Academic literature on the topic 'Hydrophobic Biomolecules'
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Journal articles on the topic "Hydrophobic Biomolecules"
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Kim, S. M., and Hyun Kyu Kweon. "A Basic Study of the CNT-Biomolecule Conjugation by Molecular Dynamics Analysis." Key Engineering Materials 381-382 (June 2008): 361–64. http://dx.doi.org/10.4028/www.scientific.net/kem.381-382.361.
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This study is about the underlying conjugation mechanism between carbon nanotube and biomolecule by molecular dynamics. In order to know about the conjugation mechanism between carbon nanotube and biomolecule, molecular dynamics simulation between carbon nanotube and water molecules was taken first and then molecular dynamics simulation between biomolecules and water molecules was taken. At simulation between carbon nanotube and water molecules, kinetic energy and potential energy became decreased with time and it means that the distance between carbon nanotube and water molecules becomes distant with time by van der Waals force and hydrophobic force. Simulation results between biomolecules and water molecules are also same as the results of carbon nanotube and water molecules simulation. From these two simulations, the conjugation mechanism between carbon nanotube and biomolecules can be predicted. Also, from simulation results between carbon nanotube and biomolecules, the distance between carbon nanotube and biomolecules becames close and it supports previous two simulation results. From these results, we can know that biomolecules enter into the carbon nanotube's cavity because of van der Waals force and hydrophobic force.
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Wang, Li, Coucong Gong, Xinzhu Yuan, and Gang Wei. "Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review." Nanomaterials 9, no. 2 (February 18, 2019): 285. http://dx.doi.org/10.3390/nano9020285.
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Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π–π stacking, DNA base pairing, and ligand–receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.
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Kellert, Martin, Jan-Simon Jeshua Friedrichs, Nadine Anke Ullrich, Alexander Feinhals, Jonas Tepper, Peter Lönnecke, and Evamarie Hey-Hawkins. "Modular Synthetic Approach to Carboranyl‒Biomolecules Conjugates." Molecules 26, no. 7 (April 3, 2021): 2057. http://dx.doi.org/10.3390/molecules26072057.
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The development of novel, tumor-selective and boron-rich compounds as potential agents for use in boron neutron capture therapy (BNCT) represents a very important field in cancer treatment by radiation therapy. Here, we report the design and synthesis of two promising compounds that combine meta-carborane, a water-soluble monosaccharide and a linking unit, namely glycine or ethylenediamine, for facile coupling with various tumor-selective biomolecules bearing a free amino or carboxylic acid group. In this work, coupling experiments with two selected biomolecules, a coumarin derivative and folic acid, were included. The task of every component in this approach was carefully chosen: the carborane moiety supplies ten boron atoms, which is a tenfold increase in boron content compared to the l-boronophenylalanine (l-BPA) presently used in BNCT; the sugar moiety compensates for the hydrophobic character of the carborane; the linking unit, depending on the chosen biomolecule, acts as the connection between the tumor-selective component and the boron-rich moiety; and the respective tumor-selective biomolecule provides the necessary selectivity. This approach makes it possible to develop a modular and feasible strategy for the synthesis of readily obtainable boron-rich agents with optimized properties for potential applications in BNCT.
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Sato, Takumi, Keiko Esashika, Eiji Yamamoto, Toshiharu Saiki, and Noriyoshi Arai. "Theoretical Design of a Janus-Nanoparticle-Based Sandwich Assay for Nucleic Acids." International Journal of Molecular Sciences 23, no. 15 (August 8, 2022): 8807. http://dx.doi.org/10.3390/ijms23158807.
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Nanoparticles exhibit diverse self-assembly attributes and are expected to be applicable under unique settings. For instance, biomolecules can be sandwiched between dimer nanoparticles and detected by surface-enhanced Raman scattering. Controlling the gap between extremely close dimers and stably capturing the target molecule in the gap are crucial aspects of this strategy. Therefore, polymer-tethered nanoparticles (PTNPs), which show promise as high-performance materials that exhibit the attractive features of both NPs and polymers, were targeted in this study to achieve stable biomolecule sensing. Using coarse-grained molecular dynamics simulations, the dependence of the PTNP interactions on the length of the grafted polymer, graft density, and coverage ratio of a hydrophobic tether were examined. The results indicated that the smaller the tether length and graft density, the smaller was the distance between the PTNP surfaces (Rsurf). In contrast, Rsurf decreased as the coverage ratio of the hydrophobic surface (ϕ) increased. The sandwiching probability of the sensing target increased in proportion to the coverage ratio. At high ϕ values, the PTNPs aggregated into three or more particles, which hindered their sensing attributes. These results provide fundamental insight into the sensing applications of NPs and demonstrate the usefulness of PTNPs in sensing biomolecules.
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Kurimoto, Rio, Kei Kanie, Naokazu Idota, Mitsuo Hara, Shusaku Nagano, Takehiko Tsukahara, Yuji Narita, et al. "Combinational Effect of Cell Adhesion Biomolecules and Their Immobilized Polymer Property to Enhance Cell-Selective Adhesion." International Journal of Polymer Science 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/2090985.
