scholarly journals Non-gradient, Sequential Algorithm for Simulation of Nascent Polypeptide Folding

2005 ◽  
pp. 766-774 ◽  
Author(s):  
Lech Znamirowski
Keyword(s):  
Sequential Algorithm ◽  
Nascent Polypeptide ◽  
Polypeptide Folding

scholarly journals Concerted Action of the Ribosome and the Associated Chaperone Trigger Factor Confines Nascent Polypeptide Folding

2012 ◽  
Vol 48 (1) ◽  
pp. 63-74 ◽  
Author(s):  
Anja Hoffmann ◽  
Annemarie H. Becker ◽  
Beate Zachmann-Brand ◽  
Elke Deuerling ◽  
Bernd Bukau ◽  
...  
Keyword(s):  
Trigger Factor ◽  
Concerted Action ◽  
Nascent Polypeptide ◽  
Polypeptide Folding

Sequential algorithm for channel equalisation employing a stack

1976 ◽  
Vol 12 (18) ◽  
pp. 468
Author(s):  
J. Gordon ◽  
N. Montague
Keyword(s):  
Sequential Algorithm

scholarly journals Membrane Topogenesis of a Type I Signal-Anchor Protein, Mouse Synaptotagmin Ii, on the Endoplasmic Reticulum

2000 ◽  
Vol 150 (4) ◽  
pp. 719-730 ◽  
Author(s):  
Yuichiro Kida ◽  
Masao Sakaguchi ◽  
Mitsunori Fukuda ◽  
Katsuhiko Mikoshiba ◽  
Katsuyoshi Mihara
Keyword(s):  
Endoplasmic Reticulum ◽  
Endoplasmic Reticulum Membrane ◽  
Type I ◽  
Hydrophobic Region ◽  
Anchor Protein ◽  
Nascent Polypeptide ◽  
Charged Residues ◽  
Er Targeting ◽  
Signal Anchor ◽  
Positively Charged

Synaptotagmin II is a type I signal-anchor protein, in which the NH2-terminal domain of 60 residues (N-domain) is located within the lumenal space of the membrane and the following hydrophobic region (H-region) shows transmembrane topology. We explored the early steps of cotranslational integration of this molecule on the endoplasmic reticulum membrane and demonstrated the following: (a) The translocation of the N-domain occurs immediately after the H-region and the successive positively charged residues emerge from the ribosome. (b) Positively charged residues that follow the H-region are essential for maintaining the correct topology. (c) It is possible to dissect the lengths of the nascent polypeptide chains which are required for ER targeting of the ribosome and for translocation of the N-domain, thereby demonstrating that different nascent polypeptide chain lengths are required for membrane targeting and N-domain translocation. (d) The H-region is sufficiently long for membrane integration. (e) Proline residues preceding H-region are critical for N-domain translocation, but not for ER targeting. The proline can be replaced with amino acid with low helical propensity.

OPTIMAL TREE RANKING IS IN $\mathcal{NC}$

1992 ◽  
Vol 02 (01) ◽  
pp. 31-41 ◽  
Author(s):  
PILAR DE LA TORRE ◽  
RAYMOND GREENLAW ◽  
TERESA M. PRZYTYCKA
Keyword(s):  
General Problem ◽  
Sequential Algorithm ◽  
Natural Numbers ◽  
Ranking Problem ◽  
Crew Pram ◽  
Optimal Tree ◽  
Optimal Ranking

This paper places the optimal tree ranking problem in [Formula: see text]. A ranking is a labeling of the nodes with natural numbers such that if nodes u and v have the same label then there exists another node with a greater label on the path between them. An optimal ranking is a ranking in which the largest label assigned to any node is as small as possible among all rankings. An O(n) sequential algorithm is known. Researchers have speculated that this problem is P-complete. We show that for an n-node tree, one can compute an optimal ranking in O( log n) time using n2/ log n CREW PRAM processors. In fact, our ranking is super critical in that the label assigned to each node is absolutely as small as possible. We achieve these results by showing that a more general problem, which we call the super critical numbering problem, is in [Formula: see text]. No [Formula: see text] algorithm for the super critical tree ranking problem, approximate or otherwise, was previously known; the only known [Formula: see text] algorithm for optimal tree ranking was an approximate one.

