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Journal articles on the topic 'Hydrophobic clusters'

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Author: Grafiati

Published: 25 May 2024

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1

Arunachalam, J., and N. Gautham. "Hydrophobic clusters in protein structures." Proteins: Structure, Function, and Bioinformatics 71, no. 4 (January 10, 2008): 2012–25. http://dx.doi.org/10.1002/prot.21881.

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2

Xie, Xuan, and Chunfu Zhang. "Controllable Assembly of Hydrophobic Superparamagnetic Iron Oxide Nanoparticle with mPEG-PLA Copolymer and Its Effect on MR Transverse Relaxation Rate." Journal of Nanomaterials 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/152524.

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Assembly of individual superparamagnetic iron oxide nanoparticles (SPION) into cluster is an effective way to prepare MRI contrast agent with high relaxivity. In this study, we fabricated SPION clusters with different sizes and configurations by assembly of amphiphilic mPEG-PLA copolymer with hydrophobic SPION in aqueous solution. The evolution of cluster size and configuration with the amount of copolymer and the effect of cluster size on the transverse relaxivity was studied.T2relaxation rates of clusters with different sizes at iron concentration of 0.1 mM were compared with the theoretical predictions. We found that the relative amount of copolymer/SPION was crucial for the formation of SPION cluster. The transverse relaxivity of the condense SPION clusters (CSC) was size-dependent. The experimentally measuredT2relaxation rates of the clusters were lower than the theoretical predictions. In motional average regime (MAR) region,T2relaxation rates were more consistent with the theoretical values when transmission electron microscope (TEM) evaluated size was used. Therefore, for fabrication of SPION clusters with assembly of mPEG-PLA and hydrophobic SPION, delicate balance between the amount of copolymer and SPION should be pursued, and for comparison of experimentalT2relaxation rate with theoretical predictions, TEM evaluated size was more suitable.

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3

Feketeová, Linda, Paul Bertier, Thibaud Salbaing, Toshiyuki Azuma, Florent Calvo, Bernadette Farizon, Michel Farizon, and Tilmann D. Märk. "Impact of a hydrophobic ion on the early stage of atmospheric aerosol formation." Proceedings of the National Academy of Sciences 116, no. 45 (October 21, 2019): 22540–44. http://dx.doi.org/10.1073/pnas.1911136116.

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Atmospheric aerosols are one of the major factors affecting planetary climate, and the addition of anthropogenic molecules into the atmosphere is known to strongly affect cloud formation. The broad variety of compounds present in such dilute media and their specific underlying thermalization processes at the nanoscale make a complete quantitative description of atmospheric aerosol formation certainly challenging. In particular, it requires fundamental knowledge about the role of impurities in water cluster growth, a crucial step in the early stage of aerosol and cloud formation. Here, we show how a hydrophobic pyridinium ion within a water cluster drastically changes the thermalization properties, which will in turn change the corresponding propensity for water cluster growth. The combination of velocity map imaging with a recently developed mass spectrometry technique allows the direct measurement of the velocity distribution of the water molecules evaporated from excited clusters. In contrast to previous results on pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is composed of 2 distinct Maxwell–Boltzmann distributions, indicating out-of-equilibrium evaporation. More generally, the evaporation of water molecules from excited clusters is found to be much slower when the cluster is doped with a pyridinium ion. Therefore, the presence of a contaminant molecule in the nascent cluster changes the energy storage and disposal in the early stages of gas-to-particle conversion, thereby leading to an increased rate of formation of water clusters and consequently facilitating homogeneous nucleation at the early stages of atmospheric aerosol formation.

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Lesnikowski, Zbigniew J. "Boron Units as Pharmacophores - New Applications and Opportunities of Boron Cluster Chemistry." Collection of Czechoslovak Chemical Communications 72, no. 12 (2007): 1646–58. http://dx.doi.org/10.1135/cccc20071646.

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Carboranes (dicarba-closo-dodecaboranes) are a class of carbon-containing polyhedral boron-cluster compounds showing remarkable hydrophobic character, chemical and thermal stability, and resistance to catabolism in biological environment. These features allow application of boron clusters as new hydrophobic core structure in biologically active molecules that interact hydrophobically with proteins, thus facilitating new drug design. A review with 45 references.

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5

Sakibaev, Farkhat, Marina Holyavka, Victoria Koroleva, and Valeriy Artyukhov. "Distribution of Charged and Hydrophobic Amino Acids on the Surfaces of Two Types of Beta-Fructosidase from Thermotoga Maritima." Chemistry Proceedings 2, no. 1 (November 9, 2020): 4. http://dx.doi.org/10.3390/eccs2020-07550.

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Thermotoga maritima beta-fructosidases are enzymes that release beta-D-fructose from sucrose, raffinose, and fructan polymers such as inulin. The surfaces of beta-fructosidases 1UYP and 1W2T from Thermotoga maritima were studied in this work. It was showed that amino acids are not distributed equally on the surfaces of the enzymes. Several clusters of charged and hydrophobic residues were detected at pH 7.0. Such clusters were detected by calculation of the distances between them. It was determined that on surfaces of beta-fructosidases PDB ID: 1UYP and PDB ID: 1W2T, 96% and 95% of charged amino acids and also 50% and 42% of hydrophobic amino acids form clusters, respectively. Six clusters of charged amino acids on the surface of beta-fructosidase 1UYP and five clusters on the surface of beta-fructosidase 1W2T were detected. The composition of such clusters is presented. Both types of beta-fructosidase have three clusters of hydrophobic amino acids on their surface. These facts should be considered when choosing immobilization conditions. It was shown that a charged matrix is more promising for the immobilization of beta-fructosidases 1UYP and 1W2T from Thermotoga maritima due to the possibility of binding without any significant loss of activity due to their overlapping active center. Hydrophobic carriers are less promising due to the probable active site overlap. Such binding may have a loss of enzyme activity as a result.

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6

Tavares, Marina Rodrigues, Kaplan Kirakci, Nikolay Kotov, Michal Pechar, Kamil Lang, Robert Pola, and Tomáš Etrych. "Octahedral Molybdenum Cluster-Based Nanomaterials for Potential Photodynamic Therapy." Nanomaterials 12, no. 19 (September 26, 2022): 3350. http://dx.doi.org/10.3390/nano12193350.

