The Experts below are selected from a list of 1344 Experts worldwide ranked by ideXlab platform
Alessandro Senes - One of the best experts on this subject based on the ideXlab platform.
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the cα h o hydrogen bond a determinant of stability and specificity in transmembrane Helix interactions
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Alessandro Senes, Iba Ubarretxenabelandia, Donald M EngelmaAbstract:The Cα—H⋅⋅⋅O hydrogen bond has been given little attention as a determinant of transmembrane Helix association. Stimulated by recent calculations suggesting that such bonds can be much stronger than has been supposed, we have analyzed 11 known membrane protein structures and found that apparent carbon α hydrogen bonds cluster frequently at glycine-, serine-, and threonine-rich packing interfaces between transmembrane helices. Parallel Right-Handed Helix–Helix interactions appear to favor Cα—H⋅⋅⋅O bond formation. In particular, Cα—H⋅⋅⋅O interactions are frequent between helices having the structural motif of the glycophorin A dimer and the GxxxG pair. We suggest that Cα—H⋅⋅⋅O hydrogen bonds are important determinants of stability and, depending on packing, specificity in membrane protein folding.
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The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane Helix interactions
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Alessandro Senes, Iban Ubarretxena-belandia, Donald M. EngelmanAbstract:The Cα—H⋅⋅⋅O hydrogen bond has been given little attention as a determinant of transmembrane Helix association. Stimulated by recent calculations suggesting that such bonds can be much stronger than has been supposed, we have analyzed 11 known membrane protein structures and found that apparent carbon α hydrogen bonds cluster frequently at glycine-, serine-, and threonine-rich packing interfaces between transmembrane helices. Parallel Right-Handed Helix–Helix interactions appear to favor Cα—H⋅⋅⋅O bond formation. In particular, Cα—H⋅⋅⋅O interactions are frequent between helices having the structural motif of the glycophorin A dimer and the GxxxG pair. We suggest that Cα—H⋅⋅⋅O hydrogen bonds are important determinants of stability and, depending on packing, specificity in membrane protein folding.
Takuji Ogawa - One of the best experts on this subject based on the ideXlab platform.
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Single-walled carbon nanotube absolute-handedness chirality assignment confirmation using metalized porphyrin's supramolecular structures via STM imaging technique.
Chirality, 2020Co-Authors: Ahmed I. A. Abd El-mageed, Takuji OgawaAbstract:This work reports confirmation of the experimental assignment of the absolute-handedness chirality of single-walled carbon nanotubes (SWNTs). This was achieved by applying the scanning tunneling microscopy (STM) imaging technique to a supramolecular composite consisting of a metalized porphyrin derivative (nickel-5,15-bisdodecylporphyrin [Ni-BDP]) affixed to the surfaces of chiral-concentrated SWNTs (with Right-Handed Helix P- and left-handed Helix M-). On the basis of the handedness chirality, different chiral supramolecular structures of Ni-BDP were observed on the surfaces of the two SWNT enantiomers. The incorporation of a metal center into the porphyrin ring did not significantly affect the SWNT absolute-handedness chirality assignment, the large pi-system porphyrin ring being the crucial factor. These findings will effectively pave the way towards the clear selective synthesis, separation, chemistry, and applications of SWNT enantiomers.
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Assignment of the Absolute‐Handedness Chirality of Single‐Walled Carbon Nanotubes by Using Organic Molecule Supramolecular Structures
Chemistry: A European Journal, 2018Co-Authors: Ahmed I. A. Abd El-mageed, Murni Handayani, Zhijin Chen, Tomoko Inose, Takuji OgawaAbstract:: Supramolecular structures of organic molecules on planar nanocarbon surfaces, such as highly oriented pyrolytic graphite (HOPG), have been extensively studied and the factors that control them are generally well-established. In contrast, the properties of supramolecular structures on curved nanocarbon surfaces like carbon nanotubes remain challenging to predict and/or to understand. This paper reports an investigation into the first study of the supramolecular structures of 5,15-bisdodecylporphyrin (C12P) on chiral, concentrated single-walled carbon nanotubes (SWNTs; with Right-Handed Helix P- and left-handed Helix M-) surfaces using STM. Furthermore, the study is the first of its kind to experimentally assign the absolute-handedness chirality of SWNTs, as well as to understand their effect on the supramolecular structures of organic molecules on their surfaces. Interestingly, these SWNT enantiomers resulted in supramolecular structures of opposite chirality based on the handedness chirality. With molecular modelling, we predicted the absolute-handedness chirality of SWNTs, before demonstrating this experimentally.
