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SHRESTHA, NRIPENDRA L., YOUHEI KAWAGUCHI, and TAKENAO OHKAWA. "SUMOMO: A PROTEIN SURFACE MOTIF MINING MODULE." International Journal of Computational Intelligence and Applications 04, no. 04 (2004): 431–49. http://dx.doi.org/10.1142/s1469026804001392.
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Protein surface motifs, which can be defined as commonly appearing patterns of shape and physical properties in protein molecular surfaces, can be considered "possible active sites". We have developed a system for mining surface motifs: SUMOMO which consists of two phases: surface motif extraction and surface motif filtering. In the extraction phase, a given set of protein molecular surface data is divided into small surfaces called unit surfaces. After extracting several common unit surfaces as candidate motifs, they are repetitively merged into surface motifs. However, a large amount of surface motifs is extracted in this phase, making it difficult to distinguish whether the extracted motifs are significant to be considered active sites. Since active sites from proteins with a particular function have similar shape and physical properties, proteins can be classified based on similarity among local surfaces. Thus, in the filtering phase, local surfaces extracted from proteins of the same group are considered significant motifs, and the rest are filtered out. The proposed method was applied to discover surface motifs from 15 proteins belonging to four function groups. Motifs corresponding to all 4 known functional sites were recognised.
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Kumar, J., and M. S. Shunmugam. "Three-Dimensional Characterization of Engineering Surfaces Using Triangular Motifs." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 219, no. 9 (2005): 965–77. http://dx.doi.org/10.1243/095440605x31823.
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The functional behaviour of manufactured surfaces is influenced by the surface topography. Encouraged by the results obtained in the implementation of two-dimensional motifs for practical profiles, a few attempts have been made to arrive at areal motifs for characterization of the surfaces. In this paper, an approach for establishing three-dimensional motifs based on triangular motif is presented. The triangular motif is formed with three peaks and a deep valley between them. To represent the surface by significant motifs, initial motifs are combined using four rules that are extended from the rules defined in ISO 12085 for combining two-dimensional motifs. Application of this technique to practical surfaces shows interesting results for characterizing the manufactured surfaces.
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da Silva, Luiz C. B., and Efi Efrati. "Construction of exact minimal parking garages: nonlinear helical motifs in optimally packed lamellar structures." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 477, no. 2246 (2021): 20200891. http://dx.doi.org/10.1098/rspa.2020.0891.
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Minimal surfaces arise as energy minimizers for fluid membranes and are thus found in a variety of biological systems. The tight lamellar structures of the endoplasmic reticulum and plant thylakoids are comprised of such minimal surfaces in which right- and left-handed helical motifs are embedded in stoichiometry suggesting global pitch balance. So far, the analytical treatment of helical motifs in minimal surfaces was limited to the small-slope approximation where motifs are represented by the graph of harmonic functions. However, in most biologically and physically relevant regimes the inter-motif separation is comparable with its pitch, and thus this approximation fails. Here, we present a recipe for constructing exact minimal surfaces with an arbitrary distribution of helical motifs, showing that any harmonic graph can be deformed into a minimal surface by exploiting lateral displacements only. We analyse in detail pairs of motifs of the similar and of opposite handedness and also an infinite chain of identical motifs with similar or alternating handedness. Last, we study the second variation of the area functional for collections of helical motifs with asymptotic helicoidal structure and show that in this subclass of minimal surfaces stability requires that the collection of motifs is pitch balanced.
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Doshi, PD, and JF DiPersio. "Three conserved motifs in the extracellular domain of the human granulocyte-macrophage colony-stimulating factor receptor subunit are essential for ligand binding and surface expression." Blood 84, no. 8 (1994): 2539–53. http://dx.doi.org/10.1182/blood.v84.8.2539.2539.
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Abstract The receptor for the human granulocyte-macrophage colony-stimulating factor (GM-CSF) (GM-R) is a heterodimeric complex consisting of two subunits, GM-R alpha and GM-R beta. Structural analyses have shown a number of highly conserved amino acid motifs present in both GM-R alpha and GM-R beta. These motifs include QYFLY, CXW, XW, and WSXWS motifs in the extracellular domain; a conserved cysteine in the transmembrane domain; and the entire cytoplasmic domain, including the LXVLX box in the carboxy terminal region of the cytoplasmic domain. We have investigated the role of these motifs in GM-R alpha by examining the effects of specific motif mutations on ligand binding and surface expression. Transient expression of these mutant GM-R alpha subunits in COS cells shows that these extracellular motis are essential for ligand binding. Alterations of the cytoplasmic region of GM-R alpha do not alter GM-CSF binding or the reconstitution of high-affinity receptors when coexpressed with GM-R beta. Permeabilization and immunostaining of cells transfected with mutant GM-R alpha subunits yields data suggesting that each of the mutant subunits is present in the cytoplasm. Immunostaining of both intact and permeabilized COS cells transiently transfected with wild-type or mutant GM-R alpha s showed that extracellular domain mutants accumulated in the cytoplasm and were not efficiently transported to the cell surface.
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Doshi, PD, and JF DiPersio. "Three conserved motifs in the extracellular domain of the human granulocyte-macrophage colony-stimulating factor receptor subunit are essential for ligand binding and surface expression." Blood 84, no. 8 (1994): 2539–53. http://dx.doi.org/10.1182/blood.v84.8.2539.bloodjournal8482539.
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The receptor for the human granulocyte-macrophage colony-stimulating factor (GM-CSF) (GM-R) is a heterodimeric complex consisting of two subunits, GM-R alpha and GM-R beta. Structural analyses have shown a number of highly conserved amino acid motifs present in both GM-R alpha and GM-R beta. These motifs include QYFLY, CXW, XW, and WSXWS motifs in the extracellular domain; a conserved cysteine in the transmembrane domain; and the entire cytoplasmic domain, including the LXVLX box in the carboxy terminal region of the cytoplasmic domain. We have investigated the role of these motifs in GM-R alpha by examining the effects of specific motif mutations on ligand binding and surface expression. Transient expression of these mutant GM-R alpha subunits in COS cells shows that these extracellular motis are essential for ligand binding. Alterations of the cytoplasmic region of GM-R alpha do not alter GM-CSF binding or the reconstitution of high-affinity receptors when coexpressed with GM-R beta. Permeabilization and immunostaining of cells transfected with mutant GM-R alpha subunits yields data suggesting that each of the mutant subunits is present in the cytoplasm. Immunostaining of both intact and permeabilized COS cells transiently transfected with wild-type or mutant GM-R alpha s showed that extracellular domain mutants accumulated in the cytoplasm and were not efficiently transported to the cell surface.
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Kusuma, Wahyu Teja, Herman Tolle, and Ahmad Afif Supianto. "Augmented Reality Application to Efficiency the Process of Making Batik Motifs Using Vertex Marker." Journal of Information Technology and Computer Science 4, no. 3 (2019): 267. http://dx.doi.org/10.25126/jitecs.201943154.
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From the total time of making traditional Batik, the batik stage is the most time consuming because there are a lot of mistakes due to lack of carefulness when making batik motifs on cloth. To overcome the problem of making Batik motifs, this research utilizes the strengths and capabilities of Marker-Based Augmented Reality technology. The development of Marker-Based Augmented Reality applications is done by replacing digital objects with Batik motif images and markers attached to the fabric. Development of Marker-Based Augmented Reality applications using vertex markers to reproduce Batik motif objects in order to overcome the limitations of the reach of hands when making Batik motifs on fabric Finally, by using Marker-Based Augmented Reality applications batik makers do not need to draw Batik motifs in pencil on fabric because of Batik motifs directly displayed on the fabric surface by the application, so that it is expected to reduce the process time of making Batik motifs compared to making Batik motifs using traditional methods.
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Marsh, B. J., R. A. Alm, S. R. McIntosh, and D. E. James. "Molecular regulation of GLUT-4 targeting in 3T3-L1 adipocytes." Journal of Cell Biology 130, no. 5 (1995): 1081–91. http://dx.doi.org/10.1083/jcb.130.5.1081.