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Photo/radiosensitizers, such as octahedral molybdenum clusters (Mo6), have been intensively studied for photodynamic applications to treat various diseases. However, their delivery to the desired target can be hampered by its limited solubility, low stability in physiological conditions, and inappropriate biodistribution, thus limiting the therapeutic effect and increasing the side effects of the therapy. To overcome such obstacles and to prepare photofunctional nanomaterials, we employed biocompatible and water-soluble copolymers based on N-(2-hydroxypropyl)methacrylamide (pHPMA) as carriers of Mo6 clusters. Several strategies based on electrostatic, hydrophobic, or covalent interactions were employed for the formation of polymer-cluster constructs. Importantly, the luminescent properties of the Mo6 clusters were preserved upon association with the polymers: all polymer-cluster constructs exhibited an effective quenching of their excited states, suggesting a production of singlet oxygen (O2(1Δg)) species which is a major factor for a successful photodynamic treatment. Even though the colloidal stability of all polymer-cluster constructs was satisfactory in deionized water, the complexes prepared by electrostatic and hydrophobic interactions underwent severe aggregation in phosphate buffer saline (PBS) accompanied by the disruption of the cohesive forces between the cluster and polymer molecules. On the contrary, the conjugates prepared by covalent interactions notably displayed colloidal stability in PBS in addition to high luminescence quantum yields, suggesting that pHPMA is a suitable nanocarrier for molybdenum cluster-based photosensitizers intended for photodynamic applications.

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7

Nishigami, Hiroshi, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Kazuhiko Yamasaki, and Masaru Tateno. "Is it possible for short peptide composed of positively- and negatively-charged “hydrophilic” amino acid residue-clusters to form metastable “hydrophobic” packing?" Physical Chemistry Chemical Physics 21, no. 19 (2019): 9683–93. http://dx.doi.org/10.1039/c9cp00103d.

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8

Gallo, Mariana, Simone Luti, Fabio Baroni, Ivan Baccelli, Eduardo Maffud Cilli, Costanza Cicchi, Manuela Leri, Alberto Spisni, Thelma A. Pertinhez, and Luigia Pazzagli. "Plant Defense Elicitation by the Hydrophobin Cerato-Ulmin and Correlation with Its Structural Features." International Journal of Molecular Sciences 24, no. 3 (January 23, 2023): 2251. http://dx.doi.org/10.3390/ijms24032251.

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Cerato-ulmin (CU) is a 75-amino-acid-long protein that belongs to the hydrophobin family. It self-assembles at hydrophobic–hydrophilic interfaces, forming films that reverse the wettability properties of the bound surface: a capability that may confer selective advantages to the fungus in colonizing and infecting elm trees. Here, we show for the first time that CU can elicit a defense reaction (induction of phytoalexin synthesis and ROS production) in non-host plants (Arabidopsis) and exerts its eliciting capacity more efficiently when in its soluble monomeric form. We identified two hydrophobic clusters on the protein’s loops endowed with dynamical and physical properties compatible with the possibility of reversibly interconverting between a disordered conformation and a β-strand-rich conformation when interacting with hydrophilic or hydrophobic surfaces. We propose that the plasticity of those loops may be part of the molecular mechanism that governs the protein defense elicitation capability.

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9

Czaplewski, C. "Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles." Biophysical Chemistry 105, no. 2-3 (September 2003): 339–59. http://dx.doi.org/10.1016/s0301-4622(03)00085-1.

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10

Matsumoto, H., E. Rozi Ismail, Y. Seki, and K. Soda. "3P031 Role of Hydrophobic Clusters in Protein Folding." Seibutsu Butsuri 45, supplement (2005): S211. http://dx.doi.org/10.2142/biophys.45.s211_3.

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11

Köddermann, T., and R. Ludwig. "N-Methylacetamide/water clusters in a hydrophobic solvent." Phys. Chem. Chem. Phys. 6, no. 8 (2004): 1867–73. http://dx.doi.org/10.1039/b314702a.

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12

Baldwin, R. L. "PROTEIN FOLDING: Making a Network of Hydrophobic Clusters." Science 295, no. 5560 (March 1, 2002): 1657–58. http://dx.doi.org/10.1126/science.1069893.

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13

Duval-Terrié, Caroline, Jovenka Huguet, and Guy Muller. "Self-assembly and hydrophobic clusters of amphiphilic polysaccharides." Colloids and Surfaces A: Physicochemical and Engineering Aspects 220, no. 1-3 (June 2003): 105–15. http://dx.doi.org/10.1016/s0927-7757(03)00062-1.

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14

Köddermann, Thorsten, Frank Schulte, Markus Huelsekopf, and Ralf Ludwig. "Formation of Water Clusters in a Hydrophobic Solvent." Angewandte Chemie International Edition 42, no. 40 (October 20, 2003): 4904–8. http://dx.doi.org/10.1002/anie.200351438.

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15

KARYAGINA, ANNA, ANNA ERSHOVA, MIKHAIL TITOV, IVAN OLOVNIKOV, EVGENIY AKSIANOV, ALEXANDRA RYAZANOVA, ELENA KUBAREVA, SERGEI SPIRIN, and ANDREI ALEXEEVSKI. "ANALYSIS OF CONSERVED HYDROPHOBIC CORES IN PROTEINS AND SUPRAMOLECULAR COMPLEXES." Journal of Bioinformatics and Computational Biology 04, no. 02 (April 2006): 357–72. http://dx.doi.org/10.1142/s0219720006001837.

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The conserved hydrophobic core is an important feature of a family of protein domains. We suggest a procedure for finding and the analysis of conserved hydrophobic cores. The procedure is based on using an original program called CluD (). Conserved hydrophobic cores of several families including homeodomains and interlock-containing domains are described. Hydrophobic clusters on some protein-DNA and protein-protein interfaces were also analyzed.

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16

Jackson, B. M., C. M. Drysdale, K. Natarajan, and A. G. Hinnebusch. "Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation." Molecular and Cellular Biology 16, no. 10 (October 1996): 5557–71. http://dx.doi.org/10.1128/mcb.16.10.5557.

