• Title, Summary, Keyword: hydrophobicity

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Protein Context-Dependent Hydrophobicity of Amino Acids in Protein

  • Cho, Hanul;Ham, Sihyun
    • Proceeding of EDISON Challenge
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    • pp.163-166
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    • 2016
  • Hydrophobicity is the key concept to understand the water plays in protein folding, protein aggregation, and protein-protein interaction. Traditionally, the hydrophobicity of protein is defined based on the scales of the hydrophobicity of residue, assuming that the hydrophobicity of free amino acids is maintained. Here, we explore how the hydrophobicity of constituting amino acids in protein rely on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we calculate and investigate the hydration free energy of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein total charge being positive or negative. We also observe that amino acids in the ${\beta}-sheets$ display more enhanced the hydrophobicity than amino acids in the loop, whereas those in the ${\alpha}-helix$ do not clearly show such a tendency. And the salt-bridge forming amino acids also exhibit increase of the hydrophobicity than that with no salt bridge. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

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Theoretical Study on Hydrophobicity of Amino Acids by the Solvation Free Energy Density Model

  • Kim, Jun-Hyoung;Nam, Ky-Youb;Cho, Kwang-Hwi;Choi, Seung-Hoon;Noh, Jae-Sung;No, Kyoung-Tai
    • Bulletin of the Korean Chemical Society
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    • v.24 no.12
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    • pp.1742-1750
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    • 2003
  • In order to characterize the hydrophobic parameters of N-acetyl amino acid amides in 1-octanol/water, a theoretical calculation was carried out using a solvation free energy density model. The hydrophobicity parameters of the molecules are obtained with the consideration of the solvation free energy over the solvent volume surrounding the solute, using a grid model. Our method can account for the solvent accessible surface area of the molecules according to conformational variations. Through a comparison of the hydrophobicity of our calculation and that of other experimental/theoretical works, the solvation free energy density model is proven to be a useful tool for the evaluation of the hydrophobicity of amino acids and peptides. In order to evaluate the solvation free energy density model as a method of calculating the activity of drugs using the hydrophobicity of its building blocks, the contracture of Bradykinin potentiating pentapeptide was also predicted from the hydrophobicity of each residue. The solvation free energy density model can be used to employ descriptors for the prediction of peptide activities in drug discovery, as well as to calculate the hydrophobicity of amino acids.

Hydrophobicity of Amino Acids in Protein Context

  • Cho, Hanul;Chong, Song-Ho;Ham, Sihyun
    • Proceeding of EDISON Challenge
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    • pp.103-113
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    • 2014
  • Hydrophobicity is the key concept to understand the role of water in protein folding, protein self-assembly, and protein-ligand interaction. Conventionally, hydrophobicity of amino acids in a protein has been argued based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acids depends on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we compute and analyze the hydration free energy - free energy change upon hydration quantifying the hydrophobicity - of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein net charge being positive or negative. We also observe that amino acids in the central ${\beta}$-strand sandwiched by ${\beta}$-sheets display more enhanced hydrophobicity than free amino acids, whereas those in the ${\alpha}$-helix do not clearly show such a tendency. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

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Relationship between Hydrophobicity and Pellicle Formation in a Film Strain of Hansenula beijerinckii FY-5 Isolated from Apple Wine (사과주(酒) 산막효묘(産膜酵母) Hansenula beijerinckii FY-5 의 소수성(疏水性)과 산막성(産膜性)과의 관련성(關聯性))

  • Song, Hyung-Ik;Chung, Ki-Taek
    • Korean Journal of Food Science and Technology
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    • v.17 no.3
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    • pp.203-207
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    • 1985
  • Relationship between cell surface hydrophobicity and pellicle formation was studied in a film strain isolated from stored apple wine and identified as Hansenula beijerinckii FY-5. In the media containing non-ionic surface-active agents the pellicle formation of strain FY-5 was efficiently repressed, whereas growth of the yeast was possible, and also cell surface hydrophobicity was greatly decreased by the addition of these agents. These results indicate that a pellicle formation factor, which keeps yeast cells floating on the medium surface, is necessary for the pellicle formation, and surely this factor is the hydrophobicity of the cell surface. The pellicle formation in the film strains was abundant with the increase of the cell surface hydrophobicity, whereas the non-film strains had less hydrophobicity as compared with the film strains. Ethanol, as a sole carbon source, efficiently increased hydrophobicity more than glucose, and the hydrophobicity was lowered with the rise of pH. In the experiments of time course, the hydrophobicity was increased in proportion to cell growth, and was maximum during the stationary phase.

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Effects of pH, Electrolyte Concentrations, and Alginate Molecular Weights on Surface Hydrophobicity of Soy Protein Isolates (pH, 전해질의 농도 및 알긴산 분자량이 분리콩단백질의 표면소수성에 미치는 영향)

  • Lim, Yeong-Seon;Yoo, Byung-Jin
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.45 no.9
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    • pp.1285-1292
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    • 2016
  • Changes in surface hydrophobicity of soy protein isolate (SPI), which plays an important role in the functional characteristics of protein, were measured according to various SPI concentrations, pH levels, electrolytes concentrations, and alginate molecular weights by using 1-anilino-8-naphthalene sulfonic acid as a fluorescent probe. SPI surface hydrophobicity decreased as SPI concentrations increased. SPI surface hydrophobicity reached a maximum at pH 7.0. SPI surface hydrophobicity rapidly increased as the NaCl concentration of SPI solution increased up to 100 mM, and showed no large increases above 100 mM. However, SPI surface hydrophobicity radically decreased until the $CaCl_2$ concentration reached 50 mM and revealed no large variations above 50 mM. A similar trend was exhibited in the case of $MgCl_2$. As both the concentration and molecular weight of sodium alginate increased, SPI surface hydrophobicity decreased. The increasing rate of SPI surface hydrophobicity decreased as the molecular weight of sodium alginate increased.

