07a
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• pp.14-14
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• 1997

Structure of potent derivatives of gaegurin, an antimicrobial peptide from Korean frog, is studied by CD and NMR spectroscopy. Gaegurin did not show any secondary structure in aqueous environment, but adopted ${\alpha}$-helix in aqueous TFE solution, SDS and liposome buffer. NMR study showed distinct difference in stability near proline residue in helix.(omitted)

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.69-69
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• 2003

Human CD99 is a ubiquitous 32-kDa transmembrane protein encoded by the mic2 gene. The major cellular functions of CD99 protein are related to homotypic cell adhension, apoptosis, vesicular protein transport, and differentiation of thymocytes or T cells. Recently it has been reported that expression of a splice variant of CD99 transmembrane protein (Type I and Type II) increases invasive ability of human breast cancer cells. To understand structural basis for cellular functions of CD99 (Type I), we have initiated studies on hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$ using circular dichroism (CD) and multi-dimensional NMR spectroscopy. CD spectrum of hCD99$^{TMcytoI}$ in the presence of 200mM DPC and CHAPS displayed an existence $\alpha$-helical conformation. The solution structure of hCD99$^{cytoI}$ determined by NMR is composed of one N-terminal $\alpha$-helix, $\alpha$A, two C-terminal short $\alpha$-helix segments, $\alpha$B and $\alpha$C. While $\alpha$A and $\alpha$B are connected by the long flexible loop, $\alpha$B and $\alpha$C connected by type III$\beta$-turn. Although it has been rarely figured out the correlation between structure and functional mechanism of hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$, there is possibility of dimerization or oligomerization. In addition, the feasible mechanism of hCD99$^{cytoI}$ is that it could have intramolecular interaction between the N- and C- terminal domain through large flexible AB loop.

• Journal of Sericultural and Entomological Science
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• v.50 no.2
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• pp.161-165
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• 2012

Antimicrobial peptides of insects are found and reported as immune defence system against infectious agents. The peptides are produced by fat body cells and thrombocytoids, a blood cell type. Defensin is 38-45 amino acids long and consists of an ${\alpha}$-helix linked by a loop to an antiparallel ${\beta}$-sheet. Defensin from a bumblebee, Bombus ignitus, is known to comprise 52 amino acid residues. This peptide consists of two ${\alpha}$-helixes; ACAANCLSM and KTNFKDLWDKRF and one ${\beta}$-sheet; GGRCENGVCLCR. We carried out antibacterial activity test by radial diffusion assay against Staphylococcus aureus (Gram positive), Escherichia coli (Gram negative), Pseudomonas syringae (Gram negative), Candida albicans (fungi), MDRPA, MRSA, and VRE (antimicrobial resistant microbes) with synthetic oligopeptides from Peptron (Daejeon, Korea). The predicted curtailment fragment (GGRCEVCLCR-$NH_2$) for ${\beta}$-sheet had strong antibacterial activity when internal amino acids were removed. But, curtailment fragments (ACAANCLSM-$NH_2$ and TNFKDLWDKR-$NH_2$) of ${\alpha}$-helix were not showed antibacterial activity. These synthetic oligopeptides were showed the great activity against Gram positive and negative bacteria.