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Cytoplasmic Side (cytoplasmic + side)

Distribution by Scientific Domains
Life Sciences71%

Selected Abstracts

Conserved cytoplasmic motifs that distinguish sub-groups of the polyprenol phosphate:N -acetylhexosamine-1-phosphate transferase family

FEMS MICROBIOLOGY LETTERS, Issue 2 2000
Matt S. Anderson
Abstract WecA, MraY and WbcO are conserved members of the polyprenol phosphate:N -acetylhexosamine-1-phosphate transferase family involved in the assembly of bacterial cell walls, and catalyze reactions involving a membrane-associated polyprenol phosphate acceptor substrate and a cytoplasmically located UDP- D -amino sugar donor. MraY, WbcO and WecA purportedly utilize different UDP-sugars, although the molecular basis of this specificity is largely unknown. However, domain variations involved in specificity are predicted to occur on the cytoplasmic side of the membrane, adjacent to conserved domains involved in the mechanistic activity, and with access to the cytoplasmically located sugar nucleotides. Conserved C-terminal domains have been identified that satisfy these criteria. Topological analyses indicate that they form the highly basic, fifth cytoplasmic loop between transmembrane regions IX and X. Four diverse loops are apparent, for MraY, WecA, WbcO and RgpG, that uniquely characterize these sub-groups of the transferase family, and a correlation is evident with the known or implied UDP-sugar specificity. [source]

Fusion of ALK to the Ran-binding protein 2 (RANBP2) gene in inflammatory myofibroblastic tumor

GENES, CHROMOSOMES AND CANCER, Issue 1 2003
Zhigui Ma
Inflammatory myofibroblastic tumor (IMT) is a rare mesenchymal proliferation of transformed myofibroblasts, with a prominent inflammatory cell component, that can mimic other spindle cell processes such as nodular fasciitis, desmoid tumor, and gastrointestinal stromal tumor. Genetic analyses have recently demonstrated rearrangements of anaplastic lymphoma kinase (ALK), located at 2p23, in a subset of IMTs. Molecular characterizations have identified ALK fusions involving tropomyosin-3 and -4 (TPM-3 and -4), the clathrin heavy chain (CLTC), and the cysteinyl-tRNA synthetase (CARS) genes as fusion partners. Here we describe two IMTs with a novel ALK fusion that involves the Ran-binding protein 2 (RANBP2) gene at 2q13, which normally encodes a large (358-kDa) nucleopore protein localized at the cytoplasmic side of the nuclear pore complex. The N-terminal 867 residues of RANBP2 are fused to the cytoplasmic segment of ALK in the 1,430,amino acid RANBP2-ALK chimeric protein. Myofibroblasts that express RANBP2-ALK exhibit nuclear membrane-associated ALK staining that is unique compared to the subcellular localization observed with other ALK fusions in IMT, presumably attributable to heteroassociation of the fusion with normal RANBP2 at the nuclear pore. These findings expand the spectrum of ALK abnormalities observed in IMT and further confirm the clonal, neoplastic nature of these lesions. © 2003 Wiley-Liss, Inc. [source]

ULTRASTRUCTURE OF THE BASAL BODY COMPLEX AND PUTATIVE VESTIGIAL FEEDING APPARATUS IN PHACUS PLEURONECTES (EUGLENOPHYCEAE)

JOURNAL OF PHYCOLOGY, Issue 2001
Article first published online: 24 SEP 200
Shin, W.1, Boo, S. M.2, & Triemer, R. E.1 1Department of Life Science, Rutgers University, Piscataway, New Jersey 08854, USA; 2Department of Biology, Chungnam National University, Daejon 305-764, Korea Phacus pleuronectes (O. F. Müller) Dujardin is a phototrophic euglenoid with small discoid chloroplasts, a flat, rigid body, and longitudinally arranged pellicular strips. The flagellar apparatus consisted of two basal bodies and three flagellar roots typical of many phototrophic euglenoids, but also had a large striated fiber that connected the two basal bodies and associated with the ventral root. The three roots, in combination with the dorsal microtubular band, extended anteriorly and formed the major cytoskeletal elements supporting the reservoir membrane and ultimately the pellicle. A cytoplasmic pocket arose in the reservoir/canal transition region. It was supported by the ventral root and a C-shaped band of electron-opaque material that lined the cytoplasmic side of the pocket. A large striated fiber extended from this C-shaped band toward the reservoir membrane. The presence of striated fibers in the basal apparatus and associated with the microtubule reinforced pocket suggested that P. pleuronectes may be at the base of the Phacus lineage and may be more closely related to the phagotrophic euglenoids than to Phacus species which are ovoid in shape and have thicker pellicle strips. [source]

Tomographic reconstruction of treponemal cytoplasmic filaments reveals novel bridging and anchoring components

MOLECULAR MICROBIOLOGY, Issue 3 2004
Jacques Izard
Summary An understanding of the involvement of bacterial cytoplasmic filaments in cell division requires the elucidation of the structural organization of those filamentous structures. Treponemal cytoplasmic filaments are composed of one protein, CfpA, and have been demonstrated to be involved in cell division. In this study, we used electron tomography to show that the filaments are part of a complex with a novel molecular organization that includes at least two distinct features decorating the filaments. One set of components appears to anchor the filaments to the cytoplasmic membrane. The other set of components appears to bridge the cytoplasmic filaments on the cytoplasmic side, and to be involved in the interfilament spacing within the cell. The filaments occupy between 3 and 18% of the inner surface of the cytoplasmic membrane. These results reveal a novel filamentous molecular organization of independent filaments linked by bridges and continuously anchored to the membrane. [source]

Protein,Protein Interaction of a Pharaonis Halorhodopsin Mutant Forming a Complex with Pharaonis Halobacterial Transducer Protein II Detected by Fourier-Transform Infrared Spectroscopy,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008
Yuji Furutani
Pharaonis halorhodopsin (pHR) functions as a light-driven inward chloride ion pump in Natoronomonas pharaonis, while pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, pSRII), is a light sensor for negative phototaxis. ppR forms a 2:2 complex with its cognate transducer protein (pHtrII) through intramembranous hydrogen bonds: Tyr199ppR,Asn74pHtrII and Thr189ppR,Glu43 pHtrII, Ser62pHtrII. It was reported that a pHR mutant (P240T/F250Y), which possesses the hydrogen-bonding sites, impairs its pumping activity upon complexation with pHtrII. In this study, effect of the complexation with pHtrII on the structural changes upon formation of the K, L1 and L2 intermediates of pHR was investigated by use of Fourier-transform infrared spectroscopy. The vibrational changes of Tyr250pHR and Asn74pHtrII were detected for the L1 and L2 intermediates, supporting that Tyr250pHR forms a hydrogen bond with Asn74pHtrII as similarly to Tyr199ppR. The conformational changes of the retinal chromophore were never affected by complexation with pHtrII, but amide-I vibrations were clearly different in the absence and presence of pHtrII. The molecular environment around Asp156pHR in helix D is also slightly affected. These additional structural changes are probably related to blocking of translocation of a chloride ion from the extracellular to the cytoplasmic side during the photocycle. [source]

A Role for Internal Water Molecules in Proton Affinity Changes in the Schiff Base and Asp85 for One-way Proton Transfer in Bacteriorhodopsin,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008
Joel E. Morgan
Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M. [source]

Slicing a protease: Structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains

PROTEIN SCIENCE, Issue 8 2006
Tatyana V. Rotanova
Abstract ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA+ superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure,function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA+ domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases. [source]