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Although surface immobilization of medical devices with bioactive molecules is one of the most widely used strategies to improve biocompatibility, the physicochemical properties of the biomaterials significantly impact the activity of the immobilized molecules. Herein we investigate the combinational effects of cell-selective biomolecules and the hydrophobicity/hydrophilicity of the polymeric substrate on selective adhesion of endothelial cells (ECs), fibroblasts (FBs), and smooth muscle cells (SMCs). To control the polymeric substrate, biomolecules are immobilized on thermoresponsive poly(N-isopropylacrylamide-co-2-carboxyisopropylacrylamide) (poly(NIPAAm-co-CIPAAm))-grafted glass surfaces. By switching the molecular conformation of the biomolecule-immobilized polymers, the cell-selective adhesion performances are evaluated. In case of RGDS (Arg-Gly-Asp-Ser) peptide-immobilized surfaces, all cell types adhere well regardless of the surface hydrophobicity. On the other hand, a tri-Arg-immobilized surface exhibits FB-selectivity when the surface is hydrophilic. Additionally, a tri-Ile-immobilized surface exhibits EC-selective cell adhesion when the surface is hydrophobic. We believe that the proposed concept, which is used to investigate the biomolecule-immobilized surface combination, is important to produce new biomaterials, which are highly demanded for medical implants and tissue engineering.
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Wang, Chong, Sze Nga Tong, Yuk Hang Tse, and Min Wang. "Conventional Electrospinning vs. Emulsion Electrospinning: A Comparative Study on the Development of Nanofibrous Drug/Biomolecule Delivery Vehicles." Advanced Materials Research 410 (November 2011): 118–21. http://dx.doi.org/10.4028/www.scientific.net/amr.410.118.
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Over the past decade, intensive research has been conducted on electrospinning of fibrous tissue engineering scaffolds and their applications in body tissue regeneration. For providing multifunctions and/or enhancing the biological performance, drugs or biomolecules can be incorporated in electrospun fibers using normally one of these techniques: (1) direct dissolution, (3) emulsion electrospinning, and (3) coaxial electrospinning. In this investigation, for constructing nanofibrous delivery vehicles, conventional electrospinning using polymer solutions with directly dissolved drugs or biomolecules and emulsion electrospinning were studied and compared. Bovine serum albumin (BSA) was used as a model protein and the drug was rifamycin, a hydrophobic antibiotic. A poly (lactic-co-glycolic acid) containing the protein or drug was electrospun into fibers. In these two routes of fabricating drug-or biomolecule-loaded nanofibers, different polymer concentrations and emulsion formulations were investigated. Various aspects of the fibrous delivery vehicles were investigated using several techniques and the in vitro release behaviour was studied.
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Lou, Lillian L., and John C. Martin. "Selected Thoughts on Hydrophobicity in Drug Design." Molecules 26, no. 4 (February 7, 2021): 875. http://dx.doi.org/10.3390/molecules26040875.
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The fundamental aim of drug design in research and development is to invent molecules with selective affinity towards desired disease-associated targets. At the atomic loci of binding surfaces, systematic structural variations can define affinities between drug candidates and biomolecules, and thereby guide the optimization of safety, efficacy and pharmacologic properties. Hydrophobic interaction between biomolecules and drugs is integral to binding affinity and specificity. Examples of antiviral drug discovery are discussed.
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Nagase, Kenichi, Jun Kobayashi, Akihiko Kikuchi, Yoshikatsu Akiyama, Hideko Kanazawa, and Teruo Okano. "Thermoresponsive hydrophobic copolymer brushes modified porous monolithic silica for high-resolution bioseparation." RSC Advances 5, no. 81 (2015): 66155–67. http://dx.doi.org/10.1039/c5ra11038f.
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Thermoresponsive-hydrophobic copolymer brushes were prepared on porous monolithic silica rods through surface initiated ATRP. The monolithic silica can separate biomolecules with high resolution and in short analysis times.
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Ishihara, Kazuhiko, Shohei Hachiya, Yuuki Inoue, Kyoko Fukazawa, and Tomohiro Konno. "Water-Soluble and Cytocompatible Phospholipid Polymers for Molecular Complexation to Enhance Biomolecule Transportation to Cells In Vitro." Polymers 12, no. 8 (August 6, 2020): 1762. http://dx.doi.org/10.3390/polym12081762.
