Genomes and Genes
hydrophobic and hydrophilic interactions
Summary: The thermodynamic interaction between a substance and WATER.
- Kwon J, Chang S, Hong S, Shim W. Microplastics as a vector of hydrophobic contaminants: Importance of hydrophobic additives. Integr Environ Assess Manag. 2017;13:494-499 pubmed publisher..More research on the fate and effects of chemicals via microplastics should focus on those additives. Integr Environ Assess Manag 2017;13:494-499. © 2017 SETAC. ..
- Sharma I, Pattanayek S. Effect of surface energy of solid surfaces on the micro- and macroscopic properties of adsorbed BSA and lysozyme. Biophys Chem. 2017;226:14-22 pubmed publisher..During the adsorption from a mixture of BSA and lysozyme on octyl surface, first lysozyme adsorbs and subsequent BSA adsorption leads to a high surface energy. ..
- Hadler C, Wissel K, Brandes G, Dempwolf W, Reuter G, Lenarz T, et al. Photochemical coating of Kapton® with hydrophilic polymers for the improvement of neural implants. Mater Sci Eng C Mater Biol Appl. 2017;75:286-296 pubmed publisher..In the case of the DMAA copolymer even a strong anti-adhesive behavior towards fibroblasts was verified. Biocompatibility of the polymer coatings was proven which enables their utilization in biomedical applications. ..
- Pal S, Saha C. Solvent effect in the synthesis of hydrophobic drug-loaded polymer nanoparticles. IET Nanobiotechnol. 2017;11:443-447 pubmed publisher..According to the authors' observations acetone is a better solvent for encapsulating quercetin in polymer nanoparticles owing to its physical and chemical properties. ..
- Su C, Tzagoloff A. Cox16 protein is physically associated with Cox1p assembly intermediates and with cytochrome oxidase. J Biol Chem. 2017;292:16277-16283 pubmed publisher..In conclusion, our results indicate that Cox16p is a constituent of several Cox1p assembly intermediates and of COX. ..
- Lee Y, Jun Y, Choi H, Huh Y, Kaang B, Jang D, et al. Development of LC3/GABARAP sensors containing a LIR and a hydrophobic domain to monitor autophagy. EMBO J. 2017;36:1100-1116 pubmed publisher..HyD-LIR(TP)-GFP allowed live-imaging of dynamic autophagosomes upon autophagy induction. These novel autophagosome sensors can thus be widely used in autophagy research. ..
- Chang C, Hsu H, Yen J, Lo S, Liou J. A Sequence in the loop domain of hepatitis C virus E2 protein identified in silico as crucial for the selective binding to human CD81. PLoS ONE. 2017;12:e0177383 pubmed publisher..The sequence of the human-specific, stronger-binding E2-site2 could serve as a candidate template for the future development of HCV-inhibiting peptide drugs. ..
- Rai J. Mini Heme-Proteins: Designability of Structure and Diversity of Functions. Curr Protein Pept Sci. 2017;18:1132-1140 pubmed publisher..Therefore heme proteins are easier to work on for designing novel proteins for industrial and medical applications. ..
- Gao Q, Wang Y, Hou J, Yao Q, Zhang J. Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products. J Comput Aided Mol Des. 2017;31:625-641 pubmed publisher..The found MMP-9 inhibitors of natural products could serve as the lead compounds for designing the new MMP-9 inhibitors by carrying out structural modifications in the future. ..
- Liu C, Li H, Wang Q, Crommen J, Zhou H, Jiang Z. Preparation and evaluation of 400?m I.D. polymer-based hydrophilic interaction chromatography monolithic columns with high column efficiency. J Chromatogr A. 2017;1509:83-90 pubmed publisher..It is particularly worth mentioning that these 400?m I.D. polymer-based HILIC monolithic columns exhibit enhanced mechanical strength owing to the thicker capillary wall of the fused-silica capillaries. ..