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GCN4 is a transcriptional activator in the bZIP family that regulates amino acid biosynthetic genes in the yeast Saccharomyces cerevisiae. The N-terminal 100 amino acids of GCN4 contains a potent activation function that confers high-level transcription in the absence of the centrally located acidic activation domain (CAAD) delineated in previous studies. To identify specific amino acids important for activation by the N-terminal domain, we mutagenized a GCN4 allele lacking the CAAD and screened alleles in vivo for reduced expression of the HIS3 gene. We found four pairs of closely spaced phenylalanines and a leucine residue distributed throughout the N-terminal 100 residues of GCN4 that are required for high-level activation in the absence of the CAAD. Trp, Leu, and Tyr were highly functional substitutions for the Phe residue at position 45. Combined with our previous findings, these results indicate that GCN4 contains seven clusters of aromatic or bulky hydrophobic residues which make important contributions to transcriptional activation at HIS3. None of the seven hydrophobic clusters is essential for activation by full-length GCN4, and the critical residues in two or three clusters must be mutated simultaneously to observe a substantial reduction in GCN4 function. Numerous combinations of four or five intact clusters conferred high-level transcription of HIS3. We propose that many of the hydrophobic clusters in GCN4 act independently of one another to provide redundant means of stimulating transcription and that the functional contributions of these different segments are cumulative at the HIS3 promoter. On the basis of the primacy of bulky hydrophobic residues throughout the activation domain, we suggest that GCN4 contains multiple sites that mediate hydrophobic contacts with one or more components of the transcription initiation machinery.

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17

Tamaru, Yutaka, Shuichi Karita, Atef Ibrahim, Helen Chan, and Roy H. Doi. "A Large Gene Cluster for the Clostridium cellulovorans Cellulosome." Journal of Bacteriology 182, no. 20 (October 15, 2000): 5906–10. http://dx.doi.org/10.1128/jb.182.20.5906-5910.2000.

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ABSTRACT A large gene cluster for the Clostridium cellulovoranscellulosome has been cloned and sequenced upstream and downstream of the cbpA and exgS genes (C.-C. Liu and R. H. Doi, Gene 211:39–47, 1998). Gene walking revealed that theengL gene cluster (Y. Tamaru and R. H. Doi, J. Bacteriol. 182:244–247, 2000) was located downstream of thecbpA-exgS genes. Further DNA sequencing revealed that this cluster contains the genes for the scaffolding protein CbpA, the exoglucanase ExgS, several endoglucanases of family 9, the mannanase ManA, and the hydrophobic protein HbpA containing a surface layer homology domain and a hydrophobic (or cohesin) domain. The sequence of the clustered genes iscbpA-exgS-engH-engK-hbpA-engL-manA-engM-engN and is about 22 kb in length. The engN gene did not have a complete catalytic domain, indicating that engN is a truncated gene. This large gene cluster is flanked at the 5′ end by a putative noncellulosomal operon consisting of nifV-orf1-sigX-regAand at the 3′ end by noncellulosomal genes with homology to transposase (trp) and malate permease (mle). Since gene clusters for the cellulosome are also found in C. cellulolyticum and C. josui, they seem to be typical of mesophilic clostridia, indicating that the large gene clusters may arise from a common ancestor with some evolutionary modifications.

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18

Chen, Peng, Chunmei Liu, Legand Burge, Mohammad Mahmood, William Southerland, and Clay Gloster. "Prediction of inter-residue contact clusters from hydrophobic cores." International Journal of Data Mining and Bioinformatics 4, no. 6 (2010): 722. http://dx.doi.org/10.1504/ijdmb.2010.037549.

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19

Permyakov, Sergey E., Alisa S. Vologzhannikova, Ekaterina L. Nemashkalova, Alexei S. Kazakov, Alexander I. Denesyuk, Konstantin Denessiouk, Viktoriia E. Baksheeva, et al. "Experimental Insight into the Structural and Functional Roles of the ‘Black’ and ‘Gray’ Clusters in Recoverin, a Calcium Binding Protein with Four EF-Hand Motifs." Molecules 24, no. 13 (July 8, 2019): 2494. http://dx.doi.org/10.3390/molecules24132494.

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Recently, we have found that calcium binding proteins of the EF-hand superfamily (i.e., a large family of proteins containing helix-loop-helix calcium binding motif or EF-hand) contain two types of conserved clusters called cluster I (‘black’ cluster) and cluster II (‘grey’ cluster), which provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domains. Cluster I is more conservative and mostly incorporates aromatic amino acids, whereas cluster II includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. Recoverin is EF-hand Ca2+-binding protein containing two ‘black’ clusters comprised of F35, F83, Y86 (N-terminal domain) and F106, E169, F172 (C-terminal domain) as well as two ‘gray’ clusters comprised of F70, Q46, F49 (N-terminal domain) and W156, K119, V122 (C-terminal domain). To understand a role of these residues in structure and function of human recoverin, we sequentially substituted them for alanine and studied the resulting mutants by a set of biophysical methods. Under metal-free conditions, the ‘black’ clusters mutants (except for F35A and E169A) were characterized by an increase in the α-helical content, whereas the ‘gray’ cluster mutants (except for K119A) exhibited the opposite behavior. By contrast, in Ca2+-loaded mutants the α-helical content was always elevated. In the absence of calcium, the substitutions only slightly affected multimerization of recoverin regardless of their localization (except for K119A). Meanwhile, in the presence of calcium mutations in N-terminal domain of the protein significantly suppressed this process, indicating that surface properties of Ca2+-bound recoverin are highly affected by N-terminal cluster residues. The substitutions in C-terminal clusters generally reduced thermal stability of recoverin with F172A (‘black’ cluster) as well as W156A and K119A (‘gray’ cluster) being the most efficacious in this respect. In contrast, the mutations in the N-terminal clusters caused less pronounced differently directed changes in thermal stability of the protein. The substitutions of F172, W156, and K119 in C-terminal domain of recoverin together with substitution of Q46 in its N-terminal domain provoked significant but diverse changes in free energy associated with Ca2+ binding to the protein: the mutant K119A demonstrated significantly improved calcium binding, whereas F172A and W156A showed decrease in the calcium affinity and Q46A exhibited no ion coordination in one of the Ca2+-binding sites. The most of the N-terminal clusters mutations suppressed membrane binding of recoverin and its inhibitory activity towards rhodopsin kinase (GRK1). Surprisingly, the mutant W156A aberrantly activated rhodopsin phosphorylation regardless of the presence of calcium. Taken together, these data confirm the scaffolding function of several cluster-forming residues and point to their critical role in supporting physiological activity of recoverin.