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Water-soluble and cytocompatible polymers were investigated to enhance a transporting efficiency of biomolecules into cells in vitro. The polymers composed of a 2-methacryloyloxyethyl phosphorylcholine (MPC) unit, a hydrophobic monomer unit, and a cationic monomer unit bearing an amino group were synthesized for complexation with model biomolecules, siRNA. The cationic MPC polymer was shown to interact with both siRNA and the cell membrane and was successively transported siRNA into cells. When introducing 20–50 mol% hydrophobic units into the cationic MPC polymer, transport of siRNA into cells. The MPC units (10–20 mol%) in the cationic MPC polymer were able to impart cytocompatibility, while maintaining interaction with siRNA and the cell membrane. The level of gene suppression of the siRNA/MPC polymer complex was evaluated in vitro and it was as the same level as that of a conventional siRNA transfection reagent, whereas its cytotoxicity was significantly lower. We concluded that these cytocompatible MPC polymers may be promising complexation reagent for introducing biomolecules into cells, with the potential to contribute to future fields of biotechnology, such as in vitro evaluation of gene functionality, and the production of engineered cells with biological functions.
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Rajendiran, N., and M. Suresh. "Study of the Interaction of Ciprofloxacin and Sparfloxacin with Biomolecules by Spectral, Electrochemical and Molecular Docking Methods." International Letters of Chemistry, Physics and Astronomy 78 (April 2018): 1–29. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.78.1.
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Interactions of ciprofloxacin and sparfloxacin with different biomolecules (DNA, RNA and BSA) are investigated by UV–Visible spectroscopy, fluorescence spectroscopy, cyclic voltammetry and molecular docking methods. Upon increasing the concentration of the biomolecules, the absorption maxima of ciprofloxacin and sparfloxacin are red shifted in the aqueous solutions whereas red or blue shift noticed in the fluorescence spectra. The negative free energy changes suggest that the interaction processes are spontaneous. Cyclic voltammetry results suggested that when the drug concentration is increased, the anodic electrode potential increased. Molecular docking results showed that hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the interaction drugs with biomolecules. The molecular docking calculation clarifies the binding mode and the binding sites are in good accordance with the experiment results.
Dissertations / Theses on the topic "Hydrophobic Biomolecules"
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Jacksén, Johan. "Improved techniques for CE and MALDI-MS including microfluidic hyphenations foranalysis of biomolecules." Doctoral thesis, KTH, Analytisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-27342.
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In this thesis, improved techniques for biomolecule analysis using capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) and hyphenations between those have been presented.A pre-concentration method which is possible to apply in both techniques, has also been investigated. In this work the off-line MS mode has been used either in the form of fractionation (Paper I) or by incorporating the MALDI target in the CE separation system (Paper II).In Paper I, a protocol for CE-MALDI analysis of cyanogen bromide digested bacteriorhodopsin (BR) peptides as model integral membrane protein peptides were established. Also, an improved protocol for partially automated manufacturing of a concentration MALDI-target plate is presented. The design of the targets was suitable for the fractions from the CE. A novel technique for the integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a micro canal functioning as a MALDI target window. A protein separation was obtained and detected with MALDI-MS analysis in the micro canal. A method has been developed for detection of monosaccharides originating from hydrolysis of a single wood fiber performed in a micro channel, with an incorporated electromigration pre-concentration step preceding CE analysis in Paper III. The pre-concentration showed to be highly complex due to the fact that several parameters are included that affecting each other. In Paper IV a protocol using enzymatic digestion, MALDI-TOF-MS and CE with laser induced fluorescence (LIF) detection for the investigation of the degree of substitution of fluorescein isothiocyanate (FITC) to bovine serum albumin (BSA), as a contact allergen model system for protein-hapten binding in the skin, is presented. The intention of a further CE-MALDI hyphenation has been considered during the work. In Paper V 2,6-dihydroxyacetophenone (DHAP) was investigated, showing promising MALDI-MS matrix properties for hydrophobic proteins and peptides. 2,5-dihydroxybenzoic acid (DHB) was undoubtedly the better matrix for the hydrophilic proteins, but its performance for the larger and hydrophobic peptides was not optimal. Consequently, DHAP can be used as a compliment matrix for improved analysis of hydrophobic analytes.QC 20101214
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Benson, Sven P. [Verfasser], and Jürgen [Akademischer Betreuer] Pleiss. "Molecular modeling of hydrophobic effects in complex biomolecular systems : from simple mixtures to protein-interface aggregation / Sven P. Benson. Betreuer: Jürgen Pleiss." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1066646015/34.
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Hall, Shaun Andrew. "Structure of Biomolecules Adsorbed at the Hydrophobic Polymer-Solution Interface from Spectroscopic Experiments and Molecular Simulations." Thesis, 2011. http://hdl.handle.net/1828/4955.
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The work herein describes efforts to improve the understanding of the structural and
optical properties of molecules adsorbed to polymeric surfaces. The main emphasis
was placed upon the determination of molecular orientation of adsorbed molecules by
developing methods for extracting structural information from vibrationally-resonant sum
frequency generation spectroscopy experiments. Through the comparison of electronic
structure calculations to the acquired spectra, orientation distributions were determined for
phenylalanine on polystyrene coated fused silica. The initial study was a single example of
a method that is applicable to any surface for which the adsorbing species has a completely
characterized infrared and Raman spectra. Predicted intensities for the symmetric and
antisymmetric CH2 stretches were compared to their corresponding amplitudes extracted
from the acquired spectra. In the second study, the method developed was more general,
incorporating the addition of molecular dynamics simulations, which were used to discover
various conformations present at the surface, allowing for fits to the acquired spectra to be
determined based on the relative populations of these species. This approach was chosen as
it is applicable to cases in which the adsorbing species has overlapping spectral features that
will not allow for characterization of specific modes. As an example of this, leucine, which
possesses highly coupled and overlapping absorptions in its infrared and Raman spectra,
adsorption to a polystyrene surface was studied. A high speed Stokes polarimeter based on
a dual photoelastic modulator was designed, assembled, and calibrated based on a novel
method, capable of measuring the adsorption kinetics of molecules adsorbing to surfaces.
