• Molecules and Cells
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• 제42권1호
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• pp.56-66
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• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.

• Bulletin of the Korean Chemical Society
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• 제33권2호
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• pp.583-588
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• 2012

Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide ($FTZ^{PEP}$) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, $FTZ^{PEP}$ formed ${\alpha}$-helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of $FTZ^{PEP}$. The solution structure of $FTZ^{PEP}$ in the presence of FTZ-F1 displays a long stretch of the ${\alpha}$-helix with a bend in the middle of helix.

• Bulletin of the Korean Chemical Society
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• 제29권8호
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• pp.1510-1518
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• 2008

Results of intrinsic and extrinsic fluorescence studies on choline oxidase revealed that the enzyme at high alkaline pH values has more accessible hydrophobic patches relative to acidic pH. Fluorescence quenching studies with acrylamide confirm these changes. The quenching constants were also determined at different pH(s) by using the Stern-Volmer equation. CD studies showed that at higher pH a transition from $\alpha$-helix to $\beta$- structure was appeared while at lower pH the content of $\alpha$-helix structure was increased. Furthermore, analysis of the spectral data using chemometric method gave evidence for existence of intermediate components at very high pH(s). Results of thermal denaturation evaluated that the enzyme has the most instability at higher pH(s). Altogether low and high pH values caused significant alteration on secondary and tertiary structures of choline oxidase via inducing of an intermediate.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.41-44
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• 2005

Cytokines play a crucial role in the immune and inflammatory responses. But because of the high evolutionary rate of these proteins, the similarity between different members of their family is very low, which makes the identification of novel members of cytokines very difficult. According to this point, a new bioinformatic strategy to identify novel cytokine of the short-chain and long-chain 4${\alpha}$ helix cytokine using hidden markov model (HMM) is proposed in the paper. As a result, two motifs were created on the two train data sets, which were used to search three different databases. In order to improve the result, a strict criterion is established to filter the novel cytokines in the subject proteins. Finally, according to their E-value, scores and the criterion, four subject proteins are predicted to be possible novel cytokines for each family respectively.

• Journal of Microbiology
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• 제45권3호
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• pp.193-198
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• 2007

A marine bacterium was isolated from Mai Po Nature Reserve of Hong Kong and identified as Vibrio cholerae MP-1. It contains a small plasmid designated as pVC of 3.8 kb. Four open reading frames (ORFs) are identified on the plasmid, but none of them shows homology to any known protein. Database search indicated that a 440 bp fragment is 96% identical to a fragment found in a small plasmid of another V. cholerae. Further experiments demonstrated that a 2.3 kb EcoRI fragment containing the complete ORF1, partial ORF4 and their intergenic region could self-replicate. Additional analyses revealed that sequence upstream of ORF1 showed the features characteristic of theta type replicons. Protein encoded by ORF1 has two characteristic motifs existed in most replication initiator proteins (Rep): the leucine zipper (LZ) motif located at the N-terminal region and the alpha helix-turn-alpha helix motif (HTH) located at the C-terminal end. The results suggest that pVC replicates via the theta type mechanism and is likely a novel type of theta replicon.

• 한국잠사곤충학회지
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• 제44권2호
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• pp.87-92
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• 2002

염화아연에 의한 작잠 견사의 용해 조건을 살펴본 후 투석법에 의하여 얻은 작잠 견피브로인 분말의 형태와 적외선 분광 특성 및 X-선 회절 특성을 살펴본 결과 다음과 같은 결론을 얻었다. 1. 작잠 견사는 고농도의 염화아연 수용액에 용해되었으나 용해 조건을 조절하여 완전하게 작잠 견사를 용해할 수 있었다. 2. 재생 작잠 분말의 구조 특성을 살펴보기 위하여 적외선 분광분석과 X-선 회절분석을 행한 결과 작잠분말은 $\beta$-sheet 구조와 $\alpha$-helix 구조로 이루어져 있었다. 3. 염화아연을 사용하여 제조한 작잠 견피브로인 용액으로부터 순수한 작잠 견피브로인을 얻기 위한 새로운 방법이 개발되어야 함을 알 수 있었다.