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Insulin stimulates glucose transport in muscle and adipose tissue by triggering the movement of the glucose transporter GLUT-4 from an intracellular compartment to the cell surface. Fundamental to this process is the intracellular sequestration of GLUT-4 in nonstimulated cells. Two distinct targeting motifs in the amino and carboxy termini of GLUT-4 have been previously identified by expressing chimeras comprised of portions of GLUT-4 and GLUT-1, a transporter isoform that is constitutively targeted to the cell surface, in heterologous cells. These motifs-FQQI in the NH2 terminus and LL in the COOH terminus-resemble endocytic signals that have been described in other proteins. In the present study we have investigated the roles of these motifs in GLUT-4 targeting in insulin-sensitive cells. Epitope-tagged GLUT-4 constructs engineered to differentiate between endogenous and transfected GLUT-4 were stably expressed in 3T3-L1 adipocytes. Targeting was assessed in cells incubated in the presence or absence of insulin by subcellular fractionation. The targeting of epitope-tagged GLUT-4 was indistinguishable from endogenous GLUT-4. Mutation of the FQQI motif (F5 to A5) caused GLUT-4 to constitutively accumulate at the cell surface regardless of expression level. Mutation of the dileucine motif (L489L490 to A489A490) caused an increase in cell surface distribution only at higher levels of expression, but the overall cells surface distribution of this mutant was less than that of the amino-terminal mutants. Both NH2- and COOH-terminal mutants retained insulin-dependent movement from an intracellular to a cell surface locale, suggesting that neither of these motifs is involved in the insulin-dependent redistribution of GLUT-4. We conclude that the phenylalanine-based NH2-terminal and the dileucine-based COOH-terminal motifs play important and distinct roles in GLUT-4 targeting in 3T3-L1 adipocytes.
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Sarhan, Mohammed. "Ice nucleation protein as a bacterial surface display protein." Archives of Biological Sciences 63, no. 4 (2011): 943–48. http://dx.doi.org/10.2298/abs1104943s.
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Surface display technology can be defined as that phenotype (protein or peptide) which is linked to a genotype (DNA or RNA) through an appropriate anchoring motif. A bacterial surface display system is based on expressing recombinant proteins fused to sorting signals (anchoring motifs) that direct their incorporation on the cell surface.
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Monk, Brian C., and David R. K. Harding. "Peptide Motifs for Cell-Surface Intervention." BioDrugs 19, no. 4 (2005): 261–78. http://dx.doi.org/10.2165/00063030-200519040-00005.
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Mouli, M. S. S. Vinod, and Ashutosh Kumar Mishra. "Formation of the silver–flavin coordination polymers and their morphological studies." CrystEngComm 24, no. 12 (2022): 2221–25. http://dx.doi.org/10.1039/d2ce00071g.
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Herein we discuss the formation of 1-D polymeric motifs for the silver–flavin complex achieved via rare bidentate coordination for the modified flavin moiety. Further studies revealed facile transfer of the polymeric motif onto the surface.
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Kowalski, Maciej, Magdalena Wiśniewska, Paweł Karolczak, and Jozef Holubjak. "Possibilities of applying motif group parameters for description roughness of turned surfaces." MATEC Web of Conferences 244 (2018): 01028. http://dx.doi.org/10.1051/matecconf/201824401028.
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This article explores the methodology of assessing the applicability of roughness parameters from the motif group to the evaluation of one-way and periodic geometrical surface structures. The results of surface roughness measurements of aluminum samples turned with variable kinematic parameters were presented. Usability of using surface motifs in combination with selected parameters described in ISO standards for assessment of geometrical structures characteristic for longitudinal turning was shown.
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Lungu, Antonela, Maria Cristina Timar, Emanuela Carmen Beldean, Sergiu Valeriu Georgescu, and Camelia Coşereanu. "Adding Value to Maple (Acer pseudoplatanus) Wood Furniture Surfaces by Different Methods of Transposing Motifs from Textile Heritage." Coatings 12, no. 10 (2022): 1393. http://dx.doi.org/10.3390/coatings12101393.
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The present paper is part of an ongoing research project carried out to find methods to transpose traditional motifs from Romanian textile heritage to furniture ornamentation, as an additional method of preserving the motifs besides conventional conservation. Modern technology, such as Computer Numerical Control (CNC) routing or laser engraving can revive furniture ornamentation, eliminating manual labor and long execution time. Three methods were applied to transpose a bicolored motif from a traditional Romanian blouse from Transylvania onto the surface of maple wood furniture. The first method utilized was nitrogen laser engraving, in which ten power settings between 10 W and 150 W were applied and color measurements were carried out on the resulting engraved surfaces. Following the International Commission on Illumination (CIELab) system analysis, two laser power settings were selected to engrave the ornament on a maple wood surface for an accurate reproduction. The second method employed a staining solution applied on flat wood surface, followed by routing the model on a CNC machine and further coating with lacquer. The third method consisted of CNC routing the model on the wood surface, then coloring the engraved ornament followed by surface sanding to remove color from the flat wood surface and, finally, lacquering. The ornaments transposed onto maple wood surfaces were aesthetically assessed, the technologies were analyzed, and the details of the processed ornaments were highlighted by Stereo Microscope investigation. The conclusions showed that each method adds value to the wood surface by original ornamentation and can be applied as furniture decoration.
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Bourgeois-Daigneault, Marie-Claude, and Jacques Thibodeau. "Identification of a novel motif important for the activity of ring-type E3 ligases using MARCH1 as a model (100.52)." Journal of Immunology 186, no. 1_Supplement (2011): 100.52. http://dx.doi.org/10.4049/jimmunol.186.supp.100.52.
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Abstract The MARCH family of proteins are RING-CH type E3 ubiquitin ligases responsible for the ubiquitination and endocytosis of cell surface proteins related to immune response. We are particularty interested in MARCH1 and 8, two members of the family that are known to downregulate the cell surface expression of MHC II, CD86 , TfR and CD95. Canonical sorting motifs in the cytoplasmic portions of murine MARCH1 and human MARCH8 were identified and reported by others to be necessary for the function. We hypothesized that such motifs in human MARCH1 are important for it’s function. Methods: We used co-immunoprecipitations and FRET to monitor interaction of MARCH1 with various proteins. Protein expression, function and localization were determined by flow cytometry, confocal microscopy and western blotting. Results: Our results showed the presence of functional sorting motifs in both N- and C-terminal cytoplasmic portions of human MARCH1. However, these signals are not essential for the activity of MARCH1. We used a series of mutants to identify functional regions on MARCH1. Our results point to a novel motif. Interestingly, that motif is found in many other proteins and appears to be important for the function of other RING-type E3 ligases. Conclusions: Our results confirmed the presence of sorting motifs in MARCH1 and highlight important species-specific functional domains. The newly identified domain of MARCH1 will shed light on the structure of RING-type E3 ubiquitin ligases.
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TASCHNER, Sabine, Andreas MEINKE, Alexander von GABAIN, and Aoife P. BOYD. "Selection of peptide entry motifs by bacterial surface display." Biochemical Journal 367, no. 2 (2002): 393–402. http://dx.doi.org/10.1042/bj20020164.
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Surface display technologies have been established previously to select peptides and polypeptides that interact with purified immobilized ligands. In the present study, we designed and implemented a surface display-based technique to identify novel peptide motifs that mediate entry into eukaryotic cells. An Escherichia coli library expressing surface-displayed peptides was combined with eukaryotic cells and the gentamicin protection assay was performed to select recombinant E. coli, which were internalized into eukaryotic cells by virtue of the displayed peptides. To establish the proof of principle of this approach, the fibronectin-binding motifs of the fibronectin-binding protein A of Staphylococcus aureus were inserted into the E. coli FhuA protein. Surface expression of the fusion proteins was demonstrated by functional assays and by FACS analysis. The fibronectin-binding motifs were shown to mediate entry of the bacteria into non-phagocytic eukaryotic cells and brought about the preferential selection of these bacteria over E. coli expressing parental FhuA, with an enrichment of 100000-fold. Four entry sequences were selected and identified using an S. aureus library of peptides displayed in the FhuA protein on the surface of E. coli. These sequences included novel entry motifs as well as integrin-binding Arg-Gly-Asp (RGD) motifs and promoted a high degree of bacterial entry. Bacterial surface display is thus a powerful tool to effectively select and identify entry peptide motifs.
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Nadia Hasna, Safira Rizqi, and Mein Kharnolis. "Penerapan Motif Batik Papua dengan Teknik Bordir pada Busana Pengantin Wanita." BAJU: Journal of Fashion & Textile Design Unesa 2, no. 1 (2022): 18–23. http://dx.doi.org/10.26740/baju.v2n1.p18-23.
