• Proceedings of the Korean Information Science Society Conference
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• 2001.10a
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• pp.595-597
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• 2001

오늘날 인간 유전체 프로젝트(Human Genome Project)의 완성은 인간의 모든 유전자 서열정보를 제공하게 되었으며, 이러한 데이터를 바탕으로 생명현상과 관련된 산업 및 연구가 각광받게 되었다. 특히 생명체의 특정 기능을 파악하기 위한 단백질 3차 구조에 대한 연구가 활발히 진행중이다. 본 논문에서는 단백질 3차 구조를 추상적으로 기술 할 수 있는 표현기법을 기술한다. 제안된 표현기법은 단백질 2차 구조요소($\alpha$-나선구조와 $\beta$-병풍구조)를 이용하여 인접한 구성요소간의 접힘(folding)에 대한 관계를 기술하여 추상적인 단백질 3차 구조를 표현한다. 제안된 표현기법으로 기술된 추상적 단백질 3차 구조 표현은 단백질 구조에 대한 보다 빠른 이해와 다른 단백질 구조와 비교될 수 있는 장점을 지닌다.

• Bulletin of the Korean Chemical Society
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• v.20 no.9
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• pp.999-1004
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• 1999

Two compact sized globular proteins, β-lactoglobulin and α-lactalbumin were kinetically characterized at the aqueous solution surface with the measurement of surface pressure (π) and surface concentration (Γ) via a radiotracer method. The adsorption kinetics was of diffusion control at early times, the rates of increase of πand Γ being lower at longer times due to growing energy barrier. At low concentrations, an apparent time lag was observed in the evolution of π for β-lactoglobulin but not for α-lactalbumin which was shown to be due to the non-linear nature of the p- G relationship for the former. The area per molecule of an adsorbed β-lactoglobulin during adsorption was smaller than that for spread monolayer since β-lactoglobulin was not fully unfolded during the adsorption. For α-lactalbumin, however, no such difference in the molecular areas for adsorbed and spread monolayer was observed indicating thereby that α-lactalbumin unfolded much more rapidly (has looser tertiary structure) than β-lactoglobulin. Surface excess concentrations of α-lactalbumin was found to evolve in two steps possibly due to the change in the orientation of the adsorbed protein from a side-on to an end-on orientation.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.880-888
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• 2006

Pleurocidin, an $\alpha$-helical cationic antimicrobial peptide, was isolated from skin mucosa of winter flounder (Pleuronectes americamus). It had strong antimicrobial activities against Gram-positive and Gram-negative bacteria, but had very weak hemolytic activity. The Gly$^{13,17}\rightarrow$Ala analog (pleurocidin-AA) showed similar antibacterial activities, but had dramatically increased hemolytic activity. The bacterial cell selectivity of pleurocidin was confirmed through the membrane-disrupting and membrane-binding affinities using dye leakage, tryptophan fluorescence blue shift, and tryptophan quenching experiments. However, the non-cell-selective antimicrobial peptide, pleurocidin-AA, interacts strongly with both negatively charged and zwitterionic phospholipid membranes, the latter of which are the major constituents of the outer leaflet of erythrocytes. Circular dihroism spectra showed that pleurocidin-AA has much higher contents of $\alpha$-helical conformation than pleurocidin. The tertiary structure determined by NMR spectroscopy showed that pleurocidin has a flexible. structure between the long helix from $Gly^3$ to $Gly^{17}$ and the short helix from $Gly^{17}$ to $Leu^{25}$. Cell-selective antimicrobial peptide pleurocidin interacts strongly with negatively charged phospholipid membranes, which mimic bacterial membranes. Structural flexibility between the two helices may play a key role in bacterial cell selectivity of pleurocidin.

• Molecules and Cells
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• v.23 no.2
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• pp.228-238
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• 2007

Since molecular structure of hnRNP is not available in foreseeable future, it is best to construct a working model for hnRNP structure. A geometric problem, assembly of $700{\pm}20$ nucleotides with 48 proteins, is visualized by a frame work in which all the proteins participate in primary binding, followed by secondary, tertiary and quaternary binding with neighboring proteins without additional import. Thus, 40S hnRNP contains crown-like secondary structure (48 stemloops) and appearance of 6 petal (octamers) rose-like architectures. The proteins are wrapped by RNA. Co-transcriptional folding for RNP fibril of FMR1 gene can produce 2,571 stem-loops with frequency of 1 stem-loop/15.3 nucleotides and 53 40S hnRNP beaded structure. By spliceosome driven reactions, there occurs removal of 16 separate lariated RNPs, joining 17 separate beaded exonic structures and anchoring EJC on each exon junction. Skipping exon 12 has 5'GU, 3'AG and very compact folding pattern with frequency of 1 stem-loop per 12 nucleotides in short exon length (63 nucleotides). 5' end of exon 12 contains SS (Splicing Silencer) element of UAGGU. In exons 10, 15 and 17 where both regular and alternative splice sites exist, SS (hnRNP A1 binding site) is observed at the regular splicing site. End products are mature FMR-1 mRNP, 4 species of Pri-microRNAs derived from introns 7,9,15 and 3'UTR of exon17, respectively. There may also be some other regulatory RNAs containing ALU/Line elements as well.