The adsorption of bovine serum albumin (BSA) to a polystyrene coated fused silica surface
was studied. The configuration of the polarimeter was amenable to the determination of
Mueller matrices of equilibrated surfaces with minimal procedural modifications.Graduate
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Heinz, Leonard. "Spatially Resolved Hydration Statistical Mechanics at Biomolecular Surfaces from Atomistic Simulations." Thesis, 2020. http://hdl.handle.net/21.11130/00-1735-0000-0005-15AF-F.
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"Molecular simulations to study thermodynamics of polyethylene oxide solutions." Tulane University, 2014.
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Polyethylene oxide polymers are intrinsic to oil spill dispersants used in Macondo well blowout of 2010. We believe that effective thermo-physical modeling of these materials should assist the application of lab-scale results into ocean-scales. Fully defensible molecular scale theory of such materials will be challenging. This thesis is the first step towards that challenge. Molecular dynamics simulations are useful in generating structural and phase behavior data for these versatile polymers. Microstructures of PEO polymers, hydrophobic interactions, direct numerical test of controversial Pratt-Chandler theory, concentration dependence of Flory-Huggins interaction parameter and neutron scattering experiments will be discussed.acase@tulane.edu
Book chapters on the topic "Hydrophobic Biomolecules"
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Ortega, Álvaro. "Hydrophobic Modifications of Biomolecules: An Introduction." In Cellular Ecophysiology of Microbe, 1–10. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-20796-4_17-1.
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Ortega, Álvaro. "Hydrophobic Modifications of Biomolecules: An Introduction." In Cellular Ecophysiology of Microbe: Hydrocarbon and Lipid Interactions, 477–86. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-50542-8_17.
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Efremov, R. G., and G. Vergoten. "What Drives Association of α-Helical Peptides in Membrane Domains of Proteins? Role of Hydrophobic Interactions." In Biomolecular Structure and Dynamics, 211–28. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5484-0_10.
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Kamanna, Kantharaju, and Aravind Kamath. "Prenylation of Natural Products: An Overview." In Modifications of Biomolecules [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.104636.
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Natural products with varied functional attributes are available in large abundance in nature. Nature has been an infinite repository of resources leading to drug development, discovery of novel chemicals, pharmacophores, and several invaluable bioactive agents. Natural products play a critical role in modern drug development, especially for antibacterial and antitumor agents. Their varied chemical structure, composition, solubility, and synthetic pathways bestow upon them a high level of diversity. Prenylation is a covalent addition of hydrophobic moieties to proteins or any other chemical compounds. Generally, the hydrophobic moieties are farnesyl or geranylgeranyl isoprenyl groups. Prenylation of flavonoids, alkaloids, terpernoids, etc., leads to gain of varied functionalities to the natural products in addition to the already existing functions. The ever-increasing need for the discovery of new drugs finds a new avenue through the prenylation of natural products. Cell-free synthesis of the prenylated natural products can be seen as a new alternative for the natural synthesis, which warrants time-consuming isolation and purification techniques.
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Kumar Mitra, Rajib, and Dipak Kumar Palit. "Probing Biological Water Using Terahertz Absorption Spectroscopy." In Terahertz Technology [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97603.
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Hydrogen bonding properties of water molecules, which are confined in microcavities of biological interfaces, are significantly different from those of bulk water and drive most of the complex biological processes. While NMR, X-ray and UV–vis-IR spectroscopic techniques have been found inadequate for describing the dynamics of the thick (20–40 Å) sheath of hydration layer around biomolecules, recently developed THz spectroscopy has emerged as a powerful technique to directly probe the collective dynamics of hydrogen bonds in the hydration layer, which control all important functions of the biomolecules in life. Both laser and accelerator-based THz sources are intense enough to penetrate up to about 100 μm thick water samples, which makes THz transmission and/or dielectric relaxation measurements possible in aqueous solutions. These measurements provide valuable information about the rattling and rotational motions of hydrated ions, making, breaking and rearrangement of hydrogen bonds in hydration layer as well as hydrophilic and hydrophobic interactions between biomolecule and water. THz spectroscopy has also been successfully applied to study the effect of modulation of the physical conditions, like temperature, pH, concentration of proteins and chemical additives, on the structure and dynamics of hydration layer. THz spectroscopy has also been applied to study the processes of denaturation, unfolding and aggregation of biomolecules.