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20

Tang, Zhaojun, Changhong Shi, Shu Wu, Zengfu Jiang, and Lijuan Wang. "Fabrication of Hydrophobic Surface on Wood Veneer via Electroless Nickel Plating Combined with Chemical Corrosion." BioResources 11, no. 1 (December 3, 2015): 1007–14. http://dx.doi.org/10.15376/biores.11.1.1007-1014.

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Birch veneers were coated with Ni-P films by a combined process of KBH4 activation and electroless plating. The plated veneers were further chemically corroded to obtain hydrophobic surfaces on wood. The effect of chemical corrosion on the contact angle of the veneers was investigated. The hydrophobic veneers were characterized by X-ray photo electron spectroscopy (XPS), scanning electron microscopy (SEM), and X-ray diffraction (XRD). The surface contact angle of birch veneer before and after it was plated with Ni-P alloy coating was 41º and 121º, respectively. The contact angle reached 136.7º when the nickel-coated veneers were corroded in CuSO4 aqueous solution for 30 min. XPS analysis showed that Cu0 cluster doped with little CuO formed on the corroded surface of Ni-P alloy film after chemical corrosion. SEM and XRD showed that rough copper clusters formed on the surface of the wood veneer and revealed the reason of the surface hydrophobicity. This study provides a new pathway for fabricating hydrophobic wood.

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21

Yagi-Utsumi, Maho, Koichi Matsuo, Katsuhiko Yanagisawa, Kunihiko Gekko, and Koichi Kato. "Spectroscopic Characterization of Intermolecular Interaction of AmyloidβPromoted on GM1 Micelles." International Journal of Alzheimer's Disease 2011 (2011): 1–8. http://dx.doi.org/10.4061/2011/925073.

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Clusters of GM1 gangliosides act as platforms for conformational transition of monomeric, unstructured amyloidβ(Aβ) to its toxicβ-structured aggregates. We have previously shown that Aβ(1–40) accommodated on the hydrophobic/hydrophilic interface of lyso-GM1 or GM1 micelles assumesα-helical structures under ganglioside-excess conditions. For better understanding of the mechanisms underlying theα-to-βconformational transition of Aβon GM1 clusters, we performed spectroscopic characterization of Aβ(1–40) titrated with GM1. It was revealed that the thioflavin T- (ThT-) reactiveβ-structure is more populated in Aβ(1–40) under conditions where the Aβ(1–40) density on GM1 micelles is high. Under this circumstance, the C-terminal hydrophobic anchor Val39-Val40shows two distinct conformational states that are reactive with ThT, while such Aβspecies were not generated by smaller lyso-GM1 micelles. These findings suggest that GM1 clusters promote specific Aβ-Aβinteractions through their C-termini coupled with formation of the ThT-reactiveβ-structure depending on sizes and curvatures of the clusters.

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22

Almlöf, T., J. A. Gustafsson, and A. P. Wright. "Role of hydrophobic amino acid clusters in the transactivation activity of the human glucocorticoid receptor." Molecular and Cellular Biology 17, no. 2 (February 1997): 934–45. http://dx.doi.org/10.1128/mcb.17.2.934.

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We have performed a mutagenesis analysis of the 58-amino-acid tau1-core peptide, which represents the core transactivation activity of the tau1 transactivation domain from the glucocorticoid receptor. Mutants with altered activity were identified by phenotypic screening in the yeast Saccharomyces cerevisiae. Most mutants with reduced activity had substitutions of hydrophobic amino acids. Most single-substitution mutants with reduced activity were localized near the N terminus of the tau1-core within a segment that has been shown previously to have a propensity for alpha-helix conformation, suggesting that this helical region is of predominant importance. The particular importance of hydrophobic residues within this region was confirmed by comparing the activities of alanine substitutions of the hydrophobic residues in this and two other helical regions. The hydrophobic residues were shown to be important for the transactivation activity of both the isolated tau1-core and the intact glucocorticoid receptor in mammalian cells. Rare mutations in helical regions I and II gave rise to increased transcriptional activation activity. These mutations increase the hydrophobicity of hydrophobic patches on each of these helices, suggesting a relationship between the hydrophobicity of the patches and transactivation activity. However, certain nonhydrophobic residues are also important for activity. Interestingly, helical region I partially matches a consensus motif found in the retinoic acid receptor, VP16, and several other activator proteins.

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23

HÓRVÖLGYI, Z., and M. ZRINYI. "INTERFACIAL AGGREGATION OF FLOATING MICROPARTICLES UNDER THE CONTROL OF SHORT-RANGE COLLOID AND VERY LONG-RANGE CAPILLARY FORCES." Fractals 01, no. 03 (September 1993): 460–69. http://dx.doi.org/10.1142/s0218348x93000484.

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Interfacial aggregation of surface modified glass beads (62–74 μm diameter) at water/air interface was carried out by using two differently hydrophobic samples, respectively. The effect of aggregation time on the self-similar structure of forming aggregates was studied comparing the actual results to those obtained previously.1 The time dependence of restructuring from the point of view of fractal geometry has been proved but the results call attention to another time dependent process— orientation of growing clusters during their collisions due to anisotropy of cluster-cluster interactions.

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24

Miller, Kyle, Ayuna Tsyrenova, Stephen M. Anthony, Shiyi Qin, Xin Yong, and Shan Jiang. "Drying mediated orientation and assembly structure of amphiphilic Janus particles." Soft Matter 14, no. 33 (2018): 6793–98. http://dx.doi.org/10.1039/c8sm01147h.

