• KIPS Transactions on Software and Data Engineering
• /
• v.8 no.10
• /
• pp.421-426
• /
• 2019

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.

• KIPS Transactions on Software and Data Engineering
• /
• v.2 no.12
• /
• pp.899-902
• /
• 2013

In this paper, we present a method to visualize the contact region between two molecules in a protein complex in a threedimensional space. The contact region of two molecules shows compatibility in geometric aspects. Usually, the computation of the area of contact region has been used to show the strength of compatibility. The numerical value and simple drawing of contact region would be useful for comparing the relative strength of different contacts, but it is not appropriate for analysing the geometric characteristics of the contact region. In this paper, we present a method to show the compatibility between two molecules by visualizing the distance information between them.

• Polymer(Korea)
• /
• v.36 no.3
• /
• pp.338-343
• /
• 2012

Interfacial properties of commercially available soft contact lens hydrogels were studied to understand thermodynamic phenomena of protein adsorption. Hydrogel particles ($1{\times}1mm^2$) with varying water wettability were exposed to bovine serum albumin solutions for an hour. The remained albumin solutions were analyzed with Bradford assay method. The amount of protein adsorbed to hydrogels increased with protein solution concentrations following Langmuir isotherm. The partition coefficient ($P$) and Gibbs free energy cost of dehydrating the surface region by protein displacement upon adsorption increased with increasing hydrophilicity of contact lens. Understanding of physical chemistry in protein adsorption to contact lens materials enabled elucidating relationships between surface energy and albumin adsorption capacity.

• Proceedings of the Korean Society for Agricultural Machinery Conference
• /
• 1993.10a
• /
• pp.1354-1363
• /
• 1993

Optical methods were developed to examine their feasibility for quality evaluation of peanut with pod. Surface color and internal quality of peanut were measured without contact. The surface color of peanut was measured by light reflectance at a region of visible wavelengths. Its characteristic was high correlated with a visual grading of peanut. A trial machine for the color grading of peanut was developed using an optical sensor and it was considered to compare with the visual grading. The spectral reflectance at a region of near infrared wavelengths from 1,200 to 2,500nm was measured , and the chemical components of peanut were related to spectral reflectance at special wavelengths. The protein, fat and moisture contents of peanut were estimated by the near infrared methods. An infrared imaging method was developed to evaluate the internal quality of peanut with pod. As thermal characteristic of peanut with pod was deeply related to internal quality , the quality of peanut can be evaluated by temperature changes on the surface of peanut. Measurement of surface color, near infrared reflectance and thermal imaging were shown to be very effective in grading of peanut with pod.

• Journal of the Korean Magnetic Resonance Society
• /
• v.18 no.1
• /
• pp.30-35
• /
• 2014

The transcription factor CP2 regulates various biological systems at diverse tissues and cells. However, none of the four CP2 isoforms has been solved in structure yet. In particular, two different regions of the CP2b isoform have been characterized to interact with the PIAS1 in nucleus to regulate the ${\alpha}$-globin gene expression. Among them, in this study, the region encompassing residues 251-309 of CP2b was prepared as a recombinant protein and its solution structure was characterized by NMR spectroscopy. The results indicated that the CP2b(251-309) fold belongs to typical IDRs (intrinsically disordered regions), likely to facilitate promiscuous interactions with various target proteins. Unfortunately, however, its interaction with the N-terminal domain of PIAS1 (residues 1-70), which has been identified as one of the CP2b-binding sites, was not observed in the NMR-based titration experiments. Therefore, it could be postulated that the 251-309 region of CP2b would not contact with the PIAS1(1-70), but alternatively interact with another CP2b-binding region that encompasses residues 400-651 of PIAS1.

