• Title/Summary/Keyword: Molecular form

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Processing of an Intracellular Immature Pullulanase to the Mature Form Involves Enzymatic Activation and Stabilization in Alkaliphilic Bacillus sp. S-1

  • Lee, Moon-Jo;Kang, Bong-Seok;Kim, Dong-Soo;Kim, Yong-Tae;Kim, Se-Kwon;Chung, Kang-Hyun;Kim, Jume-Ki;Nam, Kyung-Soo;Lee, Young-Choon;Kim, Cheorl-Ho
    • BMB Reports
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    • v.30 no.1
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    • pp.46-54
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    • 1997
  • Alkaliphilic Bacillus sp. S-1 secretes a large amount (approximately 80% of total pullulanase activity) of an extracellular pullulanase (PUL-E). The pullulanase exists in two forms: a precursor form (PUL-I: $M_r$ 180,000), and a processed form (PUL-E: $M_r$ 140,000). Two forms were purified to homogeneity and their properties were compared. PUL-I was different in molecular weight, isoelectric point, $NH_2$-terminal amino acid sequence, and stabilities over pH and temperature ranges. The catalytic activities of PUL-I were also distinguishable in the $K_m$ and $V_{max}$ values for various substrates, and in the specific activity for pullulan hydrolysis. PUL-E showed 10-fold higher specific activities than PUL-I. However. PUL-I is immunologically identical to PUL-E, suggesting that PUL-I is initially synthesized and proteolytically processed to the mature form of PUL-E. Processing was inhibited by PMSF, but not by pepstatin, suggesting that some intracellular serine proteases could be responsible for processing of the PUL-I. PUL-I has a different conformational structure for antibody recognition from that of PUL-E. It is also postulated that the translocation of alkaline pullulanase(AP) in the bacterium possibly requires processing of the $NH_2$-terminal region of the AP protein. Processing of the precursor involves a conformational shift. resulting in a mature form. Therefore. precursor processing not only cleaves the signal peptide, but also induces conformational shift. allowing development of active form of the enzyme.

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The Molecular Structure and Conformational Stability of Cyclobutylmethyl Ketone by MM2

  • Lee, Mu-Sang;Jung, Young-Mee
    • Bulletin of the Korean Chemical Society
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    • v.10 no.3
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    • pp.247-250
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    • 1989
  • The molecular structure of cyclobutylmethyl ketone (c-$C_4H_7COCH_3$) has been investigated by molecular mechanics II (MM2). For the monosubstituted cyclobutane there are two possible ring conformations, the equatorial and axial form, but for the cyclobutylmethyl ketone the equatorial form is predominant conformation. For the $COCH_3$ moiety there are two stable orientations which are the equatorial-gauche and the equatorial-trans form. The equatorial-gauche form where the C = O bond is nearly eclipsing (torsional angle ${\angle}C4-C3-C2-O10=14.5^{\circ}$) one of the ${\alpha}$C-C bonds of the four-membered ring was preferred conformer with steric energy of 13.37 kcal/mol. The equatorial-trans form where the C = O bond is nearly eclipsing (${\angle}C4-C3-C2-O10=145.0^{\circ}$) the ${\alpha}$ C-H bond of the four-membered ring was less stable conformer with steric energy of 15.40 kcal/mol.

Phylogenetic Analysis of the Genus Dendronephthya (Nephtheidae, Alcyonacea) Based on Internal Transcribed Spacer Sequences of Nuclear rDNA

  • Lee, Young-Ja;Song, Jun-Im
    • Animal cells and systems
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    • v.4 no.4
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    • pp.319-324
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    • 2000
  • Species boundaries among the Alcyonacean soft coral, the genus Dendronephthya, are often obscured by inter- and intraspecific morphological variations. In the present study, we attempted to infer the genetic relationships of eight dendronephthians based on their molecular characters, the internal transcribed spacer (ITS) regions of ribosomal DNA, and then compared this result together with the random amplified polymorphic DNA (RAPD) data from our previous investigation. Dendronephthya. putteri and D. suensoni formed a divaricate form - VI grade specific clade, whereas D. castanea, D. gigantea, D. aurea and D. spinifera, formed a umbellate and glomerate form - IV and III grade specific clade. Therefore, we confirmed that the main characters the growth form and the anthocodial grade and formula, are important in identification of the species in dendronephthians despite some problems. Also, the relationships of the growth form are clarified as the glomerate form is much closer to the umbellate form than to the divaricate form based on two sets of independent molecular data. However, we cannot determine the molecular markers which limit the species boundaries among this genus with ITS sequences.