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Rodríguez-Ramos, Ruth, Álvaro Santana-Mayor, Bárbara Socas-Rodríguez, Antonio V. Herrera-Herrera, and Miguel Ángel Rodríguez Delgado. "Recent Applications of Deep Eutectic Solvents." In Green Extraction Techniques in Food Analysis, 132–96. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815049459123030006.
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Among the different strategies applied in recent years for the development of green extraction techniques in food analysis, the design and use of deep eutectic solvents (DESs) have aroused the utmost attention due to the advantages provided by these materials in terms of sustainability and versatility. Different types of DESs have been applied in this field including hydrophilic and hydrophobic mixtures, natural DESs, or polymeric-DESs. In this sense, the great availability of components and the wide range of possible combinations constitute potential tools to increase the selectivity and enhance the extraction capacity of the procedures, which is an important concern when complex food samples are tackled. This broad spectrum of possibilities has allowed the extraction of diverse compounds including not only contaminants such as pesticides, plastic migrants, heavy metals, or pharmaceuticals, among others, but also the extraction of biomolecules from food and food by-products. However, despite the advantages of these materials, there are important drawbacks like their high viscosity and low volatility that limit their application. In this context, an important effort has been carried out by the study of different combinations and the development of numerous approaches. In this chapter, the most relevant applications of DESs in the last five years in food analysis have been compiled and discussed in order to provide a global view of the advantages and limitations of the application of these green extraction solvents in the field. Additionally, the current trends and future perspectives in the use of DESs in food analysis are also pointed out.
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Angal, S., and Simon D. Roe. "Purification by exploitation of activity." In Protein Purification Techniques. Oxford University Press, 2001. http://dx.doi.org/10.1093/oso/9780199636747.003.0013.
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Proteins carry out their biological functions through one or more binding activities and, consequently, contain binding sites for interaction with other biomolecules, called ligands. Ligands may be small molecules such as substrates for enzymes or larger molecules such as peptide hormones. The interaction of a binding site with a ligand is determined by the overall size and shape of the ligand as well as the number and distribution of complementary surfaces. These complementary surfaces may involve a combination of charged and hydrophobic moieties and exhibit other short-range molecular interactions such as hydrogen bonds. This binding activity of a protein, which is stereoselective and often of a high affinity, can be exploited for the purification of the protein in a technique commonly known as affinity chromatography. The operation of affinity chromatography involves the following steps: (a) Choice of an appropriate ligand. (b) Immobilization of the ligand onto a support matrix. (c) Contacting the protein mixture of interest with the matrix. (d) Removal of non-specifically bound proteins. (e) Elution of the protein of interest in a purified form. At best, affinity chromatography is the most powerful technique for protein purification since its high selectivity can, in principle, allow purification of a single protein of low abundance from a crude mixture of proteins at higher concentrations. Secondly, if the affinity of the ligand for the protein is sufficiently high, the technique offers simultaneous concentration from a large volume. In practice, such single-step purifications are not common and successful affinity chromatography requires careful consideration of a number of parameters involved. The remainder of this chapter attempts to guide the experimenter in the selection and use of affinity adsorbents for protein purification. For more extensive information on this technique the reader is advised to consult the many excellent texts on this subject as well as proceedings of symposia. The construction of an affinity adsorbent for the purification of a particular protein involves three major factors: (a) Choice of a suitable ligand. (b) Selection of a support matrix and spacer. (c) Attachment of the ligand to a support matrix. The criteria for making these decisions are discussed in the following sections.
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MODI, VIVEK, DILRAJ LAMA, and RAMASUBBU SANKARARAMAKRISHNAN. "PLASTICITY OF BH3 DOMAIN-BINDING HYDROPHOBIC GROOVES IN THE ANTI-APOPTOTIC MCL-1 AND A1 PROTEINS." In Biomolecular Forms and Functions, 468–81. WORLD SCIENTIFIC / INDIAN INST OF SCIENCE, INDIA, 2013. http://dx.doi.org/10.1142/9789814449144_0036.
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Sligar, Stephen G., and Clifford R. Robinson. "Osmotic and Hydrostatic Pressure as Tools to Study Molecular Recognition." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0026.