Donald M Engelma - One of the best experts on this subject based on the ideXlab platform.
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the cα h o hydrogen bond a determinant of stability and specificity in transmembrane Helix interactions
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Alessandro Senes, Iba Ubarretxenabelandia, Donald M EngelmaAbstract:The Cα—H⋅⋅⋅O hydrogen bond has been given little attention as a determinant of transmembrane Helix association. Stimulated by recent calculations suggesting that such bonds can be much stronger than has been supposed, we have analyzed 11 known membrane protein structures and found that apparent carbon α hydrogen bonds cluster frequently at glycine-, serine-, and threonine-rich packing interfaces between transmembrane helices. Parallel Right-Handed Helix–Helix interactions appear to favor Cα—H⋅⋅⋅O bond formation. In particular, Cα—H⋅⋅⋅O interactions are frequent between helices having the structural motif of the glycophorin A dimer and the GxxxG pair. We suggest that Cα—H⋅⋅⋅O hydrogen bonds are important determinants of stability and, depending on packing, specificity in membrane protein folding.
Donald M. Engelman - One of the best experts on this subject based on the ideXlab platform.
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The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane Helix interactions
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Alessandro Senes, Iban Ubarretxena-belandia, Donald M. EngelmanAbstract:The Cα—H⋅⋅⋅O hydrogen bond has been given little attention as a determinant of transmembrane Helix association. Stimulated by recent calculations suggesting that such bonds can be much stronger than has been supposed, we have analyzed 11 known membrane protein structures and found that apparent carbon α hydrogen bonds cluster frequently at glycine-, serine-, and threonine-rich packing interfaces between transmembrane helices. Parallel Right-Handed Helix–Helix interactions appear to favor Cα—H⋅⋅⋅O bond formation. In particular, Cα—H⋅⋅⋅O interactions are frequent between helices having the structural motif of the glycophorin A dimer and the GxxxG pair. We suggest that Cα—H⋅⋅⋅O hydrogen bonds are important determinants of stability and, depending on packing, specificity in membrane protein folding.
Danith H. Ly - One of the best experts on this subject based on the ideXlab platform.
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synthesis and characterization of conformationally preorganized r diethylene glycol containing γ peptide nucleic acids with superior hybridization properties and water solubility
Journal of Organic Chemistry, 2011Co-Authors: Bichismita Sahu, Srinivas Rapireddy, Iulia Sacui, Kimberly J Zanotti, Raman Bahal, Bruce A Armitage, Danith H. LyAbstract:Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity toward DNA and RNA and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol (“miniPEG”, R-MP) unit at the γ-backbone transforms a randomly folded PNA into a Right-Handed Helix. Synthesis of optically pure R-MPγPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-l-serine. Once synthesized, R-MPγPNA oligomers are preorganized into a Right-Handed Helix, hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have im...
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Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization
Journal of the American Chemical Society, 2010Co-Authors: Boris Shivachev, Srinivas Rapireddy, Matthew H. J. Crawford, Shoucheng Du, Marcela Madrid, Danith H. LyAbstract:We have determined the structure of a PNA−DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete γ-backbone modification (“γPNA”). Unlike the achiral counterpart, which adopts a random-fold, this particular γPNA is already preorganized into a Right-Handed Helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the γPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these...
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synthesis of conformationally preorganized and cell permeable guanidine based γ peptide nucleic acids γgpnas
Journal of Organic Chemistry, 2009Co-Authors: Bichismita Sahu, Venugopal Chenna, Kira L Lathrop, Sufi M Thomas, Kenneth J Livak, Danith H. LyAbstract:A general method for preparing optically pure guanidine-based γ-peptide nucleic acid (γGPNA) monomers for all four natural nucleobases (A, C, G, and T) is described. These second-generation γGPNAs differ from the first-generation GPNAs in that the guanidinium group is installed at the γ- instead of the α-position of the N-(2-aminoethyl)glycine backbone unit. This positional switch enables GPNAs to be synthesized from relatively cheap l- as opposed to d-amino acids. Unlike their α-predecessors, which are randomly folded, γGPNAs prepared from l-amino acids are preorganized into a Right-Handed Helix and bind to DNA and RNA with exceptionally high affinity and sequence selectivity and are readily taken up by mammalian cells.