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25

Zhang, Chi, Kenji Kikushima, Mizuki Endo, Tomoaki Kahyo, Makoto Horikawa, Takaomi Matsudaira, Tatsuya Tanaka, et al. "Imaging and Manipulation of Plasma Membrane Fatty Acid Clusters Using TOF-SIMS Combined Optogenetics." Cells 12, no. 1 (December 20, 2022): 10. http://dx.doi.org/10.3390/cells12010010.

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The plasma membrane (PM) serves multiple functions to support cell activities with its heterogeneous molecular distribution. Fatty acids (FAs) are hydrophobic components of the PM whose saturation and length determine the membrane’s physical properties. The FA distribution contributes to the PM’s lateral heterogeneity. However, the distribution of PM FAs is poorly understood. Here, we proposed the FA cluster hypothesis, which suggested that FAs on the PM exist as clusters. By the optogenetic tool translocating the endoplasmic reticulum (ER), we were able to manipulate the distribution of PM FAs. We used time-of-flight combined secondary ion mass spectrometry (TOF-SIMS) to image PM FAs and discovered that PM FAs were presented and distributed as clusters and are also manipulated as clusters. We also found the existence of multi-FA clusters formed by the colocalization of more than one FA. Our optogenetic tool also decreased the clustering degree of FA clusters and the formation probability of multi-FA clusters. This research opens up new avenues and perspectives to study PM heterogeneity from an FA perspective. This research also suggests a possible treatment for diseases caused by PM lipid aggregation and furnished a convenient tool for therapeutic development.

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26

Jain, Anshika, Anamika Singh, Nunziata Maio, and Tracey A. Rouault. "Assembly of the [4Fe–4S] cluster of NFU1 requires the coordinated donation of two [2Fe–2S] clusters from the scaffold proteins, ISCU2 and ISCA1." Human Molecular Genetics 29, no. 19 (August 8, 2020): 3165–82. http://dx.doi.org/10.1093/hmg/ddaa172.

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Abstract NFU1, a late-acting iron–sulfur (Fe–S) cluster carrier protein, has a key role in the pathogenesis of the disease, multiple mitochondrial dysfunctions syndrome. In this work, using genetic and biochemical approaches, we identified the initial scaffold protein, mitochondrial ISCU (ISCU2) and the secondary carrier, ISCA1, as the direct donors of Fe–S clusters to mitochondrial NFU1, which appears to dimerize and reductively mediate the formation of a bridging [4Fe–4S] cluster, aided by ferredoxin 2. By monitoring the abundance of target proteins that acquire their Fe–S clusters from NFU1, we characterized the effects of several novel pathogenic NFU1 mutations. We observed that NFU1 directly interacts with each of the Fe–S cluster scaffold proteins known to ligate [2Fe–2S] clusters, ISCU2 and ISCA1, and we mapped the site of interaction to a conserved hydrophobic patch of residues situated at the end of the C-terminal alpha-helix of NFU1. Furthermore, we showed that NFU1 lost its ability to acquire its Fe–S cluster when mutagenized at the identified site of interaction with ISCU2 and ISCA1, which thereby adversely affected biochemical functions of proteins that are thought to acquire their Fe–S clusters directly from NFU1, such as lipoic acid synthase, which supports the Fe–S-dependent process of lipoylation of components of multiple key enzyme complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase and the glycine cleavage complex.

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27

Bhattacharya, Priyanka, Smita Gohil, Javed Mazher, Shankar Ghosh, and Pushan Ayyub. "Universal, geometry-driven hydrophobic behaviour of bare metal nanowire clusters." Nanotechnology 19, no. 7 (January 31, 2008): 075709. http://dx.doi.org/10.1088/0957-4484/19/7/075709.

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28

Battista, Edmondo, Maria Laura Coluccio, Alessandro Alabastri, Marianna Barberio, Filippo Causa, Paolo Antonio Netti, Enzo Di Fabrizio, and Francesco Gentile. "Metal enhanced fluorescence on super-hydrophobic clusters of gold nanoparticles." Microelectronic Engineering 175 (May 2017): 7–11. http://dx.doi.org/10.1016/j.mee.2016.12.013.

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29

Tisi, Laurence C., and Philip A. Evans. "Conserved structural features on protein surfaces: Small exterior hydrophobic clusters." Journal of Molecular Biology 249, no. 2 (January 1995): 251–58. http://dx.doi.org/10.1006/jmbi.1995.0294.

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30

Barborini, Emanuele, Giacomo Bertolini, Monica Epifanio, Alexander Yavorskyy, Simone Vinati, and Marc Baumann. "Cluster-Assembled Nanoporous Super-Hydrophilic Smart Surfaces for On-Target Capturing and Processing of Biological Samples for Multi-Dimensional MALDI-MS." Molecules 27, no. 13 (June 30, 2022): 4237. http://dx.doi.org/10.3390/molecules27134237.

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Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) on cluster-assembled super-hydrophilic nanoporous titania films deposited on hydrophobic conductive-polymer substrates feature a unique combination of surface properties that significantly improve the possibilities of capturing and processing biological samples before and during the MALDI-MS analysis without changing the selected sample target (multi-dimensional MALDI-MS). In contrast to pure hydrophobic surfaces, such films promote a remarkable biologically active film porosity at the nanoscale due to the soft assembling of ultrafine atomic clusters. This unique combination of nanoscale porosity and super-hydrophilicity provides room for effective sample capturing, while the hydrophilic-hydrophobic discontinuity at the border of the dot-patterned film acts as a wettability-driven containment for sample/reagent droplets. In the present work, we evaluate the performance of such advanced surface engineered reactive containments for their benefit in protein sample processing and characterization. We shortly discuss the advantages resulting from the introduction of the described chips in the MALDI-MS workflow in the healthcare/clinical context and in MALDI-MS bioimaging (MALDI-MSI).

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Gugneja, S., C. M. Virbasius, and R. C. Scarpulla. "Nuclear respiratory factors 1 and 2 utilize similar glutamine-containing clusters of hydrophobic residues to activate transcription." Molecular and Cellular Biology 16, no. 10 (October 1996): 5708–16. http://dx.doi.org/10.1128/mcb.16.10.5708.

