59 results match your criteria head-to-tail closed


Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice.

Planta 2021 Jan 7;253(2):26. Epub 2021 Jan 7.

Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.

Main Conclusion: Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. Read More

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January 2021

DNA origami-based microtubule analogue.

Authors:
Tao Zhang

Nanotechnology 2020 Dec;31(50):50LT01

Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, Shandong Province 264005, People's Republic of China.

A microtubule hollow structure is one type of cytoskeletons which directs a number of important cellular functions. When recapitulating biological events in a cell-free system, artificial frames are often required to execute similar cytoskeletal functions in synthetic systems. Here, I report a prototypical microtubular assembly using a DNA origami nanostructuring method. Read More

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December 2020

Structure and function of the calcium-selective TRP channel TRPV6.

J Physiol 2020 Feb 19. Epub 2020 Feb 19.

Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY, 10032, USA.

Epithelial calcium channel TRPV6 is a member of the vanilloid subfamily of TRP channels that is permeable to cations and highly selective to Ca ; it shows constitutive activity regulated negatively by Ca and positively by phosphoinositol and cholesterol lipids. In this review, we describe the molecular structure of TRPV6 and discuss how its structural elements define its unique functional properties. High Ca selectivity of TRPV6 originates from the narrow selectivity filter, where Ca ions are directly coordinated by a ring of anionic aspartate side chains. Read More

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February 2020

Identification of cucumber circular RNAs responsive to salt stress.

BMC Plant Biol 2019 Apr 27;19(1):164. Epub 2019 Apr 27.

Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China.

Background: Circular RNAs (circRNAs) are 3'-5' head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition.

Results: In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Read More

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A new twist on tropomyosin binding to actin filaments: perspectives on thin filament function, assembly and biomechanics.

J Muscle Res Cell Motil 2020 03 15;41(1):23-38. Epub 2019 Feb 15.

Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, MA, USA.

Tropomyosin, best known for its role in the steric regulation of muscle contraction, polymerizes head-to-tail to form cables localized along the length of both muscle and non-muscle actin-based thin filaments. In skeletal and cardiac muscles, tropomyosin, under the control of troponin and myosin, moves in a cooperative manner between blocked, closed and open positions on filaments, thereby masking and exposing actin-binding sites necessary for myosin crossbridge head interactions. While the coiled-coil signature of tropomyosin appears to be simple, closer inspection reveals surprising structural complexity required to perform its role in steric regulation. Read More

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Control of spin-wave transmission by a programmable domain wall.

Nat Commun 2018 11 19;9(1):4853. Epub 2018 Nov 19.

NanoSpin, Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, FI-00076, Aalto, Finland.

Active manipulation of spin waves is essential for the development of magnon-based technologies. Here, we demonstrate programmable spin-wave filtering by resetting the spin structure of pinned 90° Néel domain walls in a continuous CoFeB film with abrupt rotations of uniaxial magnetic anisotropy. Using micro-focused Brillouin light scattering and micromagnetic simulations, we show that broad 90° head-to-head or tail-to-tail magnetic domain walls are transparent to spin waves over a broad frequency range. Read More

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November 2018

Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis.

Cell Chem Biol 2018 06 12;25(6):718-727.e3. Epub 2018 Apr 12.

State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China. Electronic address:

Here, we provide structural insights into PyrE3, a flavin-dependent [4 + 2] cyclase that catalyzes trans-decalin formation in the biosynthesis of pyrroindomycins. PyrE3 shares an architecture/domain organization head-to-tail similarity with the members of the family of para-hydroxybenzoate hydroxylase (pHBH)-fold monooxygenases, and possesses a flavin adenine dinucleotide (FAD)-binding domain, a middle domain, and a C-terminal thioredoxin-like domain. The FAD-binding domain forms a central hub of the protein structure, and binds with FAD in a "closed" conformation of pHBH-fold family monooxygenases known for their highly dynamic catalytic processes. Read More

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Molecular roles and function of circular RNAs in eukaryotic cells.

Cell Mol Life Sci 2018 03 7;75(6):1071-1098. Epub 2017 Nov 7.

Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.

Protein-coding and noncoding genes in eukaryotes are typically expressed as linear messenger RNAs, with exons arranged colinearly to their genomic order. Recent advances in sequencing and in mapping RNA reads to reference genomes have revealed that thousands of genes express also covalently closed circular RNAs. Many of these circRNAs are stable and contain exons, but are not translated into proteins. Read More

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Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium.