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Motif batik Papua yang berasal dari ragam hias khas Papua yang menjadi inspirasi dalam pembuatan busana pengantin wanita. Tujuan penelitian adalah untuk mengetahui proses dan hasil jadi penerapan motif batik papua dengan teknik bordir dibusana pengantin wanita. Metode yang digunakan adalah Double Diamond, yang terdiri dari 4 tahapan yaitu dicover, define, develop dan deliver. Dari hasil yang diperoleh, motif batik papua yaitu motif suku asmat yang diwujudkan teknik bordir digunakan sebagai detail di busana pengantin wanita. Proses pembuatan dengan cara membordir dengan mengikuti motif / pola yang telah di stilasi yang kemudian digambar atau dijiplak pada permukaan kain organza dan yang kemudian hasil bordiran kemudian dijadikan hiasan busana pengantin wanita. Hasil jadi pada busana pengantin wanita sesuai dengan ide perancangan antara lain menggunakan siluet I. Model busana pengantin wanita two piece yaitu gaun dan ekor lepas pasang. Penerapan bordir yang berbentuk motif batik Papua pada bagian bawah busana diterapkan dengan cara mapping dipermukaan busana yang menjadi hiasan dari look pada busana pengantin wanita. Hasil jadi busana secara keseluruhan telah memenuhi beberapa kriteria prinsip desain.
 Papuan batik motifs derived from Papuan decorative motifs are the inspiration for making bride's clothing. The purpose of the study was to determine the process and results of applying Papuan batik motifs with embroidery techniques in the bride's dress. The method used is Double Diamond, which consists of 4 stages, namely covered, define, develop and deliver. From the results obtained, the Papuan batik motif, namely the Asmat ethnic motif, is realized by embroidery techniques and is used as a detail in the bride's clothing. The process of making embroidery by following a stylized motif/pattern, drawn or traced on the surface of the organza cloth and then embroidered. The finished results on the bride's clothing are by the design idea, among others, using silhouette I. The bride's clothing model is two pieces, namely the dress and the loose tail. The application embroidery in the form of Papua batik motifs on the bottom of the dress is applied, mapping the surface of the clothing, which is the decoration of the look of the bride's attire. The finished product as a whole has met several design principles criteria.
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Coleman, Scott H., Nanette Van Damme, John R. Day, et al. "Leucine-Specific, Functional Interactions between Human Immunodeficiency Virus Type 1 Nef and Adaptor Protein Complexes." Journal of Virology 79, no. 4 (2005): 2066–78. http://dx.doi.org/10.1128/jvi.79.4.2066-2078.2005.
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ABSTRACT The human immunodeficiency virus type 1 virulence protein Nef interacts with the endosomal sorting machinery via a leucine-based motif. Similar sequences within the cytoplasmic domains of cellular transmembrane proteins bind to the adaptor protein (AP) complexes of coated vesicles to modulate protein traffic, but the molecular basis of the interactions between these motifs and the heterotetrameric complexes is controversial. To identify the target of the Nef leucine motif, the native sequence was replaced with either leucine- or tyrosine-based AP-binding sequences from cellular proteins, and the interactions with AP subunits were correlated with function. Tyrosine motifs predictably modulated the interactions between Nef and the μ subunits of AP-1, AP-2, and AP-3; heterologous leucine motifs caused little change in these interactions. Conversely, leucine motifs mediated a ternary interaction between Nef and hemicomplexes containing the σ1 plus γ subunits of AP-1 or the σ3 plus δ subunits of AP-3, whereas tyrosine motifs did not. Similarly, only leucine motifs supported the Nef-mediated association of AP-1 and AP-3 with endosomal membranes in cells treated with brefeldin A. Functionally, Nef proteins containing leucine motifs down-regulated CD4 from the cell surface and enhanced viral replication, whereas those containing tyrosine motifs were inactive. Apparently, the interaction of Nef with the μ subunits of AP complexes is insufficient for function. A leucine-specific mode of interaction that likely involves AP hemicomplexes is further required for Nef activity. The μ and hemicomplex interactions may cooperate to yield high avidity binding of AP complexes to Nef. This binding likely underlies the unusual ability of Nef to induce the stabilization of these complexes on endosomal membranes, an activity that correlates with enhancement of viral replication.
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Coelho, Miguel B., David B. Ascher, Clare Gooding, et al. "Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins." Biochemical Society Transactions 44, no. 4 (2016): 1058–65. http://dx.doi.org/10.1042/bst20160080.
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Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.
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He, Bin, and Elizabeth M. Wilson. "Electrostatic Modulation in Steroid Receptor Recruitment of LXXLL and FXXLF Motifs." Molecular and Cellular Biology 23, no. 6 (2003): 2135–50. http://dx.doi.org/10.1128/mcb.23.6.2135-2150.2003.
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ABSTRACT Coactivator recruitment by activation function 2 (AF2) in the steroid receptor ligand binding domain takes place through binding of an LXXLL amphipathic α-helical motif at the AF2 hydrophobic surface. The androgen receptor (AR) and certain AR coregulators are distinguished by an FXXLF motif that interacts selectively with the AR AF2 site. Here we show that LXXLL and FXXLF motif interactions with steroid receptors are modulated by oppositely charged residues flanking the motifs and charge clusters bordering AF2 in the ligand binding domain. An increased number of charged residues flanking AF2 in the ligand binding domain complement the two previously characterized charge clamp residues in coactivator recruitment. The data suggest a model whereby coactivator recruitment to the receptor AF2 surface is initiated by complementary charge interactions that reflect a reversal of the acidic activation domain-coactivator interaction model.
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Kurumatani, Natsumi, Hiroyuki Monji, and Takenao Ohkawa. "Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces and Its Application to Protein Classification." International Journal on Artificial Intelligence Tools 23, no. 03 (2014): 1460007. http://dx.doi.org/10.1142/s0218213014600070.
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Most proteins express their functions by binding with other proteins or molecular compounds (ligands). Since the characteristics of the local portion involved in binding (binding site) often determine the function of the protein, clarifying the location of the binding site of the protein helps analyze the function of proteins. Binding sites that bind to similar ligands often have common surface structures (surface motifs). Extracting the surface motifs among several proteins with similar functions improves binding site prediction. We propose a method that predicts binding sites by extracting the surface motifs that are frequently observed in only a specific set of proteins that bind to the same ligand (group). Since most binding sites have concave structures (pockets), the pockets are compared and common structures are searched for to extract the surface motifs by applying similar graph mining to the pocket data, which are represented as graphs. Common binding sites across several groups can be predicted in such a way to integrate more than one group. We also proposed a method of protein classification, in which the surface motifs extracted using the above method are evaluated on the assumption that a protein belongs to each one of the groups.
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Satława, Tadeusz, Mateusz Tarkowski, Sonia Wróbel, et al. "LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies." PLOS Computational Biology 20, no. 3 (2024): e1011881. http://dx.doi.org/10.1371/journal.pcbi.1011881.
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Antibody-based therapeutics must not undergo chemical modifications that would impair their efficacy or hinder their developability. A commonly used technique to de-risk lead biotherapeutic candidates annotates chemical liability motifs on their sequence. By analyzing sequences from all major sources of data (therapeutics, patents, GenBank, literature, and next-generation sequencing outputs), we find that almost all antibodies contain an average of 3–4 such liability motifs in their paratopes, irrespective of the source dataset. This is in line with the common wisdom that liability motif annotation is over-predictive. Therefore, we have compiled three computational flags to prioritize liability motifs for removal from lead drug candidates: 1. germline, to reflect naturally occurring motifs, 2. therapeutic, reflecting chemical liability motifs found in therapeutic antibodies, and 3. surface, indicative of structural accessibility for chemical modification. We show that these flags annotate approximately 60% of liability motifs as benign, that is, the flagged liabilities have a smaller probability of undergoing degradation as benchmarked on two experimental datasets covering deamidation, isomerization, and oxidation. We combined the liability detection and flags into a tool called Liability Antibody Profiler (LAP), publicly available at lap.naturalantibody.com. We anticipate that LAP will save time and effort in de-risking therapeutic molecules.
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Marks, M. S., L. Woodruff, H. Ohno, and J. S. Bonifacino. "Protein targeting by tyrosine- and di-leucine-based signals: evidence for distinct saturable components." Journal of Cell Biology 135, no. 2 (1996): 341–54. http://dx.doi.org/10.1083/jcb.135.2.341.