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Nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2) are ubiquitous transcription factors that have been implicated in the control of nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication. Recently, both factors have been found to be major transcriptional determinants for a subset of these genes that define a class of simple promoters involved in respiratory chain expression. Here, functional domains required for transactivation by NRF-1 have been defined. An atypical nuclear localization signal resides in a conserved amino-terminal region adjacent to the DNA binding domain and consists of functionally redundant clusters of basic residues. A second domain in the carboxy-terminal half of the molecule is necessary for transcriptional activation. The activation domains of both NRF-1 and NRF-2 were extensively characterized by both deletion and alanine substitution mutagenesis. The results show that these domains do not fall into known classes defined by a preponderance of amino acid residues, including glutamines, prolines, or isoleucines, as found in other eukaryotic activators. Rather, in both factors, a series of tandemly arranged clusters of hydrophobic amino acids were required for activation. Although all of the functional clusters contain glutamines, the glutamines differ from the hydrophobic residues in that they are inconsequential for activation. Unlike the NRF-2 domain, which contains its essential hydrophobic motifs within 40 residues, the NRF-1 domain spans about 40% of the molecule and appears to have a bipartite structure. The findings indicate that NRF-1 and NRF-2 utilize similar hydrophobic structural motifs for activating transcription.

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Feng, Sinan, Guibin Wang, Haibo Zhang, and Jinhui Pang. "Graft octa-sulfonated poly(arylene ether) for high performance proton exchange membrane." Journal of Materials Chemistry A 3, no. 24 (2015): 12698–708. http://dx.doi.org/10.1039/c5ta03088a.

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Drysdale, Connie M., Belinda M. Jackson, Richard McVeigh, Edward R. Klebanow, Yu Bai, Tetsuro Kokubo, Mark Swanson, Yoshihiro Nakatani, P. Anthony Weil, and Alan G. Hinnebusch. "The Gcn4p Activation Domain Interacts Specifically In Vitro with RNA Polymerase II Holoenzyme, TFIID, and the Adap-Gcn5p Coactivator Complex." Molecular and Cellular Biology 18, no. 3 (March 1, 1998): 1711–24. http://dx.doi.org/10.1128/mcb.18.3.1711.

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ABSTRACT The Gcn4p activation domain contains seven clusters of hydrophobic residues that make additive contributions to transcriptional activation in vivo. We observed efficient binding of a glutathioneS-transferase (GST)–Gcn4p fusion protein to components of three different coactivator complexes in Saccharomyces cerevisiae cell extracts, including subunits of transcription factor IID (TFIID) (yeast TAFII20 [yTAFII20], yTAFII60, and yTAFII90), the holoenzyme mediator (Srb2p, Srb4p, and Srb7p), and the Adap-Gcn5p complex (Ada2p and Ada3p). The binding to these coactivator subunits was completely dependent on the hydrophobic clusters in the Gcn4p activation domain. Alanine substitutions in single clusters led to moderate reductions in binding, double-cluster substitutions generally led to greater reductions in binding than the corresponding single-cluster mutations, and mutations in four or more clusters reduced binding to all of the coactivator proteins to background levels. The additive effects of these mutations on binding of coactivator proteins correlated with their cumulative effects on transcriptional activation by Gcn4p in vivo, particularly with Ada3p, suggesting that recruitment of these coactivator complexes to the promoter is a cardinal function of the Gcn4p activation domain. As judged by immunoprecipitation analysis, components of the mediator were not associated with constituents of TFIID and Adap-Gcn5p in the extracts, implying that GST-Gcn4p interacted with the mediator independently of these other coactivators. Unexpectedly, a proportion of Ada2p coimmunoprecipitated with yTAFII90, and the yTAFII20, -60, and -90 proteins were coimmunoprecipitated with Ada3p, revealing a stable interaction between components of TFIID and the Adap-Gcn5p complex. Because GST-Gcn4p did not bind specifically to highly purified TFIID, Gcn4p may interact with TFIID via the Adap-Gcn5p complex or some other adapter proteins. The ability of Gcn4p to interact with several distinct coactivator complexes that are physically and genetically linked to TATA box-binding protein can provide an explanation for the observation that yTAFII proteins are dispensable for activation by Gcn4p in vivo.

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Yan, Kai, Min Chen, Shuxue Zhou, and Limin Wu. "Self-assembly of upconversion nanoclusters with an amphiphilic copolymer for near-infrared- and temperature-triggered drug release." RSC Advances 6, no. 88 (2016): 85293–302. http://dx.doi.org/10.1039/c6ra17622d.

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The hybrid colloidal clusters were prepared by self-assembly of multiresponsive copolymer with hydrophobic nanocrystals, and which was able to near-infrared light and temperature triggered drug release.

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35

Hawlicka, Ewa, and Roman Grabowski. "Solvation of Ions in Aqueous Solutions of Hydrophobic Solutes." Zeitschrift für Naturforschung A 48, no. 8-9 (September 1, 1993): 906–10. http://dx.doi.org/10.1515/zna-1993-8-912.

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Abstract The self-diffusion of Na+, Et4N+ and I- in mixtures of water with n-propanol at 25 °C and with lert-butanol at 30 °C was measured as function of salt concentration and solvent composition. The limiting self-diffusion coefficients of the ions were used to compute the ionic radii. The influence of the composition of the solvent on the solvation of the ions is discussed. In aqueous solutions of both alcohols the effective ionic radii are reduced. The strongest influence is found for the same solvent composition for which the highest concentration of the alcohol clusters has been reported. Hydra-tion of the clusters of n-propanol causes a vanishing of the second hydration shell of Na+ and the first one of Et4N+ and I-. In the case of terf-butanol even the first hydration shell of Na+ is partially reduced.

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36

Galanakis, Dennis K., Anna Protopopova, Liudi Zhang, Kao Li, Clement Marmorat, Tomas Scheiner, Jaseung Koo, Anne G. Savitt, Miriam Rafailovich, and John Weisel. "Fibers Generated by Plasma Des-AA Fibrin Monomers and Protofibril/Fibrinogen Clusters Bind Platelets: Clinical and Nonclinical Implications." TH Open 05, no. 03 (July 2021): e273-e285. http://dx.doi.org/10.1055/s-0041-1725976.