- Sarkar A, Banik A, Pathak B, Mukhopadhyay S, Chatterjee S. Envelope protein gene based molecular characterization of Japanese encephalitis virus clinical isolates from West Bengal, India: a comparative approach with respect to SA14-14-2 live attenuated vaccine strain. BMC Infect Dis. 2013;13:368 pubmed publisher..Such naturally occurring evolution is likely to affect the disease profile and the vaccine efficacy to protect against JEV GI may demand careful evaluation. ..
- Xia Y, Shang Y, Zhang R, Zhu J. Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain. Biochem J. 2017;474:2817-2828 pubmed publisher..Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. ..
- Haraszti R, Roux L, Coles A, Turanov A, Alterman J, Echeverria D, et al. 5?-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res. 2017;45:7581-7592 pubmed publisher..Moreover, we show that 5?-(E)-vinylphosphonate stabilizes 5? phosphate, thereby enabling systemic delivery to and silencing in kidney and heart...
- Liou Y, Charoenkwan P, Srinivasulu Y, Vasylenko T, Lai S, Lee H, et al. SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides. BMC Bioinformatics. 2014;15 Suppl 16:S4 pubmed publisher..SCMHBP yields knowledge that improves our understanding of HBPs rather than merely improves the prediction accuracy in predicting HBPs. ..
- Shatnawi M, Zaki N, Yoo P. Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties. BMC Bioinformatics. 2014;15 Suppl 16:S8 pubmed publisher..Our experimental results prove that the proposed approach is useful for domain-linker identification in highly imbalanced single- and multi-domain proteins. ..
- Megremis S, Tiba A, Vogt K. An evaluation of eight elastomeric occlusal registration materials. J Am Dent Assoc. 2012;143:1358-60 pubmed
- Dorival García N, Bones J. Evaluation of solvent systems for optimized extractables studies of single use bioprocessing solutions. J Chromatogr A. 2017;1513:69-77 pubmed publisher..The developed approach was applied to seven SUBs from different vendors and production dates facilitating the identification of potentially non-satisfactory films for cultivation of CHO cell lines under process conditions. ..
- Serrano S, Huarte N, Rujas E, Andreu D, Nieva J, Jimenez M. Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance. Biochemistry. 2017;56:5503-5511 pubmed publisher..We conclude that, beyond hydrophobicity, preserving sequence order is an important feature for defining the secondary structures and oligomeric states adopted by the HIV FP in membranes. ..
- Dołżonek J, Cho C, Stepnowski P, Markiewicz M, Thöming J, Stolte S. Membrane partitioning of ionic liquid cations, anions and ion pairs - Estimating the bioconcentration potential of organic ions. Environ Pollut. 2017;228:378-389 pubmed publisher..However, this preliminary estimation need to be confirmed by in vivo bioconcentration studies. ..
- Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, et al. Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation. Nucleic Acids Res. 2017;45:7494-7506 pubmed publisher..The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms. ..
- Wang Y, Wang K, Zhang R, Liu X, Yan X, Wang J, et al. Synthesis of core-shell graphitic carbon@silica nanospheres with dual-ordered mesopores for cancer-targeted photothermochemotherapy. ACS Nano. 2014;8:7870-9 pubmed..Thus, the MMPSD system exhibited efficient drug loading capacity, high targeting ability, sensitive NIR/pH-responsive DOX release, sustained release, and excellent combined antitumor activity. ..
- Martinez Gonzalez A, Díaz Sánchez A, Rosa L, Vargas Requena C, Bustos Jaimes I, Alvarez Parrilla A. Polyphenolic Compounds and Digestive Enzymes: In Vitro Non-Covalent Interactions. Molecules. 2017;22: pubmed publisher..Existing studies conducted in vitro allow one to elucidate the characteristics of the structure-function relationships, where differences between the structures of PCs might be the reason for different in vivo effects. ..
- Huang L, Lilley D. The molecular recognition of kink-turn structure by the L7Ae class of proteins. RNA. 2013;19:1703-10 pubmed publisher..Taken together, these interactions are highly selective for the structure of the k-turn and suggest how conformational selection of the folded k-turn occurs...
