• Title, Summary, Keyword: Molecular interactions

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Molecular Design for the Formation of Two-dimensional Molecular Networks: STM Study of ${\gamma}$-phenylalanine on Au(111)

  • Jeon, A-Ram;Youn, Young-Sang;Lee, Hee-Seung;Kim, Se-Hun
    • Proceedings of the Korean Vacuum Society Conference
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    • pp.205-205
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    • 2011
  • The self-assembly of ${\gamma}$-phenylalanine on Au(111) at 150 K was investigated using scanning tunneling microscopy (STM). Phenylalanine can potentially form two-dimensional (2D) molecular networks through hydrogen bonding (through the carboxyl and amino groups) and ${\pi}-{\pi}$ stacking interactions (via aromatic rings). We found that ${\gamma}$-phenylalanine molecules self-assembled on Au(111) surfaces into well-ordered structures such as ring-shaped clusters (at low and intermediate coverages) and 2D molecular domains (intermediate and monolayer coverages), whereas ${\alpha}$-phenylalanine molecules formed less-ordered structure on Au(111). The self-assembly of ${\gamma}$- but not ${\alpha}$-phenylalanine may be related to the flexibility of the carboxyl and amino groups in the molecule. Moreover, as expected, the 2D molecular network of ${\gamma}$-phenylalanine on Au(111) was mediated by a combination of hydrogen bonding and ${\pi}-{\pi}$ stacking interactions.

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Intramolecular Hydrogen Bonds in Proteinase Inhibitor Protein, A Molecular Dynamics Simulation Study

  • Chung, Hye-Shin
    • BMB Reports
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    • v.29 no.4
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    • pp.380-385
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    • 1996
  • Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

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Flavonoids inhibit the AU-rich element binding of HuC

  • Kwak, Ho-Joong;Jeong, Kyung-Chae;Chae, Min-Ju;Kim, Soo-Youl;Park, Woong-Yang
    • BMB Reports
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    • v.42 no.1
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    • pp.41-46
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    • 2009
  • Post-transcriptional regulation of mRNA stability by Hu proteins is an important mechanism for tumorigenesis. We focused on the molecular interactions between the HuC protein and AU-rich elements (AREs) to find chemical inhibitors of RNA-protein interactions using RNA electrophoretic mobility shift assay with non-radioactive probes. Screening of 52 natural compounds identified 14 candidate compounds that displayed potent inhibitory activity. Six (quercetin, myricetin, (-)-epigallocatechin gallate, ellagic acid, (-)-epicatechin gallate, and rhamnetin) were categorized as phytochemicals, and their $IC_{50}$ values were low ($0.2-1.8\;{\mu}M$).

Single Interaction Force of Biomolecules Measured with Picoforce AFM (원자 힘 현미경을 이용한 단일 생분자 힘 측정)

  • Jung, Yu-Jin;Park, Joon-Won
    • Journal of the Korean Vacuum Society
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    • v.16 no.1
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    • pp.52-57
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    • 2007
  • The interaction force between biomolecules(DNA-DNA, antigen-antibody, ligand-receptor, protein-protein) defines not only biomolecular function, but also their mechanical properties and hence bio-sensor. Atomic force microscopy(AFM) is nowadays frequently applied to determine interaction forces between biological molecules and biomolecular force measurements, obtained for example using AFM can provide valuable molecular-level information on the interactions between biomolecules. A proper modification of an AFM tip and/or a substrate with biomolecules permits the direct measurement of intermolecular interactions, such as DNA-DNA, protein-protein, and ligand-receptor, etc. and a microcantilever-based sensor appeared as a promising approach for ultra sensitive detection of biomolecular interactions.

Epigallocatechin 3-gallate Binds to Human Salivary α-Amylase with Complex Hydrogen Bonding Interactions

  • Lee, Jee-Young;Jeong, Ki-Woong;Kim, Yang-Mee
    • Bulletin of the Korean Chemical Society
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    • v.32 no.7
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    • pp.2222-2226
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    • 2011
  • Amylase is a digestive enzyme that catalyses the starch into sugar. It has been reported that the green tea flavonoid (or polyphenols) (-)-epigallocatechin 3-gallate (EGCG) inhibits human salivary ${\alpha}$-amylase (HSA) and induced anti-nutritional effects. In this study, we performed docking study for seven EGCG-like flavonoids and HSA to understand the interaction mechanism of HSA and EGCG and suggest new possible flavonoid inhibitors of HSA. As a result, EGCG and (-)-epicatechin gallate (ECG) bind to HSA with complex hydrogen bonding interactions. These hydrogen bonding interactions are important for inhibitory activity of EGCG against HSA. We suggested that ECG can be a potent inhibitor of HSA. This study will be helpful to understand the mechanism of inhibition of HSA by EGCG and give insights to develop therapeutic strategies against diabetes.