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Targeting of transmembrane proteins to lysosomes, endosomal compartments, or the trans-Golgi network is largely dependent upon cytoplasmically exposed sorting signals. Among the most widely used signals are those that conform to the tyrosine-based motif, YXXO (where Y is tyrosine, X is any amino acid, and O is an amino acid with a bulky hydrophobic group), and to the di-leucine (or LL) motif. Signals conforming to both motifs have been implicated in protein localization to similar post-Golgi compartments. We have exploited the saturability of sorting to ask whether different YXXO or LL signals use shared components of the targeting machinery. Chimeric proteins containing various cytoplasmic domains and/or targeting signals were overexpressed in HeLa cells by transient transfection. Endogenous transferrin receptor and lysosomal proteins accumulated at the cell surface upon overexpression of chimeric proteins containing functional YXXO targeting signals, regardless of the compartmental destination imparted by the signal. Furthermore, overexpression of these chimeric proteins compromised YXXO-mediated endocytosis and lysosomal delivery. These activities were ablated by mutating the signals or by appending sequences that conformed to the YXXO motif but lacked targeting activity. Interestingly, overexpression of chimeric proteins containing cytoplasmic LL signals failed to induce surface displacement of endogenous YXXO-containing proteins, but did displace other proteins containing LL motifs. Our data demonstrate that: (a) Protein targeting and internalization mediated by either YXXO or LL motifs are saturable processes; (b) common saturable components are used in YXXO-mediated protein internalization and targeting to different post-Golgi compartments; and (c) YXXO- and LL-mediated targeting mechanisms use distinct saturable components.
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Lai, Mei-Hsiu, Nicholas E. Clay, Dong Hyun Kim, and Hyunjoon Kong. "Bacteria-mimicking nanoparticle surface functionalization with targeting motifs." Nanoscale 7, no. 15 (2015): 6737–44. http://dx.doi.org/10.1039/c5nr00736d.
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Panseri, Silvia, Laura Russo, Monica Montesi, et al. "Bioactivity of surface tethered Osteogenic Growth Peptide motifs." MedChemComm 5, no. 7 (2014): 899. http://dx.doi.org/10.1039/c4md00112e.
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Duffy, Josh, Bhargavi Patham, and Kojo Mensa-Wilmot. "Discovery of functional motifs in h-regions of trypanosome signal sequences." Biochemical Journal 426, no. 2 (2010): 135–45. http://dx.doi.org/10.1042/bj20091277.
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N-terminal signal peptides direct secretory proteins into the ER (endoplasmic reticulum) of eukaryotes or the periplasmic space of prokaryotes. A hydrophobic core (h-region) is important for signal sequence function; however, the mechanism of h-region action is not resolved. To gain new insight into signal sequences, bioinformatic analysis of h-regions from humans, Saccharomyces cerevisiae, Trypanosoma brucei and Escherichia coli was performed. Each species contains a unique set of peptide motifs (h-motifs) characterized by identity components (i.e. sequence of conserved amino acids) joined by spacers. Human h-motifs have four identity components, whereas those from the other species utilize three identity components. Example of h-motifs are human Hs3 {L-x(2)-[AGILPV]-L-x(0,2)-L}, S. cerevisiae Sc1 [L-x(0,2)-S-x(0,3)-A], T. brucei Tb2 {L-x(1,2)-L-[AILV]} and E. coli Ec1 [A-x(0,2)-L-x(0,3)-A]. The physiological relevance of h-motifs was tested with a T. brucei microsomal system for translocation of a VSG (variant surface glycoprotein)-117 signal peptide. Disruption of h-motifs by scrambling of sequences in h-regions produced defective signal peptides, although the hydrophobicity of the peptide was not altered. We conclude that: (i) h-regions harbour h-motifs, and are not random hydrophobic amino acids; (ii) h-regions from different species contain unique sets of h-motifs; and (iii) h-motifs contribute to the biological activity of ER signal peptides. h-Regions are ‘scaffolds’ in which functional h-motifs are embedded. A hypothetical model for h-motif interactions with a Sec61p protein translocon is presented.
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Tong, Kit I., Balasundaram Padmanabhan, Akira Kobayashi, et al. "Different Electrostatic Potentials Define ETGE and DLG Motifs as Hinge and Latch in Oxidative Stress Response." Molecular and Cellular Biology 27, no. 21 (2007): 7511–21. http://dx.doi.org/10.1128/mcb.00753-07.
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ABSTRACT Nrf2 is the regulator of the oxidative/electrophilic stress response. Its turnover is maintained by Keap1-mediated proteasomal degradation via a two-site substrate recognition mechanism in which two Nrf2-Keap1 binding sites form a hinge and latch. The E3 ligase adaptor Keap1 recognizes Nrf2 through its conserved ETGE and DLG motifs. In this study, we examined how the ETGE and DLG motifs bind to Keap1 in a very similar fashion but with different binding affinities by comparing the crystal complex of a Keap1-DC domain-DLG peptide with that of a Keap1-DC domain-ETGE peptide. We found that these two motifs interact with the same basic surface of either Keap1-DC domain of the Keap1 homodimer. The DLG motif works to correctly position the lysines within the Nrf2 Neh2 domain for efficient ubiquitination. Together with the results from calorimetric and functional studies, we conclude that different electrostatic potentials primarily define the ETGE and DLG motifs as a hinge and latch that senses the oxidative/electrophilic stress.
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Petersen, Helen J., Dorothea O. Tilley, Jennifer Haworth, et al. "Multiple sites on Streptococcus gordonii surface protein PadA bind to platelet GPIIbIIIa." Thrombosis and Haemostasis 110, no. 12 (2013): 1278–87. http://dx.doi.org/10.1160/th13-07-0580.
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SummaryInfective endocarditis is a life threatening disease caused by a bacterial infection of the endocardial surfaces of the heart. The oral pathogen, Streptococcus gordonii is amongst the most common pathogens isolated from infective endocarditis patients. Previously we identified a novel cell wall protein expressed on S. gordonii called platelet adherence protein A (PadA) that specifically interacts with platelet GPIIb/IIIa. The interaction between PadA and GPIIb/IIIa resulted in firm platelet adhesion, dense granule secretion and platelet spreading on immobilised S. gordonii. This study set out to identify specific motifs on the PadA protein that interacts with platelet GPIIb/IIIa. Proteomic analysis of the PadA protein identified two short amino acid motifs which have been previously shown to be important for fibrinogen binding to GPIIb/IIIa and contributing to the generation of outside-in signalling. Site directed mutagenesis on the PadA protein in which 454AGD was substituted to AAA, and the 383RGT was substituted to AAA suggests the RGT motif has no role in supporting platelet adhesion however plays a role in dense granule secretion and platelet spreading. In contrast to this the AGD motif has no role to play in supporting firm platelet adhesion or dense granule secretion however plays a role in platelet spreading. These results suggest that multiple sites on S. gordonii PadA interact with GPIIb/IIIa to mediate a number of platelet responses that likely contribute to the thrombotic complications of infective endocarditis.
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Shmulevitz, Maya, Jayme Salsman, and Roy Duncan. "Palmitoylation, Membrane-Proximal Basic Residues, and Transmembrane Glycine Residues in the Reovirus p10 Protein Are Essential for Syncytium Formation." Journal of Virology 77, no. 18 (2003): 9769–79. http://dx.doi.org/10.1128/jvi.77.18.9769-9779.2003.
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ABSTRACT Avian reovirus and Nelson Bay reovirus are two unusual nonenveloped viruses that induce extensive cell-cell fusion via expression of a small nonstructural protein, termed p10. We investigated the importance of the transmembrane domain, a conserved membrane-proximal dicysteine motif, and an endodomain basic region in the membrane fusion activity of p10. We now show that the p10 dicysteine motif is palmitoylated and that loss of palmitoylation correlates with a loss of fusion activity. Mutational and functional analyses also revealed that a triglycine motif within the transmembrane domain and the membrane-proximal basic region were essential for p10-mediated membrane fusion. Mutations in any of these three motifs did not influence events upstream of syncytium formation, such as p10 membrane association, protein topology, or surface expression, suggesting that these motifs are more intimately associated with the membrane fusion reaction. These results suggest that the rudimentary p10 fusion protein has evolved a mechanism of inducing membrane merger that is highly dependent on the specific interaction of several different motifs with donor membranes. In addition, cross-linking, coimmunoprecipitation, and complementation assays provided no evidence for p10 homo- or heteromultimer formation, suggesting that p10 may be the first example of a membrane fusion protein that does not form stable, higher-order multimers.
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Novakovic, Sinisa, Earl T. Sawai, and Kathryn Radke. "Dileucine and YXXL Motifs in the Cytoplasmic Tail of the Bovine Leukemia Virus Transmembrane Envelope Protein Affect Protein Expression on the Cell Surface." Journal of Virology 78, no. 15 (2004): 8301–11. http://dx.doi.org/10.1128/jvi.78.15.8301-8311.2004.