- Ferreira G, Ferreira G, Hespanhol M, Rezende J, Pires A, Ortega P, et al. A simple and inexpensive thermal optic nanosensor formed by triblock copolymer and polydiacetylene mixture. Food Chem. 2018;241:358-363 pubmed publisher..The results here demonstrated that the balance of intermolecular interaction between TC-TC, TC-DA, and DA-DA enables the construction of strategic sensor for detecting temperature changes in different applications. ..
- Azouzi S, Santuz H, Morandat S, Pereira C, CÃ´tÃ© F, Hermine O, et al. Antioxidant and Membrane Binding Properties of Serotonin Protect Lipids from Oxidation. Biophys J. 2017;112:1863-1873 pubmed publisher..Taken together, our results identify 5-HT as a potent inhibitor of lipid peroxidation and offer a different perspective on the role of this pleiotropic molecule. ..
- Tanaka M, Kurosawa S. Surface Modification of PDMS and Plastics with Zwitterionic Polymers. J Oleo Sci. 2017;66:699-704 pubmed publisher..The modified surfaces showed suppression effect for nonspecific adsorption of BSA compared with the surface only treated with plasma. ..
- Iizuka R, KOTCH F, Xu A, Porter T, Shion H, Birdsall R, et al. The Characterization of Drug-to-Antibody Ratio and Isoforms of ADCs Using LC and MS Technologies. Yakugaku Zasshi. 2017;137:525-528 pubmed publisher..ADC was detected as the sub-units by MS and the conjugation site was identified via a middle down approach. ..
- Purves R, Khazaei H, Vandenberg A. Quantification of vicine and convicine in faba bean seeds using hydrophilic interaction liquid chromatography. Food Chem. 2018;240:1137-1145 pubmed publisher..The analysis of 13 genotypes suggests that v-c concentrations in faba bean seeds may be independent quantitative traits. ..
- Qi Q, Yang W, Zhou H, Ming D, Sun K, Xu T, et al. The structure of a complex of the lactonohydrolase zearalenone hydrolase with the hydrolysis product of zearalenone at 1.60?Å resolution. Acta Crystallogr F Struct Biol Commun. 2017;73:376-381 pubmed publisher..This structure provides information on the final stage of the catalytic mechanism of zearalenone hydrolysis...
- Brown M. Soft Matter in Lipid-Protein Interactions. Annu Rev Biophys. 2017;46:379-410 pubmed publisher..A flexible surface model describes how curvature and hydrophobic forces lead to the emergence of new protein functional states within the membrane lipid bilayer. ..
- Schauder C, Wu X, Saheki Y, Narayanaswamy P, Torta F, Wenk M, et al. Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature. 2014;510:552-5 pubmed..These findings provide strong evidence for a role of SMP-domain-containing proteins in the control of lipid transfer at membrane contact sites and have broad implications beyond the field of ER-to-PM appositions. ..
- Pane K, Durante L, Crescenzi O, Cafaro V, Pizzo E, Varcamonti M, et al. Antimicrobial potency of cationic antimicrobial peptides can be predicted from their amino acid composition: Application to the detection of "cryptic" antimicrobial peptides. J Theor Biol. 2017;419:254-265 pubmed publisher..Our strategy is also well suited to analyze large pools of sequences, thus significantly improving the identification of new CAMPs and the study of innate immunity. ..
- Jaggessar A, Shahali H, Mathew A, Yarlagadda P. Bio-mimicking nano and micro-structured surface fabrication for antibacterial properties in medical implants. J Nanobiotechnology. 2017;15:64 pubmed publisher..While the future of nano-biomaterials is promising, long-term effects of micro and nano-structures in the body must be established before nano-textures can be used on orthopaedic implant surfaces as way of inhibiting bacterial adhesion...
- Wang L, Gulati P, Santra D, Rose D, Zhang Y. Nanoparticles prepared by proso millet protein as novel curcumin delivery system. Food Chem. 2018;240:1039-1046 pubmed publisher..The encapsulation showed no negative effect on the antioxidant activity of curcumin as assessed by the DPPH and ABTS assays. These results suggested that MP could be a promising encapsulant for the delivery of lipophilic compounds. ..