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Abstract Objective Soluble fibrin (SF) is a substantial component of plasma fibrinogen (fg), but its composition, functions, and clinical relevance remain unclear. The study aimed to evaluate the molecular composition and procoagulant function(s) of SF. Materials and Methods Cryoprecipitable, SF-rich (FR) and cryosoluble, SF-depleted (FD) fg isolates were prepared and adsorbed on one hydrophilic and two hydrophobic surfaces and scanned by atomic force microscopy (AFM). Standard procedures were used for fibrin polymerization, crosslinking by factor XIII, electrophoresis, and platelet adhesion. Results Relative to FD fg, thrombin-induced polymerization of FR fg was accelerated and that induced by reptilase was markedly delayed, attributable to its decreased (fibrinopeptide A) FpA. FR fg adsorption to each surface yielded polymeric clusters and co-cryoprecipitable solitary monomers. Cluster components were crosslinked by factor XIII and comprised ≤21% of FR fg. In contrast to FD fg, FR fg adsorption on hydrophobic surfaces resulted in fiber generation enabled by both clusters and solitary monomers. This began with numerous short protofibrils, which following prolonged adsorption increased in number and length and culminated in surface-linked three-dimensional fiber networks that bound platelets. Conclusion The abundance of adsorbed protofibrils resulted from (1) protofibril/fg clusters whose fg was dissociated during adsorption, and (2) adsorbed des-AA monomers that attracted solution counterparts initiating protofibril assembly and elongation by their continued incorporation. The substantial presence of both components in transfused plasma and cryoprecipitate augments hemostasis by accelerating thrombin-induced fibrin polymerization and by tightly anchoring the resulting clot to the underlying wound or to other abnormal vascular surfaces.

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Kellenberger, Stephan, James W. West, Todd Scheuer, and William A. Catterall. "Molecular Analysis of the Putative Inactivation Particle in the Inactivation Gate of Brain Type IIA Na+ Channels." Journal of General Physiology 109, no. 5 (May 1, 1997): 589–605. http://dx.doi.org/10.1085/jgp.109.5.589.

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Fast Na+ channel inactivation is thought to involve binding of phenylalanine 1489 in the hydrophobic cluster IFM in LIII-IV of the rat brain type IIA Na+ channel. We have analyzed macroscopic and single channel currents from Na+ channels with mutations within and adjacent to hydrophobic clusters in LIII-IV. Substitution of F1489 by a series of amino acids disrupted inactivation to different extents. The degree of disruption was closely correlated with the hydrophilicity of the amino acid at position 1489. These mutations dramatically destabilized the inactivated state and also significantly slowed the entry into the inactivated state, consistent with the idea that F1489 forms a hydrophobic interaction with a putative receptor during the fast inactivation process. Substitution of a phe residue at position 1488 or 1490 in mutants lacking F1489 did not restore normal inactivation, indicating that precise location of F1489 is critical for its function. Mutations of T1491 disrupted inactivation substantially, with large effects on the stability of the inactivated state and smaller effects on the rate of entry into the inactivated state. Mutations of several other hydrophobic residues did not destabilize the inactivated state at depolarized potentials, indicating that the effects of mutations at F1489 and T1491 are specific. The double mutant YY1497/8QQ slowed macroscopic inactivation at all potentials and accelerated recovery from inactivation at negative membrane potentials. Some of these mutations in LIII-IV also affected the latency to first opening, indicating coupling between LIII-IV and channel activation. Our results show that the amino acid residues of the IFM hydrophobic cluster and the adjacent T1491 are unique in contributing to the stability of the inactivated state, consistent with the designation of these residues as components of the inactivation particle responsible for fast inactivation of Na+ channels.

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Forouzangohar, Mohsen, and Rai S. Kookana. "Sorption of nano-C60 clusters in soil: hydrophilic or hydrophobic interactions?" Journal of Environmental Monitoring 13, no. 5 (2011): 1190. http://dx.doi.org/10.1039/c0em00689k.

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Wang, Lingjian, Nobuaki Kikkawa, and Akihiro Morita. "Hydrated Ion Clusters in Hydrophobic Liquid: Equilibrium Distribution, Kinetics, and Implications." Journal of Physical Chemistry B 122, no. 13 (January 23, 2018): 3562–71. http://dx.doi.org/10.1021/acs.jpcb.7b10740.

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40

Pica, Andrea, and Giuseppe Graziano. "On the cononsolvency behaviour of hydrophobic clusters in water–methanol solutions." Physical Chemistry Chemical Physics 20, no. 10 (2018): 7230–35. http://dx.doi.org/10.1039/c7cp07943e.

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41

Alaeddine, Simon, and Hakan Nygren. "Interaction and stability of adsorbed ferritin clusters on hydrophobic quartz surfaces." Colloids and Surfaces B: Biointerfaces 5, no. 5 (December 1995): 227–40. http://dx.doi.org/10.1016/0927-7765(95)01222-7.

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42

Hiller, Sebastian, Gerhard Wider, Lukas L Imbach, and Kurt Wüthrich. "Interactions with Hydrophobic Clusters in the Urea-Unfolded Membrane Protein OmpX." Angewandte Chemie International Edition 47, no. 5 (January 18, 2008): 977–81. http://dx.doi.org/10.1002/anie.200703367.

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43

Krupskaya, T. V., N. V. Yelahina, L. P. Morozova, and V. V. Turov. "Peculiarities of alginic acid hydration in the air and in hydrophobic organic environment." Himia, Fizika ta Tehnologia Poverhni 12, no. 2 (June 30, 2021): 149–54. http://dx.doi.org/10.15407/hftp12.02.149.