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ABSTRACT Several retroviruses downmodulate the cell surface expression of envelope (Env) proteins through peptide sequences located in the cytoplasmic tail of the transmembrane (TM) subunit. We investigated whether cell surface expression of a chimeric protein containing the cytoplasmic domain of the TM protein (CTM) of bovine leukemia virus (BLV) was regulated by two membrane-proximal dileucine motifs or by tyrosine Y487 or Y498 in YXXL motifs. A chimeric protein composed of the extracellular and membrane-spanning portions of human CD8-α plus a wild-type (wt) BLV CTM was detectable on the surface of only 40% of the cells in which it was transiently expressed. Replacement of either dileucine pair with alanines increased the level of surface display of chimeric proteins. Nearly all cells became surface positive when both dileucine motifs were altered simultaneously and when either an N-terminal segment containing both dileucine motifs or a C-terminal segment containing all YXXL motifs was deleted. In contrast, replacement of Y487 or Y498 with alanine or phenylalanine enabled only small increases in surface display compared with wt levels. Chimeric proteins had similar stabilities but were downmodulated from the cell surface at three different rates. Point mutants segregated into each of the three groups of proteins categorized according to these different rates. Interestingly, Y487 mutants were downmodulated less efficiently than Y498 mutants, which behaved like wt. CD8-CTM chimeric proteins were phosphorylated on serine residues, but the native BLV Env protein was not phosphorylated either in transfected cells or in a lymphoid cell line constitutively producing BLV. Thus, both dileucine and YXXL motifs within the BLV CTM contribute to downmodulation of a protein containing this domain. Interactions with other proteins may influence surface exposure of Env protein complexes in virus-infected cells, assisting in viral evasion of adaptive immunity.
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Zähner, Dorothea, and Regine Hakenbeck. "The Streptococcus pneumoniaeBeta-Galactosidase Is a Surface Protein." Journal of Bacteriology 182, no. 20 (2000): 5919–21. http://dx.doi.org/10.1128/jb.182.20.5919-5921.2000.
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ABSTRACT The β-galactosidase gene of Streptococcus pneumoniae,bgaA, encodes a putative 2,235-amino-acid protein with the two amino acid motifs characteristic of the glycosyl hydrolase family of proteins. In addition, an N-terminal signal sequence and a C-terminal LPXTG motif typical of surface-associated proteins of gram-positive bacteria are present. Trypsin treatment of cells resulted in solubilization of the enzyme, documenting that it is associated with the cell envelope. In order to obtain defined mutants suitable forlacZ reporter experiments, the bgaA gene was disrupted, resulting in a complete absence of endogenous β-galactosidase activity. The results are consistent with β-galactosidase being a surface protein that seems not to be involved in lactose metabolism but that may play a role during pathogenesis.
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Ilinskaya, Anna, Gisela Heidecker, and David Derse. "Opposing Effects of a Tyrosine-Based Sorting Motif and a PDZ-Binding Motif Regulate Human T-Lymphotropic Virus Type 1 Envelope Trafficking." Journal of Virology 84, no. 14 (2010): 6995–7004. http://dx.doi.org/10.1128/jvi.01853-09.
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ABSTRACT Human T-lymphotropic virus type 1 (HTLV-1) envelope (Env) glycoprotein mediates binding of the virus to its receptor on the surface of target cells and subsequent fusion of virus and cell membranes. To better understand the mechanisms that control HTLV-1 Env trafficking and activity, we have examined two protein-protein interaction motifs in the cytoplasmic domain of Env. One is the sequence YSLI, which matches the consensus YXXΦ motifs that are known to interact with various adaptor protein complexes; the other is the sequence ESSL at the C terminus of Env, which matches the consensus PDZ-binding motif. We show here that mutations that destroy the YXXΦ motif increased Env expression on the cell surface and increased cell-cell fusion activity. In contrast, mutation of the PDZ-binding motif greatly diminished Env expression in cells, which could be restored to wild-type levels either by mutating the YXXΦ motif or by silencing AP2 and AP3, suggesting that interactions with PDZ proteins oppose an Env degradation pathway mediated by AP2 and AP3. Silencing of the PDZ protein hDlg1 did not affect Env expression, suggesting that hDlg1 is not a binding partner for Env. Substitution of the YSLI sequence in HTLV-1 Env with YXXΦ elements from other cell or virus membrane-spanning proteins resulted in alterations in Env accumulation in cells, incorporation into virions, and virion infectivity. Env variants containing YXXΦ motifs that are predicted to have high-affinity interaction with AP2 accumulated to lower steady-state levels. Interestingly, mutations that destroy the YXXΦ motif resulted in viruses that were not infectious by cell-free or cell-associated routes of infection. Unlike YXXΦ, the function of the PDZ-binding motif manifests itself only in the producer cells; AP2 silencing restored the incorporation of PDZ-deficient Env into virus-like particles (VLPs) and the infectivity of these VLPs to wild-type levels.
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Sangeetha, Ramalingam, Kasthuri Balasubramani, Kaliyaperumal Thanigaimani, and Savaridasson Jose Kavitha. "Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium 4-methylbenzenesulfonate." Acta Crystallographica Section E Crystallographic Communications 74, no. 8 (2018): 1159–62. http://dx.doi.org/10.1107/s2056989018010368.
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In the title molecular salt, C9H10N5 +·C7H7O3S−, the asymmetric unit consists of a 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium cation and a 4-methylbenzenesulfonate anion. The cation is protonated at the N atom lying between the amine and phenyl substituents. The protonated N and amino-group N atoms are involved in hydrogen bonding with the sulfonate O atoms through a pair of intermolecular N—H...O hydrogen bonds, giving rise to a hydrogen-bonded cyclic motif with R 2 2(8) graph-set notation. The inversion-related molecules are further linked by four N—H...O intermolecular interactions to produce a complementary DDAA (D = donor, A = acceptor) hydrogen-bonded array, forming R 2 2(8), R 4 2(8) and R 2 2(8) ring motifs. The centrosymmetrically paired cations form R 2 2(8) ring motifs through base-pairing via N—H...N hydrogen bonds. In addition, another R 3 3(10) motif is formed between centrosymetrically paired cations and a sulfonate anion via N—H...O hydrogen bonds. The crystal structure also features weak S=O...π and π–π interactions. Hirshfeld surface and fingerprint plots were employed in order to further study the intermolecular interactions.
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Lungu, A., L. Gurău, S. Georgescu, and C. Coşereanu. "Computer-aided methods for furniture decoration with traditional motifs of textile heritage." IOP Conference Series: Materials Science and Engineering 1235, no. 1 (2022): 012041. http://dx.doi.org/10.1088/1757-899x/1235/1/012041.
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Abstract The present paper introduces computer-aided methods for the transposition of ornaments inspired from the textile heritage into the surface furniture decoration. Using digital technology, the furniture industry may bring into modern life the traditional motifs, contributing thus to the preservation of the cultural heritage from the region Ţara Bârsei, located in Transylvania. Two motifs inspired by the traditional costumes from South-Eastern Transylvania were digitized using CorelDraw software. They were imported in AutoCAD and the information was transferred both to CNC router and laser equipment. The CNC routing of ornaments was simulated with two types of tools and two processing methods (engraving and carving) using CAD-CAM-CAE software and the models were afterward processed on wood panels by CNC router and laser equipment and then visually analysed, concluding which method and tool is suitable for each type of ornament, so to transpose better the original motif on furniture wood surface.
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Hasegawa, Atsushi, Ritsuko Shimizu, Hirofumi Kurokawa, and Masayuki Yamamoto. "DNA Binding Diversity Achieved Through the Interaction of GATA1 N-Finger and GATA Motif Is Important for Embryonic Erythropoiesis." Blood 120, no. 21 (2012): 3441. http://dx.doi.org/10.1182/blood.v120.21.3441.3441.