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The question of molecular recognition is a central paradigm of molecular biology, playing central roles in most, if not all, cellular processes. Failed recognition events have been implicated in numerous disease states, ranging from flawed control of gene regulation and cellular proliferation to defects in specific metabolic activities. Historically, questions of molecular recognition have been approached through organic synthesis and through actual structural studies of biomolecular complexes. Fundamental insight into the mechanisms of molecular recognition can be realized through the use of broad interdisciplinary tools and techniques. In particular, the use of recombinant DNA technology in concert with hydrostatic and osmotic pressure methodologies have proven to be ideal for understanding the fundamental mechanisms of recognition. In our presentation, we will focus on recent results from our laboratory that examine three major classes of recognition events in biological systems: 1. Protein-protein recognition: here we seek to define the role of specific surface interactions; electrostatic, hydrogen bonding, and hydrophobic free energies provided through surface complimentarity, which define the specificity and affinity in the formation of complexes between the metalloproteins involved in electron transfer events in cytochrome P-450-dependent oxygenase catalysis and in the assembly of tetrameric hemoglobin. 2. Protein—small molecule recognition: here we seek to ascertain how the same fundamental forces of electrostatics, hydrogen bonding, and the hand-glove fit of a substrate into the active site of an enzyme can give rise to the observed high degree of control of regio- and stereo-specificity in catalysis and in the interfadal interactions of proteins at electrode interfaces. 3. Protein nucleic acid recognition: here again the same fundamental forces control recognition processes, but in this case we will focus on our exciting, recent discovery of a role for solvent water in mediating recognition between protein and nucleic acid components. Representative systems in the binding/ catalytic class of restriction endonucleases and recombinases will be discussed. In all cases, the use of pressure as a variable has provided unique understanding for the molecular details of these processes. Pressure, both hydrostatic and osmotic, has proven to be an enabling experimental technique in understanding the mechanistic origins of molecular recognition events.
Conference papers on the topic "Hydrophobic Biomolecules"
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Nguyen, Mary-Anne, and Andy Sarles. "Microfabrication for Packaged Biomolecular Unit Cells." In ASME 2013 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/smasis2013-3068.
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This paper focuses on developing a closed fluidic environment for packaging biomolecular unit cells, which consists of a synthetic lipid bilayer and other biomolecules contained in a near solid-state material with two regions that contain hydrophobic oil (i.e. nonpolar solvent) surrounding aqueous droplets. This research provides a stepping-stone towards an autonomic biomolecular material system, whereby a packaged system will allow for precise droplet interface bilayer (DIB) formation without the interference of outside contamination for long-term applications. Also, substrate materials need to maintain droplets and preserve the self-assembly and stimuli-responsive properties of biomolecules within the unit cell. A critical feature of an encapsulating material is that it does not absorb either of the liquid phases required to form DIBs. Oil depletion tests within sealed, polymeric substrates show that polydimethylsiloxane (PDMS) absorbs full volume of injected hexadecane in approximately 27 hours. However, polyurethane substrates maintain the original amount of oil injected even after several weeks. Bilayer lifetime is also monitored within an environment in which the oil is also depleting. The results of this test show the longevity of a DIB to be shorter than oil lifetime. The lipid-encased droplets disconnect after approximately 10 hours, when there is only approximately <60% amount of oil present. In addition, an initial microfluidic substrate is designed such that a single T-junction intersection can be used to form monodisperse droplets within a primary oil-filled channel and a downstream increase in channel width can be used to connect droplets to form DIBs.
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Madadi, Hojjat, and Jasmina Casals-Terré. "Study the Effects of Different Surfactants on Hydrophilicity of Polydimethylsiloxane (PDMS)." In ASME 2012 11th Biennial Conference on Engineering Systems Design and Analysis. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/esda2012-82399.
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The outstanding characteristics of polydimethylsiloxane (PDMS) caused its extensive use as base material to manufacture microfluidic devices. PDMS has numerous advantages coming from instinct properties such as its low cost, simple fabrication procedure, and robust nature that make it a compatible material in many applications such as biological and biomedical engineering. In spite of favorable physical and chemical properties, hydrophobic surface of PDMS is sometimes debatable. Because of PDMS is highly hydrophobic, pumping aqueous solution through microchannels using only capillary forces might be difficult. Although many surface treatments methods have been proposed to modify and increase the hydrophilicity of PDMS [Oxygen plasma [1], UV-radiation [2], Silanization and Chemical vapour deposition [3],…], the use of surfactants is the most effective and easiest method to overcome the hydrophobicity compared to more complex protocols which require expensive facilities [4,5]. The hydrophilic behavior of surfactant-added PDMS and especially its biocompatibility has allowed many microfluidic bio-applications such as separation of biomolecules [6,7], blood cell separation [8] and cell-based assay [9,10]. This paper discusses about the efficiency of adding different surfactants on the wettability of PDMS.
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Honig, Barry. "Macroscopic Treatments of Electrostatic and Hydrophobic Free Energies." In Advances in biomolecular simulations. AIP, 1991. http://dx.doi.org/10.1063/1.41357.
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Melo, Palloma M. J. de, Nathália S. A. A. Marques, Adriana F. de Souza, Gabriela R. P. de Andrade, and Galba M. de Campos-Takaki. "Strategy for sustainable biosurfactant production by mucor circinelloides UCP0017." In III SEVEN INTERNATIONAL MULTIDISCIPLINARY CONGRESS. Seven Congress, 2023. http://dx.doi.org/10.56238/seveniiimulti2023-267.