scholarly journals Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

2010 ◽  
Vol 1 (4) ◽  
pp. 406-416 ◽  
Author(s):  
Lanfeng Wang ◽  
Wenchi Zhang ◽  
Lu Wang ◽  
Xuejun C. Zhang ◽  
Xuemei Li ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Nascent Polypeptide

The destabilizing elements in the coding region of c-fos mRNA are recognized as RNA

1993 ◽  
Vol 13 (8) ◽  
pp. 5034-5042
Author(s):  
C L Wellington ◽  
M E Greenberg ◽  
J G Belasco
Keyword(s):  
Codon Usage ◽  
Mammalian Cells ◽  
Mrna Decay ◽  
Polypeptide Chain ◽  
Coding Region ◽  
Protein Coding ◽  
Present Evidence ◽  
Reading Frame ◽  
Nascent Polypeptide

The protein-coding region of the c-fos proto-oncogene transcript contains elements that direct the rapid deadenylation and decay of this mRNA in mammalian cells. The function of these coding region instability determinants requires movement of ribosomes across mRNAs containing them. Three types of mechanisms could account for this translational requirement. Two of these possibilities, (i) that rapid mRNA decay might be mediated by the nascent polypeptide chain and (ii) that it might result from an unusual codon usage, have experimental precedent. Here, we present evidence that the destabilizing elements in the c-fos coding region are not recognized in either of these two ways. Instead, the ability of the c-fos coding region to function as a potent mRNA destabilizer when translated in the +1 reading frame indicates that the signals for rapid deadenylation and decay reside in the sequence or structure of the RNA comprising this c-fos domain.

Evidence for a nuclear passage of nascent polypeptide-associated complex subunits in yeast

2001 ◽  
Vol 114 (14) ◽  
pp. 2641-2648
Author(s):  
Jacqueline Franke ◽  
Barbara Reimann ◽  
Enno Hartmann ◽  
Matthias Köhler ◽  
Brigitte Wiedmann
Keyword(s):  
Transcriptional Regulation ◽  
Steady State ◽  
Fluorescence Microscopy ◽  
Nuclear Import ◽  
Cell Fractionation ◽  
Active Process ◽  
Ribosomal Subunits ◽  
State Equilibrium ◽  
Nascent Polypeptide ◽  
Ribosome Binding

The nascent polypeptide-associated complex (NAC) has been found quantitatively associated with ribosomes in the cytosol by means of cell fractionation or fluorescence microscopy. There have been reports, however, that single NAC subunits may be involved in transcriptional regulation. We reasoned that the cytosolic location might only reflect a steady state equilibrium and therefore investigated the yeast NAC proteins for their ability to enter the nucleus. We found that single subunits of yeast NAC can indeed be transported into the nucleus and that this transport is an active process depending on different nuclear import factors. Translocation into the nucleus was only observed when binding to ribosomes was inhibited. We identified a domain of the ribosome-binding NAC subunit essential for nuclear import via the importin Kap123p/Pse1p-dependent import route. We hypothesize that newly translated NAC proteins travel into the nucleus to bind stoichiometrically to ribosomal subunits and then leave the nucleus together with these subunits to concentrate in the cytosol.

A sequential algorithm for the universal coding of finite memory sources

1992 ◽  
Vol 38 (3) ◽  
pp. 1002-1014 ◽  
Author(s):  
M.J. Weinberger ◽  
A. Lempe ◽  
J. Ziv
Keyword(s):  
Sequential Algorithm ◽  
Universal Coding ◽  
Finite Memory
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