• Title, Summary, Keyword: Molecular interactions

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Protein-silica Interaction in Silica-based Gel Filtration Chromatography (Silica-based Gel Filtration 크로마토그래피에서의 단백질-실리카 상호작용)

  • Choi, Jung-Kap;Yoo, Gyurng-Soo
    • YAKHAK HOEJI
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    • v.35 no.6
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    • pp.461-465
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    • 1991
  • Silica-based gel filtration chromatography has been used to characterize molecular weight of proteins. However, the molecular weight measured by this method was distorted by protein-silica interactions like hydrophobic and electrostatic forces. Therefore, we characterized protein-silica interaction using two forms of phytochrome (124 kDa) having different hydrophobicity and surface charge. PH and ionic strength affected the retention time of phytochrome suggesting that electrostatic force is the major interaction between protein and silica surface.

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Nano Mechanics Analysis of Dislocation Nucleation and Interaction (전위의 생성 및 상호작용에 관한 나노 역학 해석)

  • Lee, Young-Min;Kim, Sung-Youb;Jun, Suk-Ky;Im, Se-Young
    • Proceedings of the KSME Conference
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    • pp.537-541
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    • 2004
  • Molecular dynamics simulation of nanolithography by AFM is conducted to study nucleation of various defects, and their subsequent development and interactions as well. During nanolithography via AFM, dislocation loops are emitted along the top surface, and resourceful defect interactions such as, formation of voids chain via the motion of a jog, and creations of extended nodes and Lomer-Cottrell Lock are observed.

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Electrostatically Interactive Injectable Hydrogels for Drug Delivery

  • Seo, Ji Young;Lee, Bong;Kang, Tae Woong;Noh, Jung Hyun;Kim, Min Ju;Ji, Yun Bae;Ju, Hyeon Jin;Min, Byoung Hyun;Kim, Moon Suk
    • Tissue Engineering and Regenerative Medicine
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    • v.15 no.5
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    • pp.513-520
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    • 2018
  • BACKGROUND: Several injectable hydrogels have been developed extensively for a broad range of biomedical applications. Injectable hydrogels forming in situ through the change in external stimuli have the distinct properties of easy management and minimal invasiveness, and thus provide the advantage of bypassing surgical procedures for administration resulting in better patient compliance. METHODS: The injectable in situ-forming hydrogels can be formed irreversibly or reversibly under physiological stimuli. Among several external stimuli that induce formation of hydrogels in situ, in this review, we focused on the electrostatic interactions as the most simple and interesting stimulus. RESULTS: Currently, numerous polyelectrolytes have been reported as potential electrostatically interactive in situ-forming hydrogels. In this review, a comprehensive overview of the rapidly developing electrostatically interactive in situ-forming hydrogels, which are produced by various anionic and cationic polyelectrolytes such as chitosan, celluloses, and alginates, has been outlined and summarized. Further, their biomedical applications have also been discussed. CONCLUSION: The review concludes with perspectives on the future of electrostatically interactive in situ-forming hydrogels.

Understanding Drug-Protein Interactions in Escherichia coli FabI and Various FabI Inhibitor Complexes

  • Lee, Han-Myoung;Singh, N. Jiten
    • Bulletin of the Korean Chemical Society
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    • v.32 no.1
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    • pp.162-168
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    • 2011
  • Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-$NAD^+$ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-$NAD^+$-TCL, while the contribution of $NAD^+$ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and $NAD^+$ have many effective functional groups such as aromatic $\pi$ rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-$\pi$ interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

Molecularly Imprinted Monolithic Stationary Phases for Liquid Chromatographic Separation of Tryptophan and N-CBZ-Phenylalanine Enantiomers

  • Yan, Hong-Yuan;Row, Kyung-Ho
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.11 no.4
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    • pp.357-363
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    • 2006
  • Monolithic molecularly imprinted columns were designed and prepared by an in-situ thermal-initiated copolymerization technique for rapid separation of tryptophan and N- CBZ-phenylalanine enantiomers. The influence of polymerization conditions and separation conditions on the specific molecular recognition ability for enantiomers and diastereomers was investigated. The specious molecular recognition was found to be dependent on the stereo structures and the arrangement of functional groups of the imprinted molecule and the cavities in the molecularly imprinted polymer (MIP). Moreover, hydrogen bonding interactions and hydrophobic interactions played an important role in the retention and separation. Compared to conventional MIP preparation procedures, the present method is very simple, and its macroporous structure has excellent separation properties.

Reactions of Acetyl Radical with Acetylene - A Computational Study

  • Tran, Tu Anh;Schiesser, Carl H.
    • Bulletin of the Korean Chemical Society
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    • v.31 no.3
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    • pp.595-598
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    • 2010
  • Ab initio and DFT molecular orbital calculations predict that acetyl radical reacts with acetylene through interactions primarily involving the SOMO of the radical and the in-plane ${\pi}$-bond of acetylene. An energy barrier (${\Delta}E_1$) of 39.6 kJ $mol^{-1}$ is predicted for the preferred anti arrangement of reactants at the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVDZ level of theory. NBO analysis reveals additional interactions between the radical SOMO and the nearby C-H ${\sigma}$-bond in acetylene worth about 10% of the total transition state interaction energy. This type of orbital interaction has not previously been observed in radical addition reactions involving C-C ${\pi}$-bonds.

Fertilization and the oocyte-to-embryo transition in C. elegans

  • Marcello, Matthew R.;Singson, Andrew
    • BMB Reports
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    • v.43 no.6
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    • pp.389-399
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    • 2010
  • Fertilization is a complex process comprised of numerous steps. During fertilization, two highly specialized and differentiated cells (sperm and egg) fuse and subsequently trigger the development of an embryo from a quiescent, arrested oocyte. Molecular interactions between the sperm and egg are necessary for regulating the developmental potential of an oocyte, and precise coordination and regulation of gene expression and protein function are critical for proper embryonic development. The nematode Caenorhabditis elegans has emerged as a valuable model system for identifying genes involved in fertilization and the oocyte-to-embryo transition as well as for understanding the molecular mechanisms that govern these processes. In this review, we will address current knowledge of the molecular underpinnings of gamete interactions during fertilization and the oocyte-to-embryo transition in C. elegans. We will also compare our knowledge of these processes in C. elegans to what is known about similar processes in mammalian, specifically mouse, model systems.

Molecular Docking Studies of p21-Activated Kinase-1 (PAK1) Inhibitors

  • Balupuri, Anand;Balasubramanian, Pavithra K.;Cho, Seung Joo
    • Journal of the Chosun Natural Science
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    • v.9 no.3
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    • pp.161-165
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    • 2016
  • The p21-activated kinase-1 (PAK1) has emerged as a potential target for anticancer therapy. It is overexpressed in ovarian, breast and bladder cancers. This suggests that PAK1 may contribute to tumorigenesis. 4-azaindole derivatives are reported as potent PAK1 inhibitors. The present work deals with the molecular docking studies of 4-azaindoles with PAK1. Probable binding mode of these inhibitors has been identified by molecular modeling. Docking results indicated that hydrogen bonding interactions with Glu345 and Leu347 are responsible for governing inhibitor potency of the compounds. Additionally, Val284, Val328, Met344 and Leu396 were found to be accountable for hydrophobic interactions inside the active site of PAK1.