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Surfactants are molecules with amphipathic structures, that is, one polar extreme (hydrophilic) and the other nonpolar (hydrophobic), possessing a high capacity to reduce surface tension, emulsification production and wetting (PELE et al., 2019; BIONE, 2019). Its origin can be chemical usually derived from petroleum, being compounds that easily harm the environment making it difficult to remove it (BIONE, 2019; GAYATHIRI et al., 2022). As they can also be natural, through microorganisms such as bacteria, filamentous fungi and yeasts or are biodegradable and of low toxicity, not harming the environment or human health. (RULLI et al., 2019; CÂNDIDO et al., 2022). Therefore, the present study aims to seek the optimization of the production of biosurfactant becoming a more advantageous alternative because they use renewable substrates in their composition, and because their "green" properties do not harm the environment, besides being biodegradable, thus improving their cost-benefit, aiming at new opportunities for applications in the food, agricultural, cosmetic and pharmaceutical industries (MARQUES et al., 2020; GAYATHIRI et al., 2022; MULLIGAN, 2023).The main responsible for the production of biosurfactants and bioemulsifiers are bacteria, followed by yeasts and finally filamentous fungi because they have a potential for the production of secondary metabolites and a high value of biomass, however, studies with filamentous fungi are little explored (SAŁEK & EUSTON, 2019; DERGUINE-MECHERI; KEBBOUCHE-GANA; DJENANE, 2021). According to Geethanjali et al., (2020) and Marques et al., (2020) the species Mucor circinelloides, of the phylum Mucoromycota, order Mucorales, presents a high biotechnological potential in the production of biomolecules of industrial interest, as well as biosurfactant. In this sense, the research proposed to study the performance of biosurfactant production through the filamentous fungus Mucor circinelloides UCP 0017 using alternative substrates (MARQUES et al., 2020; RADHA et al., 2020).
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Taeger, Sebastian. "Noncovalent Sidewall Functionalization of Carbon Nanotubes by Biomolecules: Single-stranded DNA and Hydrophobin." In ELECTRONIC PROPERTIES OF NOVEL NANOSTRUCTURES: XIX International Winterschool/Euroconference on Electronic Properties of Novel Materials. AIP, 2005. http://dx.doi.org/10.1063/1.2103866.
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Nguyen, Mary-Anne, and Stephen A. Sarles. "Micro-Encapsulation and Tuning of Biomolecular Unit Cell Networks." In ASME 2014 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/smasis2014-7583.
Full textAbstract:
The goal of our research is to fabricate an autonomic material system that provides compartmentalization and multi-bilayer networks for enabling collective biomolecular functionality, as is found in living cells and tissues. The material system is based on biomolecular unit cells, which consist of synthetic lipid bilayers formed at the interfaces of lipid-coated aqueous droplets submerged in oil and contained in a solid material. This paper focuses on microfluidic encapsulation of unit cells within a solid material and tuning the amount of contact between droplets, two approaches aimed at increasing the functional density of the droplet-based material system. Hydrodynamic traps within microfluidic platforms have shown to be a promising method to capture single droplets within microfluidic devices. Herein, we develop a resistive flow model to design hydrodynamic traps for collecting pairs of droplets in a direct trapping mode to form unit cells. We also compare to the model the results of droplet trapping in a prototype microfluidic device fabricated prior to model development. In addition to flow techniques for assembling unit cells in solid materials, we examine the use of mineral oil as the hydrophobic oil phase that surrounds the droplets to increase the area of the lipid membrane formed between neighboring droplets. Compared to hexadecane, mineral oil produces larger contact areas between droplets and more-tightly packed multi-bilayer networks. The total free energies of formation for droplet arrays in mineral oil and hexadecane indicate that connected droplets in mineral oil exhibit a greater decrease in free energy upon formation (i.e. they exist at a lower energy state compared to those in hexadecane) and that hexagonal packing provides the maximum amount of decrease in free energy per droplet for droplets in large arrays. Electrical measurements of unit cells formed in mineral oil initially show gigaohm resistances typical of unit cells, however these unit cells exhibit increasing values of conductance as the bilayer areas grow.
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Ou, Junjie, Shuwen Wang, Carolyn L. Ren, and Janusz Pawliszyn. "Preparation of Poly(Dimethylsiloxane) Chip-Based Cartridge for Isoelectric Focusing and Whole-Channel Imaging Detection." In 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. ASMEDC, 2008. http://dx.doi.org/10.1115/micronano2008-70303.