• Proceedings of the Korean Biophysical Society Conference
• /
• 2003.06a
• /
• pp.68-68
• /
• 2003

HP(2-20) (AKKVFKRLEKLEKLFSKIQNDK) derived from the N-terminus of Helicobacter pylori Ribosomal Protein L1 shows potent antimicrobial activity against bacterial, fungi and cancer cells without cytotoxic effect. In order to investigate the relationships between antimicrobial activity and the structures, several analogues have been designed and synthesized. The structures of these peptides in SDS micelles have been investigated using NMR spectroscopy and they revealed that analogue 3 has the longest, well-defined alpha-helix from Val5 to Trp19. NOESY experiments performed on HP and its analogues in nondeuterated SDS micelles show that protons in the indole ring of Trp16 are in close contact with methylene protons of SDS micelles. In order to probe the position of HP and its analogues relative to the SDS micelles, spin-labeled stearate was added. Large effects are observed for the chemical shifts and the intensities of Phe5, Glu9, Phe12, and Trp16 within the helix region by 16-doxylstearate. This result implies that 16-doxylstearate is located in the center of the micelles and the hydrophobic phase of the amphiphilic ${\alpha}$-helix is located in contact with the acyl chains of the micelles. Also, Lys3 and Lys4 at N-terminus and Lys20 at C-terminus may produce an optimal arrangement for electrostatic interactions between the sulfate head groups of the SDS and the positively charged lysyl N$\sub$3/$\^$+/. Interactions between the indole ring of Trp and the membrane, as well as the amphiphilic ${\alpha}$-helical structure of HP induced by Trp at the C-terminus may allow HP to span the lipid bilayer. These structural features are crucial for their potent antibiotic activities.

• Journal of Microbiology and Biotechnology
• /
• v.30 no.8
• /
• pp.1261-1271
• /
• 2020

Cytochrome c_L (Cytc_L) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between Cytc_L and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing Cytc_L from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T at 2.13 Å resolution. The crystal structure of Ma-Cytc_L revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na⁺, Ca⁺, and Fe²⁺ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive charge to the region. In contrast, the acidic C-terminal end provided a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. These exceptional features of Ma-Cytc_L, along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to Cytc_L within appropriate proximity for electron transfer. With this knowledge in mind, the methanol oxidation complex reconstitution in vitro could be utilized to produce metabolic intermediates at the industry level.

• Maxillofacial Plastic and Reconstructive Surgery
• /
• v.31 no.6
• /
• pp.461-468
• /
• 2009

Purpose: Platelet derived growth factor(PDGF)-BB and bone morphogenetic protein(BMP)-2 are well-known representative growth factors. The purposes of this study were to investigate the effect of rhPDGFBB and rhBMP-2 on osseointegration of titanium implants at periimplant bone defects grafted with hydroxyapatite and to evaluate the feasibility of imaging bone structures around screw-type titanium implant with micro-CT. Materials and Methods: The first molar and all premolars in the mandible region of four beagle dogs were extracted. Following a healing period of 4 months, three $8{\times}8{\times}6mm$-sized bony defects were formed and screw-type titanium implants were placed with hydroxyapatite(HA) block and growth factors; Control group, PDGF group and BMP group. Two months post-implantation, the mandible was harvested. Bone volume(BV), bone-to-implant contact(BIC) and bone mineral density(BMD) were analyzed with micro-CT and histology. Results: According to micro-CT analysis, BV and BMD measures of PDGF and BMP group were significantly higher than control group(BV; PDGF group: $p{\fallingdotseq}0.011$, BMP group: $p{\fallingdotseq}0.006$/BMD; PDGF group: $p{\fallingdotseq}0.020$, BMP group: $p{\fallingdotseq}0.011$) and BIC measures of BMP group were significantly higher than PDGF group($p{\fallingdotseq}0.015$). In histologic evaluation, BIC measures of BMP group was significantly higher than PDGF group($p{\fallingdotseq}0.048$). The values of BV in histologic sections were higher than in micro-CT images and the values of BIC in micro-CT images were higher than in histologic sections. Conclusion: The findings of this experimental study indicates that the use of rhPDGF-BB and rhBMP-2 can increase new bone formation in a large bony defect around titanium implant, and rhBMP-2 is more effective than rhPDGF-BB. Micro-CT can be considered useful for assessment as a rapid and nondestructive method for 3-dimensional measurement of bone healing around implants. Further study is necessary, however, to remove metal artifacts around titanium implant and to standardize the method.