• 한국식품저장유통학회지
• /
• 제5권1호
• /
• pp.65-71
• /
• 1998

The changes in gel characteristics of soy protein as a result of various reagents that alter specific interactions which affect the formation and textural properties of gels, were studied. The reagents were added to 15% soy protein solutions prior to heat treatment. The gels were not formed with urea, indicating that hydrogen bonds significantly contributed to the formation and hardness of soy protein gel. Hydrophobic interactions and disulfide bonds compensated for hydrogen bonds and the contributions of electrostatic interactions to gel hardness are relatively insignificant. The farce primarily responsible for gel cohesiveness appeared to be disulfide bonds, because a significant decrease in cohesiveness was found only with the presence of N-ethylmaleimide. Adhesiveness decreased only with the addition of urea, and thus the contribution of hydrogen bonding to adhesiveness of gel could be concluded to be resent. However, adhesiveness was suggested to be interpreted not only wile molecular forces involved in gel formation but also with hydration properties of protein.

• Bulletin of the Korean Chemical Society
• /
• 제24권1호
• /
• pp.55-59
• /
• 2003

This work is focused on analyzing ion-pair interactions and showing the effect of solvent induced inter-atomic attractions in various dielectric environments. To estimate the stability of ion-pairs, SCI-PCM ab initio MO calculations were carried out. We show that the solvent-induced attraction or ‘cavitation' energy of the ion-pair interactions in solution that arises mainly from the stabilization of the water molecules by the generation of an electrostatic field. In fact, even the strong electrostatic interaction characteristic of ion-pair interactions in the gas phase cannot overcome the destabilization or reorganization of the water molecules around solute cavities that arise from cancellation of the electrostatic field. The solvent environment, possibly supplemented by some specific solvent molecules, may help place the solute molecule in a cavity whose surroundings are characterized by an infinite polarizable dielectric medium. This behavior suggests that hydrophobic residues at a protein surface could easily contact the side chains of other nearby residues through the solvent environment, instead of by direct intra-molecular interactions.

• Bulletin of the Korean Chemical Society
• /
• 제35권8호
• /
• pp.2494-2504
• /
• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Applied Biological Chemistry
• /
• 제32권2호
• /
• pp.126-131
• /
• 1989

암소에서 기른 귀리로부터 얻은 59 kD phytochrome의 liposome과 Cibacron Blue dye에 대한 결합성질을 규명하였다. 124 kD 및 118 kD phytochrome과는 달리 Pfr형의 59 kD phytochrome은 liposome 및 Cibacron Blue dye와 정전기적 힘으로 결합한다. 이러한 결과는 124 kD 및 118 kD phytochrome이 Pr형에서 Pfr형으로 광변환시 노출되는 소수표면이 59kD Pfr에는 존재하지 않음을 의미한다. 비교적으로 강한 소수부분이 59 kD polypeptide에 존재함이 알려져 있으므로 C-말단부위로부터 잘려져나간 55 kD tryptic domain이 l18kD 및 124kD Pfr의 소수표면 노출에 중요할 역할을 하는 것으로 믿어진다.

• Rapid Communication in Photoscience
• /
• 제4권1호
• /
• pp.1-8
• /
• 2015

For understanding molecular mechanisms of photochemical reactions, in particular reactions of proteins with biological functions, it is important to elucidate both the initial reactions from the photoexcited states and the series of subsequent chemical reactions, e.g., conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), and inter-protein interactions (oligomer formation, dissociation reactions). Although time-resolved detection of such dynamics is essential, these dynamics have been very difficult to track by traditional spectroscopic techniques. Here, relatively new approaches for probing the dynamics of protein photochemical reactions using time-resolved transient grating (TG) are reviewed. By using this method, a variety of spectrally silent dynamics can be detected and such data provide a valuable description about the reaction scheme. Herein, a blue light sensor protein TePixD is the exemplar. The initial photochemistry for TePixD occurs around the chromophore and is detected readily by light absorption, but subsequent reactions are spectrally silent. The TG experiments revealed conformational changes and changes in inter-protein interactions, which are essential for TePixD function. The TG experiments also showed the importance of fluctuations of the intermediates as the driving force of the reaction. This technique is complementary to optical absorption detection methods. The TG signal contains a variety of unique information, which is difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review.