Effects of Added Silicone Oils on the Surface Hydrophobicity of Silicone Rubber (실리콘 고무의 소수성에 미치는 첨가된 실리콘 오일의 영향)

  • Han Dong-Hee;Cho Han-Goo;Kang Dong-Pll;Min Kyung-Eun
    • Journal of the Korean Institute of Electrical and Electronic Material Engineers
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    • v.19 no.1
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    • pp.46-51
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    • 2006
  • This paper reports on the effects of silicone oils, used as processing agents, on the recovery of hydrophobicity of silicone rubber. The recovery of hydrophobicity was evaluated by the measuring the contact angle, the surface electrical resistance and SEM. Here, we formed artificial contamination on the surface of samples, which scratched by sand papers and alumina powders. There was small recovery of hydrophobicity on the surface of SIR-A that silicone oil was not added. In both oil-added samples, SIR-B and SIR-C, recovery of hydrophobicity was achieved greatly. The surface of SIR-C showed that a lot of silicone oil was observed due to migration of oil, relatively in comparison with SIR-B. The tendency of recovery of hydrophobicity expressed by contact angle was in a good agreement with electrical property as determined by surface resistivity.

표면특성 변화에 따른 유류분해 미생물의 토양내 거동성 조절

  • 류두현;목지예;최상일;김용미;이경애
    • Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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    • pp.360-362
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    • 2003
  • The adhesion of hydrocarbon degrading bacteria(HDB) differing in surface hydrophobicity was investigated. Cell wall hydrophobicity was modified chemically and physiologically. Modified adhesion deficient mutant of HDB was selected in a soil column assay Physiologically and chemical modification increased cell surface hydrophobicity. Cell surface charcteristis including BATH and zeta potential were measured. Physiological modification using ampicillin was not stable, but chemical modification was stabel. Hydrocarbon degrading potential was measured for modified and unmodifed HDB.

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Increased Cell Surface Hydrophobicity of A Lipopolysaccharide-defective Mutant of Bradyrhizobium japonicum

  • JAE-SEONG S0;PAE, KYEONC-HOON
    • Journal of Microbiology and Biotechnology
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    • v.5 no.4
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    • pp.241-243
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    • 1995
  • A lipopolysaccharide (LPS) defective mutant of Bradyrhizobium japonicum was characterized in terms of its cell surface hydrophobicity (CSH). By monitoring the kinetics of adhesion to hexadecane the LPS mutant was found to be far more hydrophobic than the wild type strain; the removal coefficients were 4.65 $min^{-1}$ for the mutant, as compared with only 2.40 $min^{-1}$ for the wild type. The possible role of cell surface hydrophobicity of B. japonicum in nodulation process is discussed.

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Hydrophobicity and tracking resistance of SIR for outdoor Insulators (초고압 옥외용 실리콘 고무의 발수성 및 트래킹 특성)

  • Han, D.H.;Kang, D.P.;Park, H.Y.;Lee, K.H.;Lee, K.C.;Min, K.E.
    • Proceedings of the KIEE Conference
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    • pp.1560-1562
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    • 2000
  • The paper reports on a study of the influence of the silicone oils on the tracking and erosion resistance and hydrophobicity of SIR. Two silicone oils(A, B) having different chemical structure were selected in consideration of goof hydrophobicity and processability. Tracking and erosion resistance of SIR was investigated by the rotating wheel dip test (RWDT). In this test tracking and erosion areas due to glow and partial arc discharges cause an increase in the leakage current with an increase in time. Leakage current of SIR was decreased with increasing ratio of oil A/B. SIR was exposed to corona discharges in air and the specimens were analyzed with contact angle. It was observed that the contact angle of SIR was increased gradually in time. The recovery of hydrophobicity was increased with increasing ratio of oil A/B.

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Properties of Silicone Rubber According to the Addition of Different Particle Size of ATH (ATH 의 입도에 따른 실리콘 고무의 특성)

  • Park, Hyo-Yul;Kang, Dong-Pil;Ahn, Myeong-Sang;Kim, Dae-Whan;Lee, Hoo-Bum;Oh, Se-Ho
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • pp.216-219
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    • 2002
  • Much quantity of anti-tracking agent, ATH is added to the silicone rubber for the protection of silicone rubber against surface discharge. Hydrophobicity recovery properties of silicone rubber could be different by the content, surface treatment state and particle size of ATH. Because hydrophobicity of silicone rubber is depend much on the surface state of ATH. In this paper, the properties of silicone rubber is investigated according to the addition of different particle size of ATH to the silicone rubber. Hydrophobicity recovery properties and arc resistance of silicone rubber were investigated according to the addition of different particle size of ATH. Hydrophobicity recovery properties of silicone rubber were evaluated by the measurement of contact angle.

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