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Abstract Abstract 3441 Transcription factor GATA1 regulates a set of genes essential for the erythroid and megakaryocytic cell differentiation through the interaction with GATA motifs (consensus sequence: A/TGATAA/T). Two zinc fingers within GATA1 have been identified to be important in the DNA binding of GATA1, which are referred to as C-finger (CF) and N-finger (NF) domains. It has been shown that transactivation activity of GATA1 is completely abolished upon deletion of the CF domain, indicating that the CF domain is a requisite for the DNA binding of GATA1. While conventional reporter transactivation analyses hardly clarified the importance of the NF domain for the DNA binding, substitution mutations on 216th arginine (R216) located in the DNA-interacting surface of the NF domain have been identified to cause familial diseases of thrombocytopenia, thalassemia, and porphyria. As a consequence of the substitution of R216 to glutamine (Q) or tryptophan (W), DNA binding activity of GATA1 to a palindromic configuration of two GATA motifs (palindromic GATA) was largely diminished, while that to a single GATA motif was maintained. In this study we have examined the DNA binding diversity of GATA1 caused by the difference in the configuration of GATA motifs. We performed surface plasmon resonance (SPR) analyses of GATA1 to a single GATA, a palindromic GATA, and a repeating configuration of two GATA motifs (tandem GATA). We found that GATA1 binds to the palindromic GATA motif in a bivalent way, while it binds to the single GATA motif in a monovalent mode. We also found that a double quantity of GATA1 is associated with the tandem GATA motif and GATA1 lacking the NF domain binds to any configurations of GATA motif in a monovalent way. To further investigate contribution of the NF domain to the binding mode of GATA1, we have constructed two types of GATA1 mutants; one type was the substitution mutations on R216 (R216Q and R216W) that were mouse homologues of the human mutations, while the other type was the alanine substitution mutation on three lysine residues (K245, K246 and K312; referred to as 3KA mutant), whereby dimerization potential of GATA1 was reduced to trace level similar to the case for GATA1 lacking the NF domain. Impotantly, R216Q and R216W mutants bind the palindromic GATA motif in a monovalent way, while these mutants bind normally to the other configuration of GATA motifs. In contrast, we found that one molecule of 3KA mutant bound to the tandem GATA motif and this observation seems to explain well the fact that dimerization potential of GATA1 is an important requisite for the full-function of GATA1 in embryos. The binding modes of this 3KA mutant to the other configurations were not influenced. These results thus demonstrate that the both NF and CF domains recognize the multiple configurations of GATA motifs and specify the binding modes of GATA1. Importantly, GATA1-deficient mice rescued with R216Q were lethal during late gestation period due to abnormality in erythroid differentiation, indicating that the contribution of the NF domain to the recognition of the palindromic GATA motif configuration indeed functions in vivo. These results thus support our contention that the NF domain acts to regulate a proper spatio-temporal gene expression of a subset of GATA1 target genes utilizing the variations in the GATA motif configuration. Disclosures: No relevant conflicts of interest to declare.
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Bakhos-Douaihy, Dalal, Elie Seaayfan, Nadia Frachon, Sylvie Demaretz, Martin Kömhoff, and Kamel Laghmani. "Diacidic Motifs in the Carboxyl Terminus Are Required for ER Exit and Translocation to the Plasma Membrane of NKCC2." International Journal of Molecular Sciences 23, no. 21 (2022): 12761. http://dx.doi.org/10.3390/ijms232112761.
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Mutations in the apical Na-K-2Cl co-transporter, NKCC2, cause type I Bartter syndrome (BS1), a life-threatening kidney disease. We have previously demonstrated that the BS1 variant Y998X, which deprives NKCC2 from its highly conserved dileucine-like motifs, compromises co-transporter surface delivery through ER retention mechanisms. However, whether these hydrophobic motifs are sufficient for anterograde trafficking of NKCC2 remains to be determined. Interestingly, sequence analysis of NKCC2 C-terminus revealed the presence of consensus di-acidic (D/E-X-D/E) motifs, 949EEE951 and 1019DAELE1023, located upstream and downstream of BS1 mutation Y998X, respectively. Di-acidic codes are involved in ER export of proteins through interaction with COPII budding machinery. Importantly, whereas mutating 949EEE951 motif to 949AEA951 had no effect on NKCC2 processing, mutating 1019DAE1021 to 1019AAA1021 heavily impaired complex-glycosylation and cell surface expression of the cotransporter in HEK293 and OKP cells. Most importantly, triple mutation of D, E and E residues of 1019DAELE1023 to 1019AAALA1023 almost completely abolished NKCC2 complex-glycosylation, suggesting that this mutant failed to exit the ER. Cycloheximide chase analysis demonstrated that the absence of the terminally glycosylated form of 1019AAALA1023 was caused by defects in NKCC2 maturation. Accordingly, co-immunolocalization experiments revealed that 1019AAALA1023 was trapped in the ER. Finally, overexpression of a dominant negative mutant of Sar1-GTPase abolished NKCC2 maturation and cell surface expression, clearly indicating that NKCC2 export from the ER is COPII-dependent. Hence, our data indicate that in addition to the di-leucine like motifs, NKCC2 uses di-acidic exit codes for export from the ER through the COPII-dependent pathway. We propose that any naturally occurring mutation of NKCC2 interfering with this pathway could form the molecular basis of BS1.
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Pechenart, Pierre-Philip, Margaux Gillet, and Marc Mimram. "Etude sur la déformabilité de la nappe." SHS Web of Conferences 47 (2018): 01017. http://dx.doi.org/10.1051/shsconf/20184701017.
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Cet article vise à explorer la déformabilité d’une nappe plane découpée par un motif. Ce dernier lui donne la capacité de subir des déformations, d’acquérir de la souplesse tout en conservant un continu de matière, et d’évoluer d’une surface plane à une surface complexe –voire à double courbure. Les notions de surface, de surface développable, et de nappe architecturale forment les bases de l’étude du motif et de son fonctionnement. L’étude du fonctionnement d’une poutre entre deux appuis permet de simplifier notre approche, notamment dans l’analyse de ses déformations, de sa résistance au cisaillement, et de l’influence du matériau choisi pour composer cette nappe. Nous verrons dans cet article comment le motif que nous proposons d’étudier permet la double courbure, en quoi il est résistant et souple à la fois, en étudiant notamment les blocages internes de la nappe. La comparaison entre différents motifs nous permettra de mieux le comprendre et l’appréhender. Cette étude participe également au développement d’un pavillon architectural à échelle 1.
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Johnson, Amy O., Michael A. Lampson, and Timothy E. McGraw. "A Di-Leucine Sequence and a Cluster of Acidic Amino Acids Are Required for Dynamic Retention in the Endosomal Recycling Compartment of Fibroblasts." Molecular Biology of the Cell 12, no. 2 (2001): 367–81. http://dx.doi.org/10.1091/mbc.12.2.367.
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Insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase, is dynamically retained within the endosomal compartment of fibroblasts. The characteristics of this dynamic retention are rapid internalization from the plasma membrane and slow recycling back to the cell surface. These specialized trafficking kinetics result in <15% of IRAP on the cell surface at steady state, compared with 35% of the transferrin receptor, another transmembrane protein that traffics between endosomes and the cell surface. Here we demonstrate that a 29-amino acid region of IRAP's cytoplasmic domain (residues 56–84) is necessary and sufficient to promote trafficking characteristic of IRAP. A di-leucine sequence and a cluster of acidic amino acids within this region are essential elements of the motif that slows IRAP recycling. Rapid internalization requires any two of three distinct motifs: M15,16, DED64–66, and LL76,77. The DED and LL sequences are part of the motif that regulates recycling, demonstrating that this motif is bifunctional. In this study we used horseradish peroxidase quenching of fluorescence to demonstrate that IRAP is dynamically retained within the transferrin receptor-containing general endosomal recycling compartment. Therefore, our data demonstrate that motifs similar to those that determine targeting among distinct membrane compartments can also regulate the rate of transport of proteins from endosomal compartments. We propose a model for dynamic retention in which IRAP is transported from the general endosomal recycling compartment in specialized, slowly budding recycling vesicles that are distinct from those that mediate rapid recycling back to the surface (e.g., transferrin receptor-containing transport vesicles). It is likely that the dynamic retention of IRAP is an example of a general mechanism for regulating the distribution of proteins between the surface and interior of cells.
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Gottwein, Eva, Jochen Bodem, Barbara Müller, Ariane Schmechel, Hanswalter Zentgraf, and Hans-Georg Kräusslich. "The Mason-Pfizer Monkey Virus PPPY and PSAP Motifs Both Contribute to Virus Release." Journal of Virology 77, no. 17 (2003): 9474–85. http://dx.doi.org/10.1128/jvi.77.17.9474-9485.2003.