• Economic and Environmental Geology
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• v.25 no.3
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• pp.351-358
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• 1992

The gravity measurement has been conducted at 327 station with an interval of 25 m along the survey lines of 1.6 km and 1.7 km traversing Hyungsan river and of 2.35 km and 2.42 km running N-S direction near Heunghae-eup in Pohang basin. Bouguer gravity anomalies were obtained, and geologic structure along four survey lines were interpreted by applying Fourier series and Talwani methods for two demensional body. A fault is in existence along the Hyungsan river, and northern block of it is displaced down by 150 m to 200 m relative to southern one. The thicknesses of Yeonil Group vary from 250 m to 550 m and from 150 m to 300 m in the northern and southern blocks of the fault, respectively. Another fault is in existence running E-W direction near Heunghae-eup, and its southern block is displaced down by about 250 m relative to its northern block. The thicknesses of Yeonil Group vary from 200 m to 400 m and from 500 m to 700 m in the southern and northern blocks of the fault, respectively. Above two faults are normal faults and make a graben structure, which results the age of rocks in the central region between the faults is younger than those of outside regions. This result coincides with that of paleontological study.

• BMB Reports
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• v.35 no.2
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• pp.155-164
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• 2002

The structural aspects of ervatamin B have been studied in different types of alcohol. This alcohol did not affect the structure or activity of ervatamin B under neutral conditions. At a low pH (3.0), different kinds of alcohol have different effects. Interestingly, at a certain concentration of non-fluorinated, aliphatic, monohydric alcohol, a conformational switch from the predominantly $\alpha$-helical to $\beta$-sheeted state is observed with a complete loss of tertiary structure and proteolytic activity. This is contrary to the observation that alcohol induces mostly the $\alpha$helical structure in proteins. The O-state of ervatamin B in 50% methanol at pH 3.0 has enhanced the stability towards GuHCl denaturation and shows a biphasic transition. This suggests the presence of two structural parts with different stabilities that unfold in steps. The thermal unfolding of ervatamin B in the O-state is also biphasic, which confirms the presence of two domains in the enzyme structure that unfold sequentially. The differential stabilization of the structural parts may also be a reflection of the differential stabilization of local conformations in methanol. Thermal unfolding of ervatamin B in the absence of alcohol is cooperative, both at neutral and low pH, and can be fitted to a two state model. However, at pH 2.0 the calorimetric profiles show two peaks, which indicates the presence of two structural domains in the enzyme with different thermal stabilities that are denatured more or less independently. With an increase in pH to 3.0 and 4.0, the shape of the DSC profiles change, and the two peaks converge to a predominant single peak. However, the ratio of van't Hoff enthalpy to calorimetric enthalpy is approximated to 2.0, indicating non-cooperativity in thermal unfolding.

• Journal of the Korean Chemical Society
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• v.37 no.2
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• pp.237-243
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• 1993

The primary and secondary structure of the 5S rRNA isolated from Xanthomonas celebensis were determined by enzymatic and chemical degradation methods. It consists of 119 nucleotides and contains no modified nucleosides. As with the 5S rRNAs of X. maltophilia and X. citri, it contains an additional uridine residue on the 5'-terminus. Its secondary structure was almost identical to the models previously proposed by us for the 5S rRNA of two Xanthomonas species. Its secondary structure consists of five helices, five loops and two bulges. The tertiary interactions in the 5S rRNA molecule were analyzed by Fe(II)-EDTA treatment and hybridization method using deoxyhexamer. From the fact that some adenine residues in loop M, region $I_1-C$, loop $H_1$, and loop $H_2$ become susceptible to diethylpyrocarbonate when the 5S rRNA was hybridized with deoxyhexamer complementary to the sequence $U_{35}CCCAU_{40}$ and that some nucleotide residues in loop M, loop $H_1$ and region $D-I_2$ become resistant Fe(II)-EDTA cleavage in the presence of $Mg^{2+}$, it is presumed that loops $H_1$ and $H_2$ interact with loop M in some way. In the tertiary interaction, the regions $I_1-C$ and $D-I_2$ seem to act as hinges in folding the stems $B-I_1-C$ and $D-I_2-E.$ It was found that loop $H_1$ changes into a smaller loop of three bases by forming noncanonical A : C base-pairs ih acidic environment.

