• 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.

• 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 $E_1^3$.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.824-828
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• 2003

Our previous quantum mechanical calculations using polyalanine model systems showed that the monodipolemacrodipoleinteractions selectively stabilize α-helices and make it possible for α-helices to be formed inhydrophobic environment where the solvent effect is not available. The monodipole-macrodipole interactionsin α-helices were studied molecular mechanically using various point-charge systems available. The resultsshow that all the point-charge systems used in the calculations produce the monodipole-macrodipoleinteractions up to about 60% compared to the results of the quantum mechanical calculations. The results ofmolecular mechanical calculations are explained and discussed compared to the results of the quantummechanical calculations.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.22-22
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• 1998

Conformational energy calculations have been carried out for proline-containing alanine-based pentadecapeptides with the sequence Ac-(Ala)/sun n/-Pro-(Ala)$_{m}$-NHMe (n ＋ m = 14), in order to figure out the positional preference of proline in $\alpha$-helices. The conformational energy was computed a sum of the potential energy (ECEPP/3) and the hydration free energy computed by the hydration shell model.(omitted)d)

• 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.34 no.2
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• pp.130-133
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• 2001

The amino acid sequences of 130 kDa and 72 kDa proteins responsible for the larvicidal activity of Bacillus thuringiensis var israelensis (Bti) were analyzed by hydrophobic moment plots. A search for highly amphiphilic $\alpha$-helices was made in these proteins using the helical hydrophobic moment as a criterion of amphiphilicity The protein segments of the largest hydrophobic moments were analyzed. In the present communication we report the surface seeking helices in 130 kDa and 72 kDa proteins of Bacillus thuringiensis var israelensis. It is assumed that the surface seeking segments may participate in one of the membrane-related functions of Bacillus thuringiensis.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.557-557
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• 2012

Silicatein-${\alpha}$, the enzyme extracted from silica spicules in glass sponges, has been studied extensively in the way of chemistry from 1999, in which the pioneering work by Morse, D. E. - the discovery of the enzymatic hydrolysis in Silicatein-${\alpha}$ - was published. Since its reaction conditions are physiologically favored, synthesis of various materials, such as gallium oxide, zirconium oxide, and silicon oxide, was achieved without any hazardous wastes. Although some groups synthesized oxide films and particles, they have not achieved yet controlled morphogenesis in the reaction conditions mentioned above. With the knowledge of catalytic triad involved in hydrolysis of silicone alkoxide and oligomerization of silicic acid, we designed the novel peptide amphiphiles to not only form self-assembled structure, but also display similar activities to silicatein-${\alpha}$. Designed templates were able to self-assemble into left-handed helices for the peptide amphiphiles with L-form amino acid, catalyzing polycondensation of silicic acids onto the surface of them. It led to the formation of silica helices with 30-50 nm diameters. These results were characterized by various techniques, including SEM, TEM, and STEM. Given the situation that nano-bio-technology, the bio-applicable technology in nanometer scale, has been attracting considerable attention; this result could be applied to the latest applications in biotechnology, such as biosensors, lab-on-a-chip, biocompatible nanodevices.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.3
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• pp.64-70
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• 2018

Human Tid1, belonging to the family of the Hsp40/DnaJ, functions as a co-chaperone of cytosolic and mitochondrial Hsp70 proteins. In addition, the conserved J-domain and G/F-rich region of Tid1 has been suggested to interact with the p53 tumor suppressor protein, to translocate it to the mitochondria. Here, backbone NMR assignments were achieved for the putative p53-binding domain of Tid1. The obtained chemical shift information identified five ${\alpha}$-helices including four helices characteristic of J-domain, which are connected to a short ${\alpha}$-helix in the G/F-rich region via a flexible loop region. We expect that this structural information would contribute to our progressing studies to elucidate atomic structure and molecular interaction of the domain with p53.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.8
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• pp.1159-1165
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• 2016

The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as ${\alpha}$-helices and ${\beta}$-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility ($p{\leq}0.003$); moreover, the relatively quantitative amounts of ${\alpha}$-helices, random coils, and ${\alpha}$-helix to ${\beta}$-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility ($p{\leq}0.004$). On the other hand, the percentage of ${\beta}$-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001) and solubility (p = 0.002). These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the ${\alpha}$-helix-to-${\beta}$-sheet ratio can be used to predict the nutritional value of feed proteins.

• Bulletin of the Korean Chemical Society
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• v.24 no.10
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• pp.1478-1484
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• 2003

CRAMP was identified from a cDNA clone derived from a mouse femoral marrow cells as a member of cathelicidin-derived antimicrobial peptide. Tertiary structure of CRAMP in TFE/$H_2O$ (1 : 1, v/v) solution has been determined by NMR spectroscopy previously and consists of two amphipathic $\alpha-helices$ from Leu4 to Lys10 and from Gly16 to Leu33. These two helices are connected by a flexible region from Gly11 to Gly16. Analysis of series of fragments composed of various portion of CRAMP revealed that an 18-residue fragment with the sequence from Gly16 to Leu33 (CRAMP-18) was found to retain antibacterial activity without cytotoxicity. The effects of two Phe residues at positions 14 and 15 of CRAMP-18 on structure, antibacterial activity, and interaction with lipid membranes were investigated by $Phe^{14,15}$ ${\rightarrow}$ Ala substitution (CRAMP-18-A) in the present study. Substitution of Phe with Ala in CRAMP-18 caused a significant reduction on antibacterial and membrane-disrupting activities. Tertiary structures of CRAMP-18 in 50% TFE/$H_2O$ (1 : 1, v : v) solution shows amphipathic ${\alpha}$-helix, from $Glu^2{\;}to{\;}Leu^{18}$, while CRAMP-18-A has relatively short amphipathic ${\alpha}$-helix from $Leu^4{\;}to{\;}Ala^{15}$. These results suggest that the hydrophobic property of $Phe^{14}{\;}and{\;}Phe^15$ in CRAMP-18 is essential for its antibacterial activity, ${\alpha}$-helical structure, and interactions with phospholipid membranes.