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Theoretical Study of the N-(2,5-Methylphenyl)salicylaldimine Schiff Base Ligand: Atomic Charges, Molecular Electrostatic Potential, Nonlinear Optical (NLO) Effects and Thermodynamic Properties

  • Zeyrek, Tugrul C.
    • Journal of the Korean Chemical Society
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    • v.57 no.4
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    • pp.461-471
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    • 2013
  • Optimized geometrical structure, atomic charges, molecular electrostatic potential, nonlinear optical (NLO) effects and thermodynamic properties of the title compound N-(2,5-methylphenyl)salicylaldimine (I) have been investigated by using ab initio quantum chemical computational studies. Calculated results showed that the enol form of (I) is more stable than keto form. The solvent effect was investigated for obtained molecular energies, hardneses and the atomic charge distributions of (I). Natural bond orbital and frontier molecular orbital analysis of the title compound were also performed. The total molecular dipole moment (${\mu}$), linear polarizability (${\alpha}$), and first-order hyperpolarizability (${\beta}$) were calculated by B3LYP method with 6-31G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d) and 6-311++G(d,p) basis sets to investigate the NLO properties of the compound (I). The standard thermodynamic functions were obtained for the title compound with the temperature ranging from 200 to 450 K.

Mode of Action on EcoRI Restriction Endonuclease: EcoRI and EcoRI Variant N199H have Active Monomeric Forms

  • Kim, Jae-Jong;Koh, Suk-Hoon;Kim, Joong-Su;Lee, Dae-Sil
    • BMB Reports
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    • v.31 no.2
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    • pp.149-155
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    • 1998
  • The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the wild-type. A comparison of their biochemical characteristics, using synthetic oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT), helps to define the cleavage reaction pathway of these enzymes. Both EcoRI and EcoRI variant N199H were found to cleave singlestranded KA or KT about three times faster than the double-stranded forms, although the KT oligonucleotide was more susceptible. Using the ssDNA substrate in kinetic analyses, lower $K_m$ values were obtained for the N199H variant than for the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations. This difference between the endonucleases is attributed to a grealter accessibility for tbe substrate by the variant, and also a higher affinity for the DNA backbone. It also appears that the relative activities of the two enzymes, particularly at high ionic strength, are proportional to their populations in the monomeric enzyme form. That is, according to gel filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those of the wild-type are mainly dimeric. Consequently, the Asp199 residue of the EcoRI endonuclease may be implicated in the protein-protein interaction leading to dimerization, as well as in coupling to DNA substrates. In summary, it is proposed that active monomeric endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and cleavage.

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Filaments and Dense Cores in Perseus Molecular Cloud

  • Chung, Eun Jung;Lee, Chang Won
    • The Bulletin of The Korean Astronomical Society
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    • v.41 no.2
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    • pp.38.2-38.2
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    • 2016
  • How dense cores and filaments in molecular clouds form is one of key questions in star formation. To challenge this issue we started to make a systematic mapping survey of nearby molecular clouds in various environments with TRAO 14m telescope equipped with 16 beam array, in high ($N_2H^+$, $HCO^+$ 1-0) and low ($C^{18}O$, $^{13}CO$ 1-0) density tracers (TRAO Multi-beam Legacy Survey of Nearby Filamentary Molecular Clouds, PI: C. W. Lee). We pursue to dynamically and chemically understand how filaments, dense cores, and stars form under different environments. We have performed On-The-Fly (OTF) mapping observations toward L1251, southern part of Perseus molecular cloud, and Serpens main molecular cloud from January to May, 2016. In total, ~3.5 square degree area map of $^{13}CO$ and $C^{18}O$ was simultaneously obtained with S/N of >10 in a velocity resolution of ~0.2 km/s. Dense core regions of ~1.7 square degree area where $C^{18}O$ 1-0 line is strongly detected were also mapped in $N_2H^+$ 1-0 and $HCO^+$ 1-0. The L1251 and Perseus MC are known to be low- to intermediate-mass star-forming clouds, while the Serpens MC is an active low-mass star-forming cloud. The observed molecular filaments will help to understand how the filaments, cores and eventually stars form in a low- and/or intermediate-mass star-forming environment. In this talk, I'll give a brief report on the observation and show preliminary results of Perseus MC.

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Rational Design of Coordination Polymers with Flexible Oxyethylene Side Chains

  • Choi, Eun-Young;Gao, Chun-Ji;Lee, Suck-Hyun;Kwon, O-Pil
    • Bulletin of the Korean Chemical Society
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    • v.33 no.4
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    • pp.1264-1267
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    • 2012
  • We rationally designed and synthesized metallopolymers with organic 1,4-benzenedicarboxylic acid (BDC) linkers with different lengths of oxyethylene side chains in order to examine the influence of side chains on the coordination characteristics. While in a previous report the BDC linkers with alkyl side chains were found to form three-dimensional (3D) isoreticular metal-organic framework (IRMOF) structures or one-dimensional (1D) coordination polymeric structures with short $-O(CH_2)_6CH_3$ or long $-O(CH_2)_9CH_3$ side chains, respectively, new BDC linkers with oxyethylene side chains of the same lengths, $-(OCH_2CH_2)_2CH_3$ and $-(OCH_2CH_2)_3CH_3$, form only 3D IRMOF structures. This result is attributed to the higher flexibility and smaller volume of oxyethylene side chains compared to alkyl side chains.