Acta Crystallogr F Struct Biol Commun 2017 Nov 30;73(Pt 11):612-620. Epub 2017 Oct 30.

Division of Medicine, University College London, Gower Street, London WC1E 6BT, England.

The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. Read More

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November 2017

Conformational Changes of CFTR upon Phosphorylation and ATP Binding.

Cell 2017 Jul 20;170(3):483-491.e8. Epub 2017 Jul 20.

Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from an ATP-binding cassette transporter. CFTR channel gating is strictly coupled to phosphorylation and ATP hydrolysis. Previously, we reported essentially identical structures of zebrafish and human CFTR in the dephosphorylated, ATP-free form. Read More

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Plant SAM-Domain Proteins Start to Reveal Their Roles.

Trends Plant Sci 2017 08 28;22(8):718-725. Epub 2017 Jun 28.

LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France. Electronic address:

Proteins often act in complexes assembled via protein-protein interaction domains. The sterile alpha motif (SAM) domain is one of the most prominent interaction domains in animals and is present in proteins of diverse functions. This domain allows head-to-tail closed oligomerisation or polymer formation resulting in homo- and/or heterocomplexes that have been shown to be important for proper protein localisation and function. Read More

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Colloidal aggregation and structural assembly of aspect ratio variant goethite (α-FeOOH) with nC fullerene in environmental media.

Environ Pollut 2016 Dec 13;219:1049-1059. Epub 2016 Sep 13.

Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States. Electronic address:

Environmental mobility of C fullerene can be significantly affected in the presence of naturally abundant α-FeOOH. However, α-FeOOH vary significantly in sizes, shapes and associated properties that can greatly influence the fate and transport of C fullerene in environmental media. Therefore, colloidal hetero-association between well crystallized low aspect (L) α-FeOOH and nC fullerene may differ substantially to weakly crystallized high-aspect (H) counterpart. Read More

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December 2016

Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

Soft Matter 2016 Aug;12(32):6841-50

Institute of Theoretical Physics, Technical University Berlin, Secr. EW 7-1 Hardenbergstr. 36, D-10623 Berlin, Germany.

Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. Read More

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Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5.

Mol Cell 2016 05;62(4):586-602

European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France. Electronic address:

RIG-I and MDA5 sense virus-derived short 5'ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of chicken (ch) LGP2 with dsRNA display a fully or semi-closed conformation depending on the presence or absence of nucleotide. Read More

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The Nucleotide-Free State of the Multidrug Resistance ABC Transporter LmrA: Sulfhydryl Cross-Linking Supports a Constant Contact, Head-to-Tail Configuration of the Nucleotide-Binding Domains.

PLoS One 2015 29;10(6):e0131505. Epub 2015 Jun 29.

School of Life Sciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.

ABC transporters are integral membrane pumps that are responsible for the import or export of a diverse range of molecules across cell membranes. ABC transporters have been implicated in many phenomena of medical importance, including cystic fibrosis and multidrug resistance in humans. The molecular architecture of ABC transporters comprises two transmembrane domains and two ATP-binding cassettes, or nucleotide-binding domains (NBDs), which are highly conserved and contain motifs that are crucial to ATP binding and hydrolysis. Read More

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Landscape of intertwined associations in multi-domain homo-oligomeric proteins.

J Mol Biol 2015 Jan 11;427(2):350-70. Epub 2014 Nov 11.

Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8. Electronic address:

This study charts the landscape of multi-domain protein structures that form intertwined homodimers by exchanging structural domains between subunits. A representative dataset of such homodimers was derived from the Protein Data Bank, and their structural and topological properties were compared to those of a representative set of non-intertwined homodimers. Most of the intertwined dimers form closed assemblies with head-to-tail arrangements, where the subunit interface involves contacts between dissimilar domains. Read More

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January 2015

Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations.

Biophys J 2014 Nov;107(9):2164-76

Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain. Electronic address:

Bacterial cytoskeletal protein FtsZ assembles in a head-to-tail manner, forming dynamic filaments that are essential for cell division. Here, we study their dynamics using unbiased atomistic molecular simulations from representative filament crystal structures. In agreement with experimental data, we find different filament curvatures that are supported by a nucleotide-regulated hinge motion between consecutive FtsZ monomers. Read More

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November 2014

The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.