- Wijma R, Bahmany S, Wilms E, van Gelder T, Mouton J, Koch B. A fast and sensitive LC-MS/MS method for the quantification of fosfomycin in human urine and plasma using one sample preparation method and HILIC chromatography. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1061-1062:263-269 pubmed publisher..Selectivity and sensitivity were confirmed and no carry-over was observed. The method was successfully applied in two pharmacokinetic studies in healthy volunteers and patients respectively. ..
- Huang X, Luo C, Lin L, Zhang L, Li H, Yao K, et al. UV-assisted treatment on hydrophobic acrylic IOLs anterior surface with methacryloyloxyethyl phosphorylcholine: Reducing inflammation and maintaining low posterior capsular opacification properties. Mater Sci Eng C Mater Biol Appl. 2017;75:1289-1298 pubmed publisher..In conclusion, our Anterior UV-MPC IOLs may reduce postoperative inflammation while maintaining the low PCO rates of hydrophobic acrylic IOLs. ..
- Ehrmann F, Stojko J, Metz A, Debaene F, Barandun L, Heine A, et al. Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition. PLoS ONE. 2017;12:e0175723 pubmed publisher..Likely, this novel twisted dimer is catalytically inactive and, therefore, suggests that stabilizing this non-productive subunit arrangement may be used as a further strategy for TGT inhibition. ..
- Shao B, Liu Z, Zhong H, Zeng G, Liu G, Yu M, et al. Effects of rhamnolipids on microorganism characteristics and applications in composting: A review. Microbiol Res. 2017;200:33-44 pubmed publisher..It is believed that rhamnolipids will play more and more important role in composting. ..
- Avellaneda Matteo D, Grunseth A, Gonzalez E, Anselmo S, Kennedy M, Moman P, et al. Molecular mechanisms of isocitrate dehydrogenase 1 (IDH1) mutations identified in tumors: The role of size and hydrophobicity at residue 132 on catalytic efficiency. J Biol Chem. 2017;292:7971-7983 pubmed publisher..We report that one mutation can support both the normal and neomorphic reactions. These studies illuminate catalytic features of mutations found in the majority of patients with lower grade gliomas. ..
- Seno K, Hayashi F. Palmitoylation is a prerequisite for dimerization-dependent raftophilicity of rhodopsin. J Biol Chem. 2017;292:15321-15328 pubmed publisher..These results indicate that palmitoylated GPCRs such as Rh can acquire raftophilicity upon G protein-stabilized dimerization and thereby organize receptor-cluster rafts by recruiting raftophilic lipids. ..
- Biswas R, Bagchi A. A comprehensive computational study on pathogenic mis-sense mutations spanning the RING2 and REP domains of Parkin protein. Gene. 2017;610:49-58 pubmed publisher..This study is based purely on computational approach which has the potential to identify disease mutations and the information could further be used in treatment of diseases and prognosis. ..
- Bakou M, Hille K, Kracklauer M, Spanopoulou A, Frost C, Malideli E, et al. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly. J Biol Chem. 2017;292:14587-14602 pubmed publisher..We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions. ..
- Kundu P, Chattopadhyay N. Interaction of a bioactive pyrazole derivative with calf thymus DNA: Deciphering the mode of binding by multi-spectroscopic and molecular docking investigations. J Photochem Photobiol B. 2017;173:485-492 pubmed publisher..In-silico molecular docking simulation corroborates the experimental findings and depicts that DSDP favorably binds to the minor groove region of the biomacromolecule. ..
- Wang B, Wu D, Ekama G, Huang H, Lu H, Chen G. Optimizing mixing mode and intensity to prevent sludge flotation in sulfidogenic anaerobic sludge bed reactors. Water Res. 2017;122:481-491 pubmed publisher..Our findings provide a method to optimize the design and operation of anaerobic sulfidogenic reactors that can be extended to similar low-gas-production anaerobic bioreactors. ..
- Iwamoto N, Butler D, Svrzikapa N, Mohapatra S, Zlatev I, Sah D, et al. Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides. Nat Biotechnol. 2017;35:845-851 pubmed publisher..Further, we elucidated a triplet stereochemical code in the stereopure ASOs, 3'-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs. ..