• Journal of the Korean Chemical Society
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• v.50 no.5
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• pp.362-368
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• 2006

SH group modifying chemicals were used to characterize the eight cysteine residues of cabbage PLD. 5,5-dithiobis(2-nitrobenzoate)(DTNB) was used to titrate the SH group of cysteine residues . Based on the optical density at 412nm due to the reduced DTNB, 4 SH groups are found to be present in a native PLD while 8 SH groups in the denatured PLD whose tertiary structure was perturbed by 8M urea. The results imply that among the 8 cysteine residues of PLD, the half(4) are exposed on the surface whereas the other half are present at the interior of the enzyme tertiary structure. The PLD was inactivated by SH modifying reagents such as p-chloromercuribenzoate(PCMB), iodoacetate, iodoacetamide, and N-ethylmaleimide. At the addition of dithiothreitol(DTT) only the PCMB inhibited PLD activity was recovered reversibly. The micro-environment of the exposed SH group of cysteine residues was examined with various disulfide compounds with different functional groups and we found that anionic or neutral disulfides appear to be more effective than the positively charged cystamine for inactivating the PLD activity. The effect of redox state of cysteine residues on the PLD activity was further explored with H2O2. The oxidation of SH groups by H2O2 inhibited the PLD activity more than 70%, which was mostly recovered by DTT. From these results, we could confirm chemically that all the cysteine residues of PLD are present as in their reduced SH forms and the 4 SH groups exposed on the surface of the enzyme may play important roles in the regulation of PLD activity.

• Journal of the Mineralogical Society of Korea
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• v.31 no.1
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• pp.57-65
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• 2018

The geology of Hidalgo state in Mexico is formed by a Precambrian metamorphic rock base which discordantly supports a strong Paleozoic sedimentary rock sequence. Triassic-Jurassic and Cretaceous sedimentary rocks overlie the above-mentioned rocks at a discordant angle. These Mesozoic rocks are in turn covered by a Cenozoic structure which is marine at its base. At the top, the structure changes to andesitic and basaltic composition volcanic rocks. And, a great variety of mineral deposits, both metallic and nonmetallic, is present in Hidalgo state. The host rocks of these deposits are also very varied in age from Mesozoic to Tertiary. Mineralization age corresponds to Tertiary in 90% of the area. Hidalgo state occupies as an important place in national silver and manganese production. Main mineral deposits correspond to argentiferous veins hosted in sedimentary rocks. Following in order of importance are lead and zinc, as well as some small iron deposits. There is evidence of tin and molybdenum mineralization, but these deposits have not been exploited because of their low grade and volume. And, Hidalgo state has different types of nonmetallic mineral deposits such as sedimentary, hydrothermal, metamorphic and volcanic origins.

• Economic and Environmental Geology
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• v.25 no.3
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• pp.337-349
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• 1992

