• Title, Summary, Keyword: Molecular interactions

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Protein-protein Interaction Networks: from Interactions to Networks

  • Cho, Sa-Yeon;Park, Sung-Goo;Lee, Do-Hee;Park, Byoung-Chul
    • BMB Reports
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    • v.37 no.1
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    • pp.45-52
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    • 2004
  • The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.

Theoretical Study on Interactions between N-Butylpyridinium Nitrate and Thiophenic Compounds

  • Lu, Renqing;Liu, Dong;Wang, Shutao;Lu, Yukun
    • Bulletin of the Korean Chemical Society
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    • v.34 no.6
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    • pp.1814-1822
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    • 2013
  • By using density functional theory calculations, we have performed a systemic study on the electronic structures and topological properties of interactions between N-butylpyridinium nitrate ($[BPY]^+[NO_3]^-$) and thiophene (TS), benzothiophene (BT), dibenzothiophene (DBT), naphthalene (NAP). The most stable structure of $[BPY]^+[NO_3]^-$ ion pair indicates that hydrogen bonding interactions between oxygen atoms on $[NO_3]^-$ anion and C2-H2 on pyridinium ring play a dominating role in the formation of ion pair. The occurrence of hydrogen bonding, ${\pi}{\cdots}$H-C, and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and TS, BT, DBT, NAP has been corroborated at the molecular level. But hydrogen bonding and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and NAP are weak in terms of structural properties and NBO, AIM analyses. DBT is prior to adsorption on N-butylpyridinium nitrate ionic liquid.

Molecular dynamics simulation of short peptide in DPC micelle using explicit water solvent parameters

  • Kim, Ji-Hun;Yi, Jong-Jae;Won, Hyung-Sik;Son, Woo Sung
    • Journal of the Korean Magnetic Resonance Society
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    • v.22 no.4
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    • pp.139-143
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    • 2018
  • Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

MAP kinase kinase kinase as a positive defense regulator in rice-blast fungus interactions

  • Kim, Jung-A;Jung, Young-Ho;Lee, Joo-Hee;Jwa, Nam-Soo
    • Proceedings of the Korean Society of Plant Pathology Conference
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    • pp.48-52
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    • 2004
  • We have found the role of rice mitogen-activated protein kinase kinase kinase (MAPKKK), OsEDR1, as controling hypersensitive response (HR) and increased disease resistance to rice blast fungus Magnaporthe grisea. Generation of transgenic rice plants through introduction of the over-expression construct of OsEDR1 using Agrobacterium-mediated transformation results in lesion mimic phenotype. Up-regulation of defense mechanism was detected through detection of increased transcription level of rice PBZ1 and PR1a. Inoculation of rice blast fungus on the lesion mimic transgenic lines displayed significantly increased resistance. The disease symptoms were arrested like HR responses which are commonly detected in the incompatible interactions. High accumulation of phenolic compounds around developing lesions was detected under UV light. There was variation among transgenic lines on the timing of lesion progression as well as the lesion numbers on the rice leaves. Transgenic lines with few lesions also show increased resistance as well as equal amount of grain yields compared to that of wild type rice cultivar Nipponbare. This is the first report of the MAPKKK as a positive regulator molecule on defense mechanism through inducing HR-like cell death lesion mimic phenotype. The application of OsEDR1 is highly expected for the development of resistant cultivars against rice pathogens.

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Mechanical Properties of Hydrated Cement Paste: Development of Structure-property Relationships

  • Ghebrab, Tewodros T.;Soroushian, Parviz
    • International Journal of Concrete Structures and Materials
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    • v.4 no.1
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    • pp.37-43
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    • 2010
  • Theoretical models based on modern interpretations of the morphology and interactions of cement hydration products are developed for prediction of the mechanical properties of hydrated cement paste (hcp). The models are based on the emerging nanostructural vision of calcium silicate hydrate (C-S-H) morphology, and account for the intermolecular interactions between nano-scale calcium C-S-H particles. The models also incorporate the effects of capillary porosity and microcracking within hydrated cement paste. The intrinsic modulus of elasticity and tensile strength of hydrated cement paste are determined based on intermolecular interactions between C-S-H nano-particles. Modeling of fracture toughness indicates that frictional pull-out of the micro-scale calcium hydroxide (CH) platelets makes major contributions to the fracture energy of hcp. A tensile strength model was developed for hcp based on the linear elastic fracture mechanics theories. The predicted theoretical models are in reasonable agreements with empirical models developed based on the experimental performance of hcp.

Molecular Modeling of the Subtype Dopamine Receptor-ligand Interactions

  • Baek, Minkyung;Shin, Woong-Hee
    • Proceeding of EDISON Challenge
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    • pp.13-24
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    • 2013
  • Dopamine agonists and antagonists and its receptor play a critical role in the information transfer in the nervous system, and dopamine receptor-ligands interactions are deeply related to Parkinson's disease, schizophrenia and some other mental diseases. However, the only experimental 3D structure available for dopamine receptors is human D3 dopamine receptor. Therefore, it is important to create model of subtype dopamine receptor-ligands interactions. We report here the 3D structures of the human D1 and D2 dopamine receptor predicted by using GalaxyTBM, and its predicted binding site determined by using GalaxyDock. The highly conserved Asp on TM 3 and Phe on TM 6 have critical role in ligand binding. Also, highly conserved serines on TM 5 are essential for binding agonists and some kinds of antagonists. We identify differences between binding sites of agonists and antagonists of human D1 and D2 dopamine receptor, and find the reasons of selective binding of antagonists.

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Heterogeneous interaction network of yeast prions and remodeling factors detected in live cells

  • Pack, Chan-Gi;Inoue, Yuji;Higurashi, Takashi;Kawai-Noma, Shigeko;Hayashi, Daigo;Craig, Elizabeth;Taguchi, Hideki
    • BMB Reports
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    • v.50 no.9
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    • pp.478-483
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    • 2017
  • Budding yeast has dozens of prions, which are mutually dependent on each other for the de novo prion formation. In addition to the interactions among prions, transmissions of prions are strictly dependent on two chaperone systems: the Hsp104 and the Hsp70/Hsp40 (J-protein) systems, both of which cooperatively remodel the prion aggregates to ensure the multiplication of prion entities. Since it has been postulated that prions and the remodeling factors constitute complex networks in cells, a quantitative approach to describe the interactions in live cells would be required. Here, the researchers applied dual-color fluorescence cross-correlation spectroscopy to investigate the molecular network of interaction in single live cells. The findings demonstrate that yeast prions and remodeling factors constitute a network through heterogeneous protein-protein interactions.