Fluid heating in a nano-scale Poiseuille flow: A non-equilibrium molecular dynamics study

  • Faraji, Fahim;Rajabpour, Ali
    • Current Applied Physics
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    • v.17 no.12
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    • pp.1646-1654
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    • 2017
  • In this paper we develop a non-equilibrium molecular dynamics computer simulation to study the fluid heating in a nano scale Poiseuille flow system and discuss the effects of the fluid-wall interaction strength and wall temperature on the fluid heating. We calculate the fluid temperature distribution, as well as the heat flux from the fluid towards the walls and the interfacial thermal resistance and discuss the variations of the fluid heating caused by the viscous and surface frictions as the fluid-wall interaction strength and wall temperature vary. It is found that as the fluid-wall interactions strengthen, the fluid heating diminishes. In weak interactions, the heat flux from the fluid to the wall is almost independent of the wall temperature while the interfacial thermal resistance decreases with increased wall temperature and the surface friction is the major contribution to the fluid heating; in contrast, in large interactions, both the heat flux and thermal resistance increase with increased wall temperature and the viscous friction is the major contribution to the fluid heating.

Molecular Dynamics Simulations of Small n-Alkane Clusters in a Mesoscopic Solvent

  • Ko, Seo-Young;Lee, Song-Hi
    • Bulletin of the Korean Chemical Society
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    • v.24 no.6
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    • pp.771-776
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    • 2003
  • The structural and dynamic properties of small n-alkane clusters embedded in a mesoscopic solvent are investigated. The solvent interactions are taken into account through a multi-particle collision operator that conserves mass, momentum and energy and the solvent dynamics is updated at discrete time intervals. The cluster molecules interact among themselves and with the solvent molecules through intermolecular forces. The properties of n-heptane and n-decane clusters interacting with the mesoscopic solvent molecules through repulsive Lennard-Jones interactions are studied as a function of the number of the mesoscopic solvent molecules. Modifications of both the cluster and solvent structure as a result of cluster-solvent interactions are considered. The cluster-solvent interactions also affect the dynamics of the small n-alkane clusters.

Assessment of the Performance of B2PLYP-D for Describing Intramolecular π-π and σ-π Interactions

  • Choi, Tae-Hoon;Han, Young-Kyu
    • Bulletin of the Korean Chemical Society
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    • v.32 no.12
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    • pp.4195-4198
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    • 2011
  • Intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

Impacts of C60-Ionic Liquids (ILs) Interactions and IL Alkyl Chain Length on C60 Dispersion Behavior: Insights at the Molecular Level

  • Wang, Zhuang;Tang, Lili;Wang, Degao
    • Bulletin of the Korean Chemical Society
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    • v.35 no.9
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    • pp.2679-2683
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    • 2014
  • Mechanisms underlying the impacts of interactions between carbon nanoparticles (CNPs) and ionic liquids (ILs) on the physicochemical behavior of CNPs need to be more full worked out. This manuscript describes a theoretical investigation at multiple levels on the interactions of fullerene $C_{60}$ with 21 imidazolium-based ILs of varying alkyl side chain lengths and anionic types and their impacts on $C_{60}$ dispersion behavior. Results show that ${\pi}$-cation interaction contributed to mechanism of the $C_{60}$-IL interaction more than ${\pi}$-anion interaction. The calculated interaction energy ($E_{INT}$) indicates that $C_{60}$ can form stable complex with each IL molecule. Moreover, the direction of charge transfer occurred from IL to $C_{60}$ during the $C_{60}$-IL interaction. Quantitative models were developed to evaluate the self-diffusion coefficient of $C_{60}$ ($D_{fullerene}$) in bulk ILs. Three interpretative molecular descriptors (heat of formation, $E_{INT}$, and charge) that describe the $C_{60}$-IL interactions and the alkyl side chain length were found to be determinants affecting $D_{fullerene}$.