Full textAbstract:
A poly(dimethylsiloxane) (PDMS) microfluidic chip-based cartridge was fabricated by sandwiching commercial dialysis membrane and inserting fused-silica capillary into the end of channel according to the principle and structure of a commercial fused-silicon capillary-based cartridge, which can adapt to an IEF analyzer for isoelectric focusing with whole channel imaging detection (IEF-WCID). The novel design of sandwiching membrane in this chip not only eliminated the unfavorable hydrodynamic pressure, leading to poor IEF reproducibility, but made the sample injection much easy. Thus the reproducibility of analysis was very good. The prepared microfluidic chips were applied for qualitative and quantitative analysis of proteins. The six pI markers in the range of 3–10 were separated by IEF under the optimized conditions. The pH gradients exhibited good linear by plotting the pI versus peak position, and the correlation coefficient reached to 0.9994 and 0.9995. The separation of more complicated human hemoglobin control and myoglobin sample could be achieved. By comparison with the separation efficiency obtained on the microfluidic chip and commercial cartridge, the results were similar, which indicates the capillary cartridge may be replaced with the cost-efficient PDMS microfluidic chip. It is anticipated the high throughput analysis can be easily performed on this microfluidic chip patterned multi-channels. The techniques of capillary electrophoresis (CE) have been extensively explored for the chip-based separation. Isoelectric focusing (IEF) as one of high-resolution CE techniques has been widely applied for the separation of zwitterionic biomolecules, such as proteins and peptides. After the samples were focused at their corresponding pIs, the focused zones were mobilized to pass through the detection point for obtaining an electropherogram. This single-point detection imposes extensive restriction for chip-based IEF because a mobilization process requires additional time and lowers resolution and reproducibility of the separation [1]. An alternative is whole-column imaging detection developed by Pawliszyn et al [2] is an ideal detection method for IEF because no mobilization is required, which avoids the disadvantages as mentioned previously. Most microfluidic systems could be fabricated in glass/silicon or polymers in which the channels are defined using photolithography and micromachining. Mao and Pawliszyn [3] have developed a method for IEF on an etched quartz chip following whole-channel imaging detection (WCID). Ren et al [4] presented an integrated WCID system on glass microfluidic chip. However, these materials have some disadvantages such as expensive and fragile and so on. An attractive alternative for fabrication of microfluidic devices is using poly(dimethylsiloxane) (PDMS) as material, which has unique properties such as nontoxic, optical transparent down to 280 nm, elastomeric, hydrophobic surface chemistry Yao et al. [5] designed the glass/PDMS microchip integrated whole-column fluorescence imaging detection for IEF of R-phycoerythrin. Our preliminary studies have successfully developed a PDMS chip-based cartridge for IEF-WCID. It is due to hydrodynamic flow between two reservoirs that the focused zones were mobilized, thus gave poor reproducibility and difficulty in sample infusion. As membranes have been integrated into microchips for microdialysis, protein digestion, solid-phase extraction, desalting, pumping and so on, it could minimize hydrodynamic flow by using membranes as a filter. Although a simple PDMS chip-based cartridge has been successfully fabricated in our labs according to the principle of commercial capillary-based cartridge, it is difficult to introduce the sample into channel for IEF-WCID. As the vacuum was applied in one end of channel for infusing of solution into channel, the lifetime of this chip-based cartridge is shortened. Additionally, the hydrodynamic flow is occurred due to the different heights of anolyte and catholyte in two reservoirs, respectively. The IEF separation was deteriorated by the infusion of anolyte or catholyte, thus leading to poor reproducibility of IEF-WCID analysis. Similar to the hollow fiber in the commercial capillary-based cartridge in which it is aimed to separate the sample in the capillary and electrolytes in the reservoirs, porous membrane was integrated into PDMS chips for decrease of hydrodynamic flow [6]. As a result, integration of dialysis membrane is considered into the design of our new chip-based cartridge. Up to now, many approaches have been described to integrate membranes into glass/quartz or polymeric microfluidic chips. A simple method is direct incorporation by gluing or clamping commercial flat membranes. A major problem of this method is sealing, otherwise, a phenomenon of leakage around the membranes is always occurred due to the capillary force. A novel approach of sandwiching dialysis membrane was developed as schematically indicated in Figure 1. After optimizing IEF conditions, the separation of pI markers was performed on the obtained PDMS microfluidic chip. As exhibited in Figure 2a, six pI markers could be well separated on the PDMS chips patterned the channel of 100 μm deep, 100 μm wide by IEF-WCID. All the peaks were sharp and symmetric, indicating that both EOF and analytes adsorption were completely suppressed by the dynamic coating of PVP. The plots of peak position versus pI of these pI markers suggested good linearity of pH gradient (as shown in Figure 2b). The linear correlation coefficient was 0.9995 (n = 6). As expected to the capillary-based cartridge, the PDMS microfluidic chips could be applied for qualitative and quantitative analysis of proteins. Figure 3a exhibited that human hemoglobin control AFSC contains four known isoforms (HbA, HbF, HbS and HbC) mixed with two pI marker 6.14 and 8.18 were well separated on the PDMS chip by IEF-WCID, indicating the strong separation ability of chip similar to the commercial capillary-based cartridge. According to the linearity of pH gradient, these four isoforms with the pIs of 7.0, 7.1, 7.3 and 7.5, respectively, could be detected. An unknown isoform in human hemoglobin control marked asterisk in Figure 3A observed besides the definite four isoforms A, F, S and C. The myoglobin from horse heart contains two isoforms, whose pIs are 6.8 and 7.2, respectively. It can be seen from Figure 3b that these two isoforms were separated on PDMS chip by IEF-WCID. The peak 1 and 2 could be assigned to the two isoforms according to their pI. The pI of unknown peak marked asterisk could be measured to 6.25.