• 한국축산식품학회지
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• 제39권4호
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• pp.576-584
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• 2019

This study was performed to evaluate the physicochemical properties of myofibrillar protein (MP) gels containing pork skin gelatin at different salt concentrations. MP gels were prepared to the different salt levels (0.15, 0.30, and 0.45 M) with or without 1.0% of pork skin gelatin. Cooking yield (CY), gel strength, shear stress were measured to determine the physical properties, and SDS-polyacrylamide gel electrophoresis, scanning electron microscopy, fourier transform infrared spectroscopy, sulfhydryl group and protein surface hydrophobicity was performed to figure out the structural changes among the proteins. The addition of gelatin into MP increased CYs and shear stress. MP at 0.45 M salt level had the highest CY and shear stress, as compared to MPs at lower salt concentrations. As the salt concentration of MP gels increased, the microstructure became the compact and wet structures, and decreased the amount of ${\alpha}-helix$/unordered structures and ${\beta}-sheet$. MP with gelatin showed a decreased amount of ${\alpha}-helix$/unordered structures and ${\beta}-sheet$ compared to MP without gelatin. The addition of gelatin to MP did not affect the sulfhydryl group, but the sulfhydryl group decreased as increased salt levels. MP mixtures containing gelatin showed a higher hydrophobicity value than those without gelatin, regardless of salt concentration. Based on these results, the addition of gelatin increased viscosity of raw meat batter and CY of MP gels for the application to low salt meat products.

• 대한화학회지
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• 제38권10호
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• pp.710-718
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• 1994

본 연구에서는 ${\alpha}$-aminoisobutyric acid (Aib)와 alanine (Ala)이 교대로 결합된 올리고펩티드(Buo-(Ala-Aib)$_n$-oMe:여기서 Buo는 t-butoxy를 oMe는 methoxy를 의미한다)의 구조적인 전이현상을 적절하게 설명할 수 있는 통계 열역학적인 이론을 제시하고자 한다. Poly $\alpha-aminoisobutyric$ acid는 $3_{10}$ 나선 구조를 가지며 polyalanine은 $\alpha$ 나선구조를 가진다. 올리고펩티드(Buo-(Ala-Aib)$_n$-oMe)의 사슬 길이를 N = 4(N = 2n)에서부터 증가시킬 때, $3_{10}$ 나선구조에서 $\alpha$ 나선구조로의 전이는 사슬길이가 N = 8일 때 일어난다. 올리고 펩티드는 수용액에서 코일 구조로만 있으나, 유기용매(예를 들면, $CD_3$CN)에서는 여러가지 구조가 있을 수 있기 때문에, 코일구조만으로 된 것, 코일과 $3_{10}$ 나선구조로 된 것, 코일과 $\alpha$ 나선구조로 된 것을 zipper 모형을 사용하여 전이현상을 설명하였다. Zimm-Bragg변수인 $\alpha$와 $\xi$는 실험적인 값에 의거하였다. 각각 그 값은 $\sigma_T$ = 0.00011이고, ${\sigma}_T$ = 0.0060이며, $\xi_A$ = 10.1, $\xi_T$ = 3.90이 된다(첨자 A와 T는 각각 $\alpha$ 나선, $3_{10}$을 의미한다.) 일반적으로 사슬 전체길이를 N이라 하면 $\alpha$ 나선내에서의 나선내 수소 결합수는 N-2, N-3, N-4, ${\cdots}$, 3, 2, 1등이 있을 수 있으며, $3_{10}$ 나선에서는 N-1, N-2, N-3, N-4, ${\cdots}$, 3, 2, 1등이 있을 수 있다. 그러나 $\xi_A$와 $\xi_T$가 1보다 큰 값을 가지기 때문에, 긴 나선으로 된 사슬로 존재하는 것이 상대적으로 많다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권8호
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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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• 제24권10호
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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.