Abstract：
:Small RNAs were selected from a highly degenerate library on the basis of their ability to bind tightly to Escherichia coli phenylalanyl-tRNA synthetase (FRS). The 63 nucleotide library consisted of the acceptor stem and portions of the D and T stems of E. coli tRNA(Phe) flanking a 32 nucleotide randomized region. Because FRS binding relies on a correctly folded tRNA substrate, the selected variants from this library were expected to resemble tRNA(Phe) structure. After seven cycles of selection, the RNA library bound to FRS with similar affinity to that of the E. coli tRNA(Phe), but did not show detectable aminoacylation. Fourteen FRS-specific isolates were sequenced and found to contain an anticodon stem-loop including the anticodon triplet of tRNA(Phe). The tight-binding RNAs fell into two classes depending on the location of this step-loop within the sequence. The acceptor stem defined by the non-randomized sequence was also found to be essential for binding. Mutation of two residues within a common hexanucleotide sequence present in one of the classes reduced binding to FRS. Taken together, these results suggest that in order to bind RNAs tightly, FRS requires the simultaneous interaction of the anticodon stem-loop and acceptor stem, and additional sequences needed for proper folding. This approach should assist in the detection of motifs that resemble tRNA, but are too dissimilar to be identified by sequence comparison.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Peterson ET,Pan T,Coleman J,Uhlenbeck OCdoi
10.1006/jmbi.1994.1571subject
Has Abstractpub_date
1994-09-23 00:00:00pages
186-92issue
3eissn
0022-2836issn
1089-8638pii
S0022-2836(84)71571-3journal_volume
242pub_type
杂志文章abstract：:alpha-Synuclein is an intrinsically disordered protein that appears in aggregated forms in the brains of patients with Parkinson's disease. The conversion from monomer to aggregate is complex, and aggregation rates are sensitive to changes in amino acid sequence and environmental conditions. It has previously been obs...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.06.063
更新日期：2009-08-28 00:00:00
abstract：:An essential step in the replication cycle of all retroviruses is the dimerization of genomic RNA prior to or during encapsidation and budding. In HIV-1, a stem-loop structure in the genomic RNA called the dimerization initiation site, or DIS, has been well characterized. However, the identification of the structure(s...
journal_title：Journal of molecular biology
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更新日期：2002-06-07 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0656
更新日期：1996-12-06 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0487
更新日期：1996-09-06 00:00:00
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pub_type： 杂志文章
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2001-02-09 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2002-05-03 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
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更新日期：2019-04-19 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0297
更新日期：1996-05-31 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3712
更新日期：2000-05-19 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1655
更新日期：1993-12-20 00:00:00
abstract：:Low dose electron diffraction and imaging techniques have been applied to the study of the crystalline structure of gp32*I, a DNA helix destabilizing protein derived from bacteriophage T4 gene 32 protein. A quantitative analysis of intensities from electron diffraction patterns from tilted, multilayered gp32*I crystal...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(83)80182-x
更新日期：1983-09-05 00:00:00
abstract：:The structure of empty canine parvovirus capsids shows that residues 37 to the carboxy-terminal residue 584 (VP2 numbering) are ordered in each of the 60 subunits. The central structural motif of each subunit is the eight-stranded antiparallel beta-barrel that has been found in many other virus structures. Five beta-h...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1502
更新日期：1993-09-20 00:00:00
abstract：:The main regulator of pIP501 replication is an antisense RNA (RNAIII) that induces transcriptional attenuation of the essential RNAII. Previous studies identified the termination point in vivo and demonstrated attenuation in vitro. This in vivo analysis confirms the appearance of attenuated RNAII dependent on RNAIII. ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0023
更新日期：1996-01-19 00:00:00
abstract：:The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2012.01.041
更新日期：2012-04-06 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.06.074
更新日期：2004-08-20 00:00:00
abstract：:Islet amyloid polypeptide (IAPP) forms fibrillar amyloid deposits in the pancreatic islets of Langerhans of patients with type 2 diabetes mellitus, and its misfolding and aggregation are thought to contribute to beta-cell death. Increasing evidence suggests that IAPP fibrillization is strongly influenced by lipid memb...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.11.077
更新日期：2008-02-08 00:00:00
abstract：:Sho1p, an integral membrane protein, plays a vital role in the high-osmolarity glycerol (HOG) mitogen-activated protein kinase pathway in the yeast Saccharomyces cerevisiae. Activated under conditions of high osmotic stress, it interacts with other HOG pathway proteins to mediate cell signaling events, ensuring that y...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2015.01.016
更新日期：2015-06-05 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.06.008
更新日期：2004-07-30 00:00:00
abstract：:A membrane-independent morphogenetic viral signal peptide is identified within bacteriophage T4 internal protein III (IPIII). Utilizing a phagederived expression-packaging-processing system, which packages foreign proteins fused with IPIII into the phage capsid, a synthetic cleavage site introduced at the C terminus o...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0470
更新日期：1996-08-23 00:00:00
abstract：:A monoclonal antibody (MF5), capable of recognizing a divalent cation-induced conformational change in myosin light chain 2 (LC2f), has been used to screen a cDNA library constructed in the expression vector lambda gt11. A clone has been isolated that contains the whole coding sequence of this myosin subunit. The ligh...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(85)90229-3
更新日期：1985-02-05 00:00:00
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journal_title：Journal of molecular biology
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更新日期：2015-10-09 00:00:00
abstract：:A novel interrupted gene motif has been reported in which a 50-nucleotide insertion into bacteriophage T4 gene 60 appears to be present in the message at the time of translation, yet it is not translated. We present here a dynamic model for how translation may be occurring in the neighborhood of the interruption. The ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/S0022-2836(05)80177-9
更新日期：1990-05-20 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2010-04-30 00:00:00
abstract：:Promiscuous mutant EcoRI endonucleases produce lethal to sublethal effects because they cleave Escherichia coli DNA despite the presence of the EcoRI methylase. Three promiscuous mutant forms, Ala138Thr, Glu192Lys and His114Tyr, have been characterized with respect to their binding affinities and first-order cleavage ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.02.051
更新日期：2005-04-29 00:00:00
abstract：:The structure of tomato bushy stunt virus has been determined crystallographically to 2.9 A resolution. Details are presented of both the molecular structure and the methods by which it has been solved. The icosahedrally symmetric viral shell is composed of 180 protein subunits (Mr 43,000), with three similar but dist...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(83)80314-3
更新日期：1983-11-25 00:00:00
abstract：:Six different hybrid colicins were constructed by recombining various domains of the two pore-forming colicins A and E1. These hybrid colicins were purified and their properties were studied. All of them were active against sensitive cells, although to varying degrees. From the results, one can conclude that: (1) the ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90747-t
更新日期：1991-02-05 00:00:00
abstract：:Gram-negative bacteria have developed several different transport systems for solute uptake. One of these, the tripartite ATP independent periplasmic transport system (TRAP-T), makes use of an extracytoplasmic solute receptor (ESR) which captures specific solutes with high affinity and transfers them to their partner ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.04.047
更新日期：2007-06-29 00:00:00
abstract：:Enzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes were previously shown to induce only a weak conservation gradient, a com...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2019.07.019
更新日期：2019-09-06 00:00:00
abstract：:Adenoviruses are respiratory, ocular and enteric pathogens that form complex capsids, which are assembled from seven different structural proteins and composed of several core proteins that closely interact with the packaged dsDNA genome. The recent near-atomic resolution structures revealed that the interlacing conti...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2017.06.025
更新日期：2017-09-01 00:00:00