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ABSTRACT Late (L) domains are required for the efficient release of several groups of enveloped viruses. Three amino acid motifs have been shown to provide L-domain function, namely, PPXY, PT/SAP, or YPDL. The retrovirus Mason-Pfizer monkey virus (MPMV) carries closely spaced PPPY and PSAP motifs. Mutation of the PPPY motif results in a complete loss of virus release. Here, we show that the PSAP motif acts as an additional L domain and promotes the efficient release of MPMV but requires an intact PPPY motif to perform its function. Examination of HeLaP4 cells expressing PSAP mutant virus by electron microscopy revealed mostly late budding structures and chains of viruses accumulating at the cell surface with little free virus. In the case of the PPPY mutant virus, budding appeared to be mostly arrested at an earlier stage before induction of membrane curvature. The cellular protein TSG101, which interacts with the human immunodeficiency virus type 1 (HIV-1) PTAP L domain, was packaged into MPMV in a PSAP-dependent manner. Since TSG101 is crucial for HIV-1 release, this result suggests that the Gag-TSG101 interaction is responsible for the virus release function of the MPMV PSAP motif. Nedd4, which has been shown to interact with viral PPPY motifs, was also detected in MPMV particles, albeit at much lower levels. Consistent with a role of VPS4A in the budding of both PPPY and PTAP motif-containing viruses, the overexpression of ATPase-defective GFP-VPS4A fusion proteins blocked both wild-type and PSAP mutant virus release.
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Muhammad Yasir, Fitria Wardani, Apliniari Yuniar, and Ardhansyah Putra Hrp. "PEMBERDAYAAN MASYARAKAT MELALUI INOVASI BATIK DAN PRODUK MAKANAN MANGROVE DI DESA TANJUNG REJO KECAMATAN PERCUT SEI TUAN KABUPATEN DELI SERDANG." J-ABDI: Jurnal Pengabdian kepada Masyarakat 1, no. 9 (2022): 2157–62. http://dx.doi.org/10.53625/jabdi.v1i9.1252.
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Mangroves are typical plants found in coastal areas. Mangrove batik motifs as coastal plants have not been exposed optimally. Meanwhile, the coastal environment with its flora and fauna has tremendous potential as a batik motif. Aside from being a motif, mangrove plants can also be used as natural batik dyes and mangroves can be processed into food and beverage ingredients which are currently becoming a trend in the community. The use of mangroves as natural dyes, in addition to providing natural colors and beautiful motifs, can also reduce environmental pollution. The method of implementing the activities is group-based, comprehensive assistance is provided in all aspects, starting from providing facilities and infrastructure, as well as improving various HR skills through training. To increase the selling value of the mangrove crafts produced, foster partners were given training to diversify batik products in the form of brooches, wallets, bags and exhibitions of food and drink made from mangroves. The results of this service activity can provide more varied motifs and patterns of mangrove batik. Besides that, it resulted in the diversification of mangrove batik products into brooches, wallets and bags which have a higher selling value than just sheets of cloth. The fostered partners participated in the exhibition to further introduce the results of mangrove batik to the community and related agencies.
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Coblitz, Brian, Sojin Shikano, Meng Wu, et al. "C-terminal Recognition by 14-3-3 Proteins for Surface Expression of Membrane Receptors." Journal of Biological Chemistry 280, no. 43 (2005): 36263–72. http://dx.doi.org/10.1074/jbc.m507559200.
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Diverse functions of 14-3-3 proteins are directly coupled to their ability to interact with targeted peptide substrates. RSX(pS/pT)XP and RXΦX(pS/pT)XP are two canonical consensus binding motifs for 14-3-3 proteins representing the two common binding modes, modes I and II, between 14-3-3 and internal peptides. Using a genetic selection, we have screened a random peptide library and identified a group of C-terminal motifs, termed SWTY, capable of overriding an endoplasmic reticulum localization signal and redirecting membrane proteins to cell surface. Here we report that the C-terminal SWTY motif, although different from mode I and II consensus, binds tightly to 14-3-3 proteins with a dissociation constant (KD) of 0.17 μm, comparable with that of internal canonical binding peptides. We show that all residues but proline in -SWTX-COOH are compatible for the interaction and surface expression. Because SWTY-like sequences have been found in native proteins, these results support a broad significance of 14-3-3 interaction with protein C termini. The C-terminal binding consensus, mode III, represents an expansion of the repertoire of 14-3-3-targeted sequences.
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Borassi, Cecilia, Ana R. Sede, Martin A. Mecchia, et al. "An update on cell surface proteins containing extensin-motifs." Journal of Experimental Botany 67, no. 2 (2015): 477–87. http://dx.doi.org/10.1093/jxb/erv455.
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Ciobanu, C. V., B. N. Jariwala, T. E. B. Davies, and S. Agarwal. "Roughness and structural motifs on the Si(103) surface." Computational Materials Science 45, no. 1 (2009): 150–57. http://dx.doi.org/10.1016/j.commatsci.2008.03.048.
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Höhn, Annika, Tobias Jung, Stefanie Grimm, Betül Catalgol, Daniela Weber, and Tilman Grune. "Lipofuscin inhibits the proteasome by binding to surface motifs." Free Radical Biology and Medicine 50, no. 5 (2011): 585–91. http://dx.doi.org/10.1016/j.freeradbiomed.2010.12.011.
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Sheshadri, S. N., C. S. Chidan Kumar, S. Naveen, M. K. Veeraiah, Kakarla Raghava Reddy, and Ismail Warad. "Crystal structure and Hirshfeld surface analysis of 2-(4-nitrophenyl)-2-oxoethyl benzoate." Acta Crystallographica Section E Crystallographic Communications 75, no. 11 (2019): 1719–23. http://dx.doi.org/10.1107/s2056989019013975.
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The title compound, C15H11NO5, is relatively planar, with the planes of the two aromatic rings being inclined to each other by 3.09 (5)°. In the crystal, molecules are linked by a pair of C—H...O hydrogen bonds, forming inversion dimers, which enclose an R 2 2(16) ring motif. The dimers are linked by a further pair of C—H...O hydrogen-bonds forming ribbons enclosing R 4 4(26) ring motifs. The ribbons are linked by offset π–π interactions [centroid–centroid distances = 3.6754 (6)–3.7519 (6) Å] to form layers parallel to the ac plane. Through Hirshfeld surface analyses, the d norm surfaces, electrostatic potential and two-dimensional fingerprint (FP) plots were examined to verify the contributions of the different intermolecular contacts within the supramolecular structure. The shape-index surface shows that two sides of the molecule are involved with the same contacts in neighbouring molecules, and the curvedness plot shows flat surface patches that are characteristic of planar stacking.
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Takeda, Tetsuro, Hajime Yamazaki, and Marilyn G. Farquhar. "Identification of an apical sorting determinant in the cytoplasmic tail of megalin." American Journal of Physiology-Cell Physiology 284, no. 5 (2003): C1105—C1113. http://dx.doi.org/10.1152/ajpcell.00514.2002.
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Megalin is the main endocytic receptor of the proximal tubule and is responsible for reabsorption of many filtered proteins. In contrast to other members of the low-density lipoprotein (LDL) receptor gene family, it is expressed on the apical plasma membrane (PM) of polarized epithelial cells. To identify megalin's apical sorting signal, we generated deletion mutants and chimeric minireceptors composed of complementary regions of megalin and LDL receptor-related protein (LRP) and assessed the distribution of the mutants in Madin-Darby canine kidney (MDCK) cells by immunofluorescence and cell surface biotinylation. Megalin and LRP minireceptors are correctly targeted to the apical and basolateral PM, respectively, of MDCK cells. We found that the information that directs apical sorting is present in the cytoplasmic tail (CT) of megalin, which contains three NPXY motifs, YXXØ, SH3, and dileucine motifs, and a PDZ-binding motif at its COOH terminus. Deletion analysis established that amino acids 107–136 of the megalin-CT containing the second NPXY-like motif are critical for apical sorting and targeting, whereas the regions containing the first and third NPXY motifs are required for efficient endocytosis. We conclude that the megalin-CT contains a novel apical sorting determinant and that cytoplasmic sorting machinery exists in MDCK cells for some apical transmembrane proteins.
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Boonen, Marielle, Roberta Rezende de Castro, Gaëlle Cuvelier, Isabelle Hamer, and Michel Jadot. "A dileucine signal situated in the C-terminal tail of the lysosomal membrane protein p40 is responsible for its targeting to lysosomes." Biochemical Journal 414, no. 3 (2008): 431–40. http://dx.doi.org/10.1042/bj20071626.