J Phys Chem B 2013 Jan 19;117(1):83-93. Epub 2012 Dec 19.

Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.

Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Read More

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January 2013

Structure of a compact conformation of linear diubiquitin.

Acta Crystallogr D Biol Crystallogr 2012 Feb 13;68(Pt 2):102-8. Epub 2012 Jan 13.

Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.

Post-translational modifications involving ubiquitin regulate a wide range of biological processes including protein degradation, responses to DNA damage and immune signalling. Ubiquitin polymerizes into chains which may contain eight different linkage types; the ubiquitin C-terminal glycine can link to one of the seven lysine residues or the N-terminal amino group of methionine in the distal ubiquitin molecule. The latter head-to-tail linkage type, referred to as a linear ubiquitin chain, is involved in NF-κB activation through specific interactions with NF-κB essential modulator (NEMO). Read More

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February 2012

Stereochemistry-dependent, mechanoresponsive supramolecular host assemblies for fullerenes: a guest-induced enhancement of thixotropy.

J Am Chem Soc 2012 Feb 18;134(4):2161-71. Epub 2012 Jan 18.

Institute for Advanced Study, Faculty of Engineering, Kyushu University, 744 Moto-oka, Fukuoka 819-0395, Japan.

Self-assembly behaviors of a series of systems (G1, G2, and G3) possessing same organic building blocks based on a substituted anthracene have been investigated in decalin. G2 and G3 are dominated by head-to-tail (ht) and head-to-head (hh) type dimers of G1, respectively. G1 gives a thermoresponsive gel that behaves ideally, showing frequency-independent elastic and viscous moduli. Read More

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February 2012

Bocavirus episome in infected human tissue contains non-identical termini.

PLoS One 2011 28;6(6):e21362. Epub 2011 Jun 28.

Center for Infection and Immunity, Columbia University, New York, New York, United States of America.

Unlabelled: Human bocaviruses (HBoV) are highly prevalent human infections whose pathogenic potential remains unknown. Recent identification of the first non-human primate bocavirus [1] in captive gorillas raised the possibility of the persistent nature of bocavirus infection. To characterize bocavirus infection in humans, we tested intestinal biopsies from 22 children with gastrointestinal disease for the presence of HBoV DNA. Read More

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December 2011

Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution.

Biochemistry 2011 Jul 10;50(26):5958-68. Epub 2011 Jun 10.

Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.

Escherichia coli DNA polymerase III is a highly processive replicase because of the presence of the β clamp protein that tethers DNA polymerases to DNA. The β clamp is a head-to-tail ring-shaped homodimer, in which each protomer contains three structurally similar domains. Although multiple studies have probed the functions of the β clamp, a detailed understanding of the conformational dynamics of the β clamp in solution is lacking. Read More

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Structural basis for agonism and antagonism of hepatocyte growth factor.

Proc Natl Acad Sci U S A 2010 Jul 12;107(30):13264-9. Epub 2010 Jul 12.

Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA.

Hepatocyte growth factor (HGF) is an activating ligand of the Met receptor tyrosine kinase, whose activity is essential for normal tissue development and organ regeneration but abnormal activation of Met has been implicated in growth, invasion, and metastasis of many types of solid tumors. HGF has two natural splice variants, NK1 and NK2, which contain the N-terminal domain (N) and the first kringle (K1) or the first two kringle domains of HGF. NK1, which is a Met agonist, forms a head-to-tail dimer complex in crystal structures and mutations in the NK1 dimer interface convert NK1 to a Met antagonist. Read More

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Evidence for ligand non-innocence in a formally ruthenium(I) hydride complex.

J Am Chem Soc 2010 Mar;132(12):4107-9

Department of Chemistry and Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Formally zerovalent, dinitrogen-bridged ruthenium complex, {[N(3)(Xyl)]Ru}(2)(mu-eta(1):eta(1)-N(2)) (1), where [N(3)(Xyl)] = 2,6-(XylN horizontal lineCMe)(2)C(5)H(3)N, reacts with excess H(2) to give the binuclear hydride species, {[N(3)]Ru(H)}(2)(mu-eta(1):eta(1)-N(2)) (2) bearing a single hydrogen per ruthenium. Complex 2 is an unusual example of a structurally characterized paramagnetic transition metal hydride, and the first such example for ruthenium. Structural data and DFT calculations suggest unpaired electron density is strongly delocalized onto the non-innocent [N(3)] ligand, with a relatively small degree of the metalloradical character implied by the Ru(I) formal oxidation state, and that the [N(3)](-)/Ru(II) formalism may be more informative. Read More

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Herpes simplex virus 1 regulatory protein ICP27 undergoes a head-to-tail intramolecular interaction.