The Tertiary basins in Korea have widely been studied by numerous researchers producing individual results in sedimentology, paleontology, stratigraphy, volcanic petrology and structural geology, but interdisciplinary studies, inter-basin analysis and basin-forming process have not been carried out yet. Major work of this study is to elucidate evidences obtained from different parts of a basin as well as different Tertiary basins (Pohang, Changgi, Eoil, Haseo and Ulsan basins) in order to build up the correlation between the basins, and an overall picture of the basin architecture and evolution in Korea. According to the paleontologic evidences the geologic age of the Pohang marine basin is dated to be late Lower Miocence to Middle Miocene, whereas other non-marine basins are older as being either Early Miocene or Oligocene(Lee, 1975, 1978: Bong, 1984: Chun, 1982: Choi et al., 1984: Yun et al., 1990: Yoon, 1982). However, detailed ages of the Tertiary sediments, and their correlations in a basin and between basins are still controversial, since the basins are separated from each other, sedimentary sequence is disturbed and intruded by voncanic rocks, and non-marine sediments are not fossiliferous to be correlated. Therefore, in this work radiometric, magnetostratigraphic, and biostratigraphic data was integrated for the refinement of chronostratigraphy and synopsis of stratigraphy of Tertiary basins of Korea. A total of 21 samples including 10 basaltic, 2 porphyritic, and 9 andesitic rocks from 4 basins were collected for the K-Ar dating of whole rock method. The obtained age can be grouped as follows: $14.8{\pm}0.4{\sim}15.2{\pm}0.4Ma$, $19.9{\pm}0.5{\sim}22.1{\pm}0.7Ma$, $18.0{\pm}1.1{\sim}20.4+0.5Ma$, and $14.6{\pm}0.7{\sim}21.1{\pm}0.5Ma$. Stratigraphically they mostly fall into the range of Lower Miocene to Mid Miocene. The oldest volcanic rock recorded is a basalt (911213-6) with the age of $22.05{\pm}0.67Ma$ near Sangjeong-ri in the Changgi (or Janggi) basin and presumed to be formed in the Early Miocene, when Changgi Conglomerate began to deposit. The youngest one (911214-9) is a basalt of $14.64{\pm}0.66Ma$ in the Haseo basin. This means the intrusive and extrusive rocks are not a product of sudden voncanic activity of short duration as previously accepted but of successive processes lasting relatively long period of 8 or 9 Ma. The radiometric age of the volcanic rocks is not randomly distributed but varies systematically with basins and localities. It becomes generlly younger to the south, namely from the Changgi basin to the Haseo basin. The rocks in the Changgi basin are dated to be from $19.92{\pm}0.47$ to $22.05{\pm}0.67Ma$. With exception of only one locality in the Geumgwangdong they all formed before 20 Ma B.P. The Eoil basalt by Tateiwa in the Eoil basin are dated to be from $20.44{\pm}0.47$ to $18.35{\pm}0.62Ma$ and they are younger than those in the Changgi basin by 2~4 Ma. Specifically, basaltic rocks in the sedimentary and voncanic sequences of the Eoil basin can be well compared to the sequence of associated sedimentary rocks. Generally they become younger to the stratigraphically upper part. Among the basin, the Haseo basin is characterized by the youngest volcanic rocks. The basalt (911214-7) which crops out in Jeongja-ri, Gangdong-myon, Ulsan-gun is $16.22{\pm}0.75Ma$ and the other one (911214-9) in coastal area, Jujon-dong, Ulsan is $14.64{\pm}0.66Ma$ old. The radiometric data are positively collaborated with the results of paleomagnetic study, pull-apart basin model and East Sea spreading theory. Especially, the successively changing age of Eoil basalts are in accordance with successively changing degree of rotation. In detail, following results are discussed. Firstly, the porphyritic rocks previously known as Cretaceous basement (911213-2, 911214-1) show the age of $43.73{\pm}1.05$ 및 $49.58{\pm}1.13Ma$(Eocene) confirms the results of Jin et al. (1988). This means sequential volcanic activity from Cretaceous up to Lower Tertiary. Secondly, intrusive andesitic rocks in the Pohang basin, which are dated to be $21.8{\pm}2.8Ma$ (Jin et al., 1988) are found out to be 15 Ma old in coincindence with the age of host strata of 16.5 Ma. Thirdly, The Quaternary basalt (911213-5 and 911213-6) of Tateiwa(1924) is not homogeneous regarding formation age and petrological characteristics. The basalt in the Changgi basin show the age of $19.92{\pm}0.47$ and $22.05{\pm}0.67$ (Miocene). The basalt (911213-8) in Sangjond-ri, which intruded Nultaeri Trachytic Tuff is dated to be $20.55{\pm}0.50Ma$, which means Changgi Group is older than this age. The Yeonil Basalt, which Tateiwa described as Quaternary one shows different age ranging from Lower Miocene to Upper Miocene(cf. Jin et al., 1988: sample no. 93-33: $10.20{\pm}0.30Ma$). Therefore, the Yeonil Quarterary basalt should be revised and divided into different geologic epochs. Fourthly, Yeonil basalt of Tateiwa (1926) in the Eoil basin is correlated to the Yeonil basalt in the Changgi basin. Yoon (1989) intergrated both basalts as Eoil basaltic andesitic volcanic rocks or Eoil basalt (Yoon et al., 1991), and placed uppermost unit of the Changgi Group. As mentioned above the so-called Quarternary basalt in the Eoil basin are not extruded or intruaed simultaneously, but differentiatedly (14 Ma~25 Ma) so that they can not be classified as one unit. Fifthly, the Yongdong-ri formation of the Pomgogri Group is intruded by the Eoil basalt (911214-3) of 18.35~0.62 Ma age. Therefore, the deposition of the Pomgogri Group is completed before this age. Referring petrological characteristics, occurences, paleomagnetic data, and relationship to other Eoil basalts, it is most provable that this basalt is younger than two others. That means the Pomgogri Group is underlain by the Changgi Group. Sixthly, mineral composition of the basalts and andesitic rocks from the 4 basins show different ground mass and phenocryst. In volcanic rocks in the Pohang basin, phenocrysts are pyroxene and a small amount of biotite. Those of the Changgi basin is predominant by Labradorite, in the Eoil by bytownite-anorthite and a small amount pyroxene.