• 한국응용과학기술학회지
• /
• 제30권3호
• /
• pp.380-386
• /
• 2013

N,N,N-Trimethyl-10-nitrophenoxy decylammonium bromide (N10TAB) and N,N,N,N-Tetramethyl-bis-[10-nitrophenoxy decyl]-1,6-hexanediammonium dibromide (N10-6-10N), bearing aromatic nitrophenoxy group in the end of their hydrophobic chains have been prepared, and their properties in aqueous solutions have been studied by conductivity and H-NMR spectroscopy. Below the critical micelle concentration N10-6-10N form premicelle with two or three surfactant molecules. Beyond the critical micelle concentration two molecules have strong self-aggregation ability and form micelles of rather small size and with small aggregation numbers. H-NMR at different concentrations give the informations on the environmental changes of the surfactants on their micellization progress.

• Archives of Pharmacal Research
• /
• 제26권10호
• /
• pp.846-854
• /
• 2003

The oligomerization of G-proteincoupled receptors (GPCRs) has been shown to occur by various mechanisms, such as via disulfide covalent linkages, non covalent (ionic, hydrophobic) interactions of the N-terminal, and/or transmembrane and/or intracellular domains. Interactions between GPCRs could involve an association between identical proteins (homomers) or non-identical proteins (heteromers), or between two monomers (to form dimers) or multiple monomers (to form oligomers). It is believed that muscarinic receptors may also be arranged into dimeric or oigomeric complexes, but no systematic experimental evidence exists concerning the direct physical interaction between receptor proteins as its mechanism. We undertook this study to determine whether muscarinic receptors form homomers or a heteromers by direct protein-protein interaction within the same or within different subtypes using a yeast two-hybrid system. Intracellular loops (i1, i2 and i3) and the C-terminal cytoplasmic tails (C) of human muscarinic (Hm) receptor subtypes, Hm1, Hm2 and Hm3, were cloned into the vectors (pB42AD and pLexA) of a two-hybrid system and examined for heteromeric or homodimeric interactions between the cytoplasmic domains. No physical interaction was observed between the intracellular domains of any of the Hm/Hm receptor sets tested. The results of our study suggest that the Hm1, Hm2 and Hm3 receptors do not form dimers or oligomers by interacting directly through either the hydrophilic intracellular domains or the C-terminal tail domains. To further investigate extracellular domain interactions, the N-terminus (N) and extracellular loops (o1 and o2) were also cloned into the two-hybrid vectors. Interactions of Hm2N with Hm2N, Hm2o1, Hm2o2, Hm3N, Hm3o1 or Hm3o2 were examined. The N-terminal domain of Hm2 was found to have no direct interaction with any extracellular domain. From our results, we excluded the possibility of a direct interaction between the muscarinic receptor subtypes (Hm1, Hm2 and Hm3) as a mechanism for homo- or hetero-meric dimerization/oligomerization. On the other hand, it remains a possibility that interaction may occur indirectly or require proper conformation or subunit formation or hydrophobic region involvement.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 1996년도 정기총회 및 학술발표회
• /
• pp.21-21
• /
• 1996

The hyperthermostable protein, rubredoxin from Pyrococcus furiosus is 53-residue protein with a three-stranded anti-parallel $\beta$-sheet and several loops. To investigate the effect of changes of electrostatic and hydrophobic interactions on the structure and dynamic property of P. furiosus rubredoxin, molecular dynamics simulations in water were performed on three mesophilic rubredoxins, P, furiosus rubresoxin, and 5 mutants of P. furiosus rubredoxin. (omitted)

• Korea-Australia Rheology Journal
• /
• 제15권1호
• /
• pp.27-33
• /
• 2003

Associating polymers are hydrophilic long-chain molecules to which a small amount of hydrophobic groups (hydrophobes) is incorporated. In aqueous solution, the association interactions result in the formation of three-dimensional network through flowerlike micelles at high concentrations. In colloidal suspensions, the associating polymers act as flocculated by bridging mechanism. The rheological properties of suspensions flocculated by associating polymers end-capped with hydrophobes are studied in relation to the bridging conformation. At low polymer concentrations, the polymer chains effectively form bridges between particles by multichain association. The suspensions are highly flocculated and show typical viscoelastic responses. When the polymer concentration is increased above the absorbance at saturation, the excess polymer chains remaining in the solution phase build up three-dimensional network by associating interactions. Since the presence of particles does not significantly influence the network structures in the medium, the relative viscosity, which gives a measure of the degree of flocculation is decreased with increasing polymer concentration. The bridging conformation and flocculation level vary strongly depending on the polymer concentrations.

• Biotechnology and Bioprocess Engineering:BBE
• /
• 제11권4호
• /
• pp.357-363
• /
• 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.