J Virol 2010 May 17;84(9):4124-35. Epub 2010 Feb 17.

Department of Microbiology and Molecular Genetics, School of Medicine, Medical Sciences, B240, University of California, Irvine, CA 92697-4025, USA.

Herpes simplex virus type 1 (HSV-1) regulatory protein ICP27 is a multifunction functional protein that interacts with many cellular proteins. A number of the proteins with which ICP27 interacts require that both the N and C termini of ICP27 are intact. These include RNA polymerase II, TAP/NXF1, and Hsc70. Read More

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Strict coupling between CFTR's catalytic cycle and gating of its Cl- ion pore revealed by distributions of open channel burst durations.

Proc Natl Acad Sci U S A 2010 Jan 4;107(3):1241-6. Epub 2009 Dec 4.

Department of Medical Biochemistry, Semmelweis University, Budapest H-1094, Hungary.

CFTR, the ABC protein defective in cystic fibrosis, functions as an anion channel. Once phosphorylated by protein kinase A, a CFTR channel is opened and closed by events at its two cytosolic nucleotide binding domains (NBDs). Formation of a head-to-tail NBD1/NBD2 heterodimer, by ATP binding in two interfacial composite sites between conserved Walker A and B motifs of one NBD and the ABC-specific signature sequence of the other, has been proposed to trigger channel opening. Read More

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January 2010

Exploring the linkage dependence of polyubiquitin conformations using molecular modeling.

J Mol Biol 2010 Jan 22;395(4):803-14. Epub 2009 Oct 22.

Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20910, USA.

Posttranslational modification of proteins by covalent attachment of a small protein ubiquitin (Ub) or a polymeric chain of Ub molecules (called polyubiquitin) is involved in controlling a vast variety of processes in eukaryotic cells. The question of how different polyubiquitin signals are recognized is central to understanding the specificity of various types of polyubiquitination. In polyubiquitin, monomers are linked to each other via an isopeptide bond between the C-terminal glycine of one Ub and a lysine of the other. Read More

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January 2010

[5mCCTCTCTCC]4: an i-motif tetramer with intercalated T*T pairs.

J Am Chem Soc 2009 Sep;131(36):12870-1

Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France 91190.

The i-motif is a four-stranded structure built by intercalation in a head-to-tail orientation of two parallel duplexes associated by hemiprotonated C(*)C(+) pairs. T*T pairs are nearly isomorphic of C*C(+) pairs; however the structural investigations of i-motif tetramers containing thymidines suggest that the i-motif cannot accommodate T*T pairs in a face-to-face orientation. The tetramer of 5mCCTCTCTCC make an exception. Read More

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September 2009

Identification of mitochondrial genome concatemers in AIDS-associated lymphomas and lymphoid cell lines.

Leuk Res 2009 Nov 11;33(11):1499-504. Epub 2009 Apr 11.

Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, United States.

Since most oncogenic viruses persist as extrachromosomal covalently closed circular DNA (cccDNA) in tumor cells, we developed an assay to visualize and identify cccDNA in primary lymphomas. We identified concatemers of the mitochondrial genome in all samples analyzed, but not in normal lymphocytes. One AIDS-associated lymphoma (EL) was further studied in detail as its mitochondrial genome consisted of tandem head-to-tail duplications. Read More

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November 2009

Architecture of clathrin fullerene cages reflects a geometric constraint--the head-to-tail exclusion rule--and a preference for asymmetry.

Authors:
Stan Schein

J Mol Biol 2009 Mar 29;387(2):363-75. Epub 2009 Jan 29.

California NanoSystems Institute, UCLA, Los Angeles, CA 90095-7151, USA.

Fullerene cages have n trivalent vertices, 12 pentagonal faces, and (n-20)/2 hexagonal faces. The smallest cage in which all of the pentagons are surrounded by hexagons and thus isolated from each other has 60 vertices and is shaped like a soccer ball. The protein clathrin self-assembles into fullerene cages of a variety of sizes and shapes, including smaller ones with adjacent pentagons as well as larger ones, but the variety is limited. Read More

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