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The effect of the medium on the parameters of water bound to the surface of alginic acid powder was studied by low-temperature 1H NMR spectroscopy. The aim of this work was to study the effect of hydrophobic environment on the binding of water with alginic acid and to compare the parameters of the interfacial layers of water in air, in chloroform and chloroform with the addition of hydrochloric acid. It is shown that when adsorbed on the surface (500 mg/g H2O), most of it is strongly bound. It is shown that for most dispersed systems, when replacing the air with chloroform, the interfacial energy of water increases from 11.8 to 15.2 kJ/mol, which is due to the capability of weakly polar organic molecules to diffuse on the surface of solid particles, thereby reducing the interaction energy with the adsorbed surface water clusters. It is concluded that chloroform molecules cannot diffuse on the surface of alginic acid particles and affect only the structure of water clusters localized in the outer adsorption layer. In the presence of hydrochloric acid on the surface of alginic acid, a system of water clusters is formed, most of which does not dissolve hydrochloric acid, and the radii of these clusters is 2 nm, which are likely to form in the gaps between the polymer chains of polysaccharide.

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Hernandez, Leonardo F., Roberto R. Lima, Edson Pecoraro, Esteban Rosim-Fachini, and Maria L. P. da Silva. "Composite Thin Film Obtained Using Tetraethoxysilane and Aimed at VOCs Detection." Materials Science Forum 730-732 (November 2012): 185–90. http://dx.doi.org/10.4028/www.scientific.net/msf.730-732.185.

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The aim of this work was production of tetraethoxysilane (TEOS) plasma polymerized thin films and optimization of their physical-chemical characteristic for sensor development. The films were analyzed using several techniques. It was possible to produce composites (graphite clusters imbibed by silicon oxide film) made from only one reactant (TEOS). Deposition rate can vary significantly, reaching a maximum of 30 nm/min; cluster formation and their size widely depending on deposition parameters. The film surface was hydrophobic but can be wetted by organic compounds, probably due to carbon radicals. These films are good candidates for sensor development.

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Kluska, Katarzyna, Manuel D. Peris-Díaz, Dawid Płonka, Alexander Moysa, Michał Dadlez, Aurélien Deniaud, Wojciech Bal, and Artur Krężel. "Formation of highly stable multinuclear AgnSn clusters in zinc fingers disrupts their structure and function." Chemical Communications 56, no. 9 (2020): 1329–32. http://dx.doi.org/10.1039/c9cc09418k.

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Silver (Ag(i)) binding to consensus zinc fingers (ZFs) causes Zn(ii) release inducing a gradual disruption of the hydrophobic core, followed by an overall conformational change and formation of highly stable Ag_nS_n clusters.

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46

Mizutani, Azuki, Cheng Tan, Yuji Sugita, and Shoji Takada. "Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study." PLOS Computational Biology 19, no. 7 (July 24, 2023): e1011321. http://dx.doi.org/10.1371/journal.pcbi.1011321.

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The phase separation model for transcription suggests that transcription factors (TFs), coactivators, and RNA polymerases form biomolecular condensates around active gene loci and regulate transcription. However, the structural details of condensates remain elusive. In this study, for Nanog, a master TF in mammalian embryonic stem cells known to form protein condensates in vitro, we examined protein structures in the condensates using residue-level coarse-grained molecular simulations. Human Nanog formed micelle-like clusters in the condensate. In the micelle-like cluster, the C-terminal disordered domains, including the tryptophan repeat (WR) regions, interacted with each other near the cluster center primarily via hydrophobic interaction. In contrast, hydrophilic disordered N-terminal and DNA-binding domains were exposed on the surface of the clusters. Electrostatic attractions of these surface residues were responsible for bridging multiple micelle-like structures in the condensate. The micelle-like structure and condensate were dynamic and liquid-like. Mutation of tryptophan residues in the WR region which was implicated to be important for a Nanog function resulted in dissolution of the Nanog condensate. Finally, to examine the impact of Nanog cluster to DNA, we added DNA fragments to the Nanog condensate. Nanog DNA-binding domains exposed to the surface of the micelle-like cluster could recruit more than one DNA fragments, making DNA-DNA distance shorter.

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47

Lashkov, A. A., S. V. Rubinsky, and P. A. Eistrikh-Heller. "Application of the DBSCAN Algorithm to Detect Hydrophobic Clusters in Protein Structures." Crystallography Reports 64, no. 3 (May 2019): 524–32. http://dx.doi.org/10.1134/s1063774519030179.

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48

Zehfus, Micheal H. "Automatic recognition of hydrophobic clusters and their correlation with protein folding units." Protein Science 4, no. 6 (June 1995): 1188–202. http://dx.doi.org/10.1002/pro.5560040617.

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Sun, Xiuzhi Susan, Donghai Wang, Lu Zhang, Xiaoqun Mo, Li Zhu, and Dan Bolye. "Morphology and Phase Separation of Hydrophobic Clusters of Soy Globular Protein Polymers." Macromolecular Bioscience 8, no. 4 (December 10, 2007): 295–303. http://dx.doi.org/10.1002/mabi.200700235.

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50

Palomeque-Messia, P., S. Englebert, M. Leyh-Bouille, M. Nguyen-Distèche, C. Duez, S. Houba, O. Dideberg, J. Van Beeumen, and J. M. Ghuysen. "Amino acid sequence of the penicillin-binding protein/dd-peptidase of Streptomyces K15. Predicted secondary structures of the low Mr penicillin-binding proteins of class A." Biochemical Journal 279, no. 1 (October 1, 1991): 223–30. http://dx.doi.org/10.1042/bj2790223.

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The low-Mr penicillin-binding protein (PBP)/DD-transpeptidase of Streptomyces K15 is synthesized in the form of a 291-amino acid-residue precursor possessing a cleavable 29-amino acid-residue signal peptide. Sequence-similarity searches and hydrophobic-cluster analysis show that the Streptomyces K15 enzyme, the Escherichia coli PBPs/DD-carboxy-peptidases 5 and 6, the Bacillus subtilis PBP/DD-carboxypeptidase 5 and the spoIIA product (a putative PBP involved in the sporulation of B. subtilis) are structurally related and form a distinct class A of low-Mr PBPs/DD-peptidases. The distribution of the hydrophobic clusters along the amino acid sequences also shows that the Streptomyces K15 PBP, and by extension the other PBPs of class A, have similarity in the polypeptide folding, with the beta-lactamases of class A, with as reference the Streptomyces albus G and Staphylococcus aureus beta-lactamases of known three-dimensional structure. This comparison allows one to predict most of the secondary structures in the PBPs and the amino acid motifs that define the enzyme active sites.

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