Density Functional Theory Calculation of Molecular Structure and Vibrational Spectra of Dibanzofuran in the Ground Lowest Triplet State.

  • Lee, Sang Yeon
    • Bulletin of the Korean Chemical Society
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    • v.22 no.6
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    • pp.605-610
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    • 2001
  • The molecular geometries and harmonic vibrational frequencies of dibenzofuran in the ground and lowest triplet state have been calculated using the Hartree-Fock and Becke-3-Lee-Yang-Parr(B3LYP)density functional methods with the 6-31G basis set. Upon the excitation to the lowest triplet state, the molecular structure retains the planar form but distorts from a benzene-like to a quinone-like form in skeleton. Scaled vibrational frequencies for the ground and lowest triplet state obtained from the B3LYP calculation show excellent agreement with the available experimental data. A few vibrational fundamentals for both states are newly assigned based on the B3LYP results.

Intracellular Posttranslational Modification of Aspartyl Proteinase of Candida albicans and the Role of the Glycan Region of the Enzyme

  • 나병국;송철용
    • Korean Journal of Microbiology
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    • v.38 no.4
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    • pp.218-218
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    • 2002
  • Using two drugs, tunicamycin and brefeldin A, which affect protein processing, we investigated the intracellular processing mechanism of secreted aspartyl proteinase 1 (SAPl) of Candide albicans. Three intracellular forms of SAPI were detected by immunoblotting using menoclonal antibody (MAb) CAPl. Their molecular weights were approximately 40, 41 and 45 kDa, respectively. The 41 kDa protein is a glycoprotein and may be the same as the extracellular form judging by its molecular mass. The 40 kDa protein was the unglycosylated form and its molecular mass coincided with deglycosylated SAPl and the 45 kDa protein was also the unglycosylated form. Neither the 40 and 45 kDa proteins were detected in the culture supernatant of C. albicans. These suggested that the 40 and 45 kDa proteins might be intracellular precursor forms of SAPI. These results show that SAPI is translated as a 45 kDa precusor form in the endoplasmic reticulum and the 45 kDa precursor farm undergoes proteolytic cleavage after translocation into the Golgi apparatus, generating the 40 kDa precursor form. This 40 kDa precursor is converted into a 41 kDa mature form through glycosylation in the Golgi apparatus. The mature form of the 41 kDa protein is sorted into secretary vesicles and finally released into the extracellular space through membrane fusion. When the glycan region of SAPl was digested with N-glycosidase F, both stability and activity of the enzyme decreased. These results indicate that the glycan attached to the enzyme may, at least in parti be related to enzyme stability and activity.

Intracellular Posttranslational Modification of Aspartyl Proteinase of Candida albicans and the Role of the Glycan Region of the Enzyme

  • Na, Byung-Kuk;Song, Chul-Yong
    • Journal of Microbiology
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    • v.38 no.4
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    • pp.218-223
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    • 2000
  • Using two drugs, tunicamycin and brefeldin A, which affect protein processing, we investigated the intracellular processing mechanism of secreted aspartyl proteinase 1 (SAPl) of Candide albicans. Three intracellular forms of SAPI were detected by immunoblotting using menoclonal antibody (MAb) CAPl. Their molecular weights were approximately 40, 41 and 45 kDa, respectively. The 41 kDa protein is a glycoprotein and may be the same as the extracellular form judging by its molecular mass. The 40 kDa protein was the unglycosylated form and its molecular mass coincided with deglycosylated SAPl and the 45 kDa protein was also the unglycosylated form. Neither the 40 and 45 kDa proteins were detected in the culture supernatant of C. albicans. These suggested that the 40 and 45 kDa proteins might be intracellular precursor forms of SAPI. These results show that SAPI is translated as a 45 kDa precusor form in the endoplasmic reticulum and the 45 kDa precursor farm undergoes proteolytic cleavage after translocation into the Golgi apparatus, generating the 40 kDa precursor form. This 40 kDa precursor is converted into a 41 kDa mature form through glycosylation in the Golgi apparatus. The mature form of the 41 kDa protein is sorted into secretary vesicles and finally released into the extracellular space through membrane fusion. When the glycan region of SAPl was digested with N-glycosidase F, both stability and activity of the enzyme decreased. These results indicate that the glycan attached to the enzyme may, at least in parti be related to enzyme stability and activity.

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