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Transport of newly synthesized lysosomal membrane proteins from the TGN (trans-Golgi network) to the lysosomes is due to the presence of specific signals in their cytoplasmic domains that are recognized by cytosolic adaptors. p40, a hypothetical transporter of 372 amino acids localized in the lysosomal membrane, contains four putative lysosomal sorting motifs in its sequence: three of the YXXϕ-type (Y6QLF, Y106VAL, Y333NGL) and one of the [D/E]XXXL[L/I]-type (EQERL360L361). To test the role of these motifs in the biosynthetic transport of p40, we replaced the most critical residues of these consensus sequences, the tyrosine residue or the leucine–leucine pair, by alanine or alanine–valine respectively. We analysed the subcellular localization of the mutated p40 proteins in transfected HeLa cells by confocal microscopy and by biochemical approaches (subcellular fractionation on self-forming Percoll density gradients and cell surface biotinylation). The results of the present study show that p40 is mistargeted to the plasma membrane when its dileucine motif is disrupted. No role of the tyrosine motifs could be put forward. Taken together, our results provide evidence that the sorting of p40 from the TGN to the lysosomes is directed by the dileucine EQERL360L361 motif situated in its C-terminal tail.
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Ali Yasin, Siti Maryam, Hamdzun Haron, Zuliskandar Ramli, Suhaimi Tular, and Hanafi Mohd Raffie. "Translating Traditional Malay Pottery Motifs To Inspire Ceramic Surface Decoration Design." Idealogy Journal 6, no. 2 (2021): 98–103. http://dx.doi.org/10.24191/idealogy.v6i2.289.
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A particular ceramic product offered by the designers and manufacturers is measured based on its appearance and performance from aesthetic value, design and craftsmanship quality. Products in our daily life play an essential role in bringing us happiness, comfort, convenience and satisfaction to the consumers and buyers. In a Malay community in Malaysia, the Malay Traditional Pottery is one of the Malay arts heritage. Its products used to have a high demand among the locals as well as people from abroad. However, today, demand for Malay Traditional Pottery from the locals has declined significantly. Hence, to improve the product appearance, this study highlights one of the essential factors in ceramic design features, namely surface decoration, by using motifs derived from the Malay Traditional Pottery onto the new contemporary design of the local ceramic products. The surface decoration consists of motifs, patterns, colours, techniques and materials. Surface decoration study would give designers and local ceramic entrepreneurs the product appearance improvement. With such improvements, local ceramic products would become a preferred choice for the consumer’s daily use. This study also aimed to entice the designer to be involved in pattern design and ceramic product surfaces.
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Mitchell, Richard S., Rittik Chaudhuri, O. Wolf Lindwasser, et al. "Competition Model for Upregulation of the Major Histocompatibility Complex Class II-Associated Invariant Chain by Human Immunodeficiency Virus Type 1 Nef." Journal of Virology 82, no. 16 (2008): 7758–67. http://dx.doi.org/10.1128/jvi.02668-07.
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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) Nef protein upregulates the expression of the invariant chain (Ii)/major histocompatibility complex class II (MHC-II) complex at the cell surface. This complex appears to reach the antigen-loading endosomal compartment at least in part via an indirect pathway in which it is internalized from the cell surface via the adaptor protein 2 (AP-2) complex. Here we provide evidence for a competition model to explain how Nef upregulates the expression of Ii at the cell surface. In this model, Nef and Ii compete for binding to AP-2. In support of this model, Nef decreased the rate of internalization of Ii from the cell surface. The AP-binding dileucine motif in Nef, ENTSLL165, was necessary and sufficient for the upregulation of Ii. In addition, two leucine-based AP-binding motifs in the Ii cytoplasmic tail, DDQRDLI8 and EQLPML17, were critical for the efficient upregulation of Ii by Nef. Experiments using Nef variants in which the native dileucine-based sorting motif was replaced with similar motifs from cellular transmembrane proteins allowed modulation of AP-binding specificity. Analysis of these variants suggested that the binding of Nef to AP-2 is sufficient to upregulate Ii at the plasma membrane. Finally, interference with the expression of AP-2 caused an upregulation of Ii at the plasma membrane, and this decreased the effect of Nef. These data indicate that Nef usurps AP-2 complexes to dysregulate Ii trafficking and potentially interfere with antigen presentation in the context of MHC-II.
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Venzke, Stephanie, Nico Michel, Ina Allespach, Oliver T. Fackler, and Oliver T. Keppler. "Expression of Nef Downregulates CXCR4, the Major Coreceptor of Human Immunodeficiency Virus, from the Surfaces of Target Cells and Thereby Enhances Resistance to Superinfection." Journal of Virology 80, no. 22 (2006): 11141–52. http://dx.doi.org/10.1128/jvi.01556-06.
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ABSTRACT Lentiviral Nef proteins are key factors for pathogenesis and are known to downregulate functionally important molecules, including CD4 and major histocompatibility complex class I (MHC-I), from the surfaces of infected cells. Recently, we demonstrated that Nef reduces cell surface levels of the human immunodeficiency virus type 1 (HIV-1) entry coreceptor CCR5 (N. Michel, I. Allespach, S. Venzke, O. T. Fackler, and O. T. Keppler, Curr. Biol. 15:714-723, 2005). Here, we report that Nef downregulates the second major HIV-1 coreceptor, CXCR4, from the surfaces of HIV-infected primary CD4 T lymphocytes with efficiencies comparable to those of the natural CXCR4 ligand, stromal cell-derived factor-1 alpha. Analysis of a panel of mutants of HIV-1SF2 Nef revealed that the viral protein utilized the same signature motifs for downmodulation of CXCR4 and MHC-I, including the proline-rich motif P73P76P79P82 and the acidic cluster motif E66E67E68E69. Expression of wild-type Nef, but not of specific Nef mutants, resulted in a perinuclear accumulation of the coreceptor. Remarkably, the carboxy terminus of CXCR4, which harbors the classical motifs critical for basal and ligand-induced receptor endocytosis, was dispensable for the Nef-mediated reduction of surface exposure. Functionally, the ability of Nef to simultaneously downmodulate CXCR4 and CD4 correlated with maximum-level protection of Nef-expressing target cells from fusion with cells exposing X4 HIV-1 envelopes. Furthermore, the Nef-mediated downregulation of CXCR4 alone on target T lymphocytes was sufficient to diminish cells' susceptibility to X4 HIV-1 virions at the entry step. The downregulation of chemokine coreceptors is a conserved activity of Nef to modulate infected cells, an important functional consequence of which is an enhanced resistance to HIV superinfection.
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Adamkiewicz, Malgorzata, David O’Hagan, and Georg Hähner. "Organic chemistry on surfaces: Direct cyclopropanation by dihalocarbene addition to vinyl terminated self-assembled monolayers (SAMs)." Beilstein Journal of Organic Chemistry 10 (December 5, 2014): 2897–902. http://dx.doi.org/10.3762/bjoc.10.307.
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C11-Vinyl-terminated self-assembled monolayers (SAMs) on silica surfaces are successfully modified in C–C bond forming reactions with dihalocarbenes to generate SAMs, terminated with dihalo- (fluoro, chloro, bromo) cyclopropane motifs with about 30% surface coverage.
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Herrera-León, Claudia, Francisco Ramos-Martín, Hassan El Btaouri, et al. "The Influence of Short Motifs on the Anticancer Activity of HB43 Peptide." Pharmaceutics 14, no. 5 (2022): 1089. http://dx.doi.org/10.3390/pharmaceutics14051089.
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Despite the remarkable similarity in amino acid composition, many anticancer peptides (ACPs) display significant differences in terms of activity. This strongly suggests that particular relative dispositions of amino acids (motifs) play a role in the interaction with their biological target, which is often the cell membrane. To better verify this hypothesis, we intentionally modify HB43, an ACP active against a wide variety of cancers. Sequence alignment of related ACPs by ADAPTABLE web server highlighted the conserved motifs that could be at the origin of the activity. In this study, we show that changing the order of amino acids in such motifs results in a significant loss of activity against colon and breast cancer cell lines. On the contrary, amino acid substitution in key motifs may reinforce or weaken the activity, even when the alteration does not perturb the amphipathicity of the helix formed by HB43 on liposomes mimicking their surface. NMR and MD simulations with different membrane models (micelles, bicelles, and vesicles) indicate that the activity reflects the insertion capability in cancer-mimicking serine-exposing membranes, supported by the insertion of N-terminal phenylalanine in the FAK motif and the anchoring to the carboxylate of phosphatidylserine by means of arginine side chains.