Abstract：
:Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function of these non-coding RNAs. As demonstrated for protein antigens, specific antibodies may aid in RNA crystal structure elucidation or the development of diagnostic tools and therapeutic drugs targeting disease-causing RNAs. Recent success and limitation of RNA antibody development has made it imperative to generate an effective antibody library specifically targeting RNA molecules. Adopting the reduced chemical diversity design and further restricting the interface diversity to tyrosines, serines, glycines, and arginines only, we have constructed a RNA-targeting Fab library. Phage display selection and downstream characterization showed that this library yielded high-affinity Fabs for all three RNA targets tested. Using a quantitative specificity assay, we found that these Fabs are highly specific, possibly due to the alternate codon design we used to avoid consecutive arginines in the Fab interface. In addition, the effectiveness of the minimal Fab library may challenge our view of the protein-RNA binding interface and provide a unique solution for future design of RNA-binding proteins.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Sherman EM,Holmes S,Ye JDdoi
10.1016/j.jmb.2014.03.003subject
Has Abstractpub_date
2014-05-15 00:00:00pages
2145-57issue
10eissn
0022-2836issn
1089-8638pii
S0022-2836(14)00127-2journal_volume
426pub_type
杂志文章abstract：:Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells co...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2013.09.020
更新日期：2013-11-29 00:00:00
abstract：:The human alternative splicing factor ASF/SF2, an SR (serine-arginine-rich) protein involved in mRNA splicing control, is activated by the multisite phosphorylation of its C-terminal RS domain, a segment containing numerous arginine-serine dipeptide repeats. The protein kinase responsible for this modification, SR-spe...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.08.029
更新日期：2008-02-08 00:00:00
abstract：:The two opponents, toxin (CcdB, LetB or LetD, protein G, LynB) and antidote (CcdA, LetA, protein H, LynA), in the plasmid addiction system ccd of the F plasmid were studied by different biophysical methods. The thermodynamic stability was measured at different temperatures combining denaturant and thermally induced un...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3815
更新日期：2000-06-23 00:00:00
abstract：:The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructu...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.05.058
更新日期：2009-07-17 00:00:00
abstract：:A gene encoding a major entomocidal polypeptide from Bacillus thuringiensis subspecies kyushuensis delta-endotoxin crystals (CytB) was cloned into Escherichia coli and sequenced. The deduced amino acid sequence gave a predicted molecular mass of 29,236 Da and showed 39% identity and 70% similarity with the 27,371 Da C...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1037
更新日期：1993-01-20 00:00:00
abstract：:The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel beta-sheet...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.05.028
更新日期：2010-07-30 00:00:00
abstract：:We have previously identified 20 different fusidic acid-resistant alleles of fusA, encoding mutant forms of the ribosomal translocase EF-G. One of these, P413L, is used here as the starting point in selections for internal revertants, identifying 20 different pseudo-wild-type forms of EF-G. We have also identified two...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0259
更新日期：1996-05-10 00:00:00
abstract：:The movement of the bacterial insertion sequence IS1 often generates cointegrate structures in which donor and target replicons are connected by direct repeats of IS1. The experiments reported here were designed to understand how IS1 transposition is controlled. Our physical characterization of the structures of coint...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90337-1
更新日期：1984-04-05 00:00:00
abstract：:Aminoacyl-tRNA synthetases are responsible for attaching amino acid residues to the tRNA 3'-end. The two classes of synthetases approach tRNA as mirror images, with opposite but symmetrical stereochemistries that allow the class I enzymes to attach amino acid residues to the 2'-hydroxyl group of the terminal ribose, w...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.02.023
更新日期：2005-05-06 00:00:00
abstract：:The secondary structure of bacterial RNase P RNA, a ribozyme responsible for the maturation of the 5' end of tRNAs, is well established on the basis of sequence comparison analysis. RNase P RNA secondary structures fall into two types, A and B, which share a common core formed by the assembly of two main folding domai...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.1797
更新日期：1998-06-19 00:00:00
abstract：:As the receptor on the platelet surface for von Willebrand factor, glycoprotein (GP) Ib-IX complex is critically involved in hemostasis and thrombosis. How the complex is assembled from GP Ibalpha, GP Ib beta and GP IX subunits, all of which are type I transmembrane proteins, is not entirely clear. Genetic and mutatio...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2008.07.037
更新日期：2008-10-03 00:00:00
abstract：:The crystal structure of the ferredoxin:NADP+ reductase (FNR) from the cyanobacterium Anabaena PCC 7119 has been determined at 2.6 A resolution by multiple isomorphous replacement and refined using 15.0 A to 1.8 A data, collected at 4 degrees C, to an R-factor of 0.172. The model includes 303 residues, the flavin aden...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0553
更新日期：1996-10-18 00:00:00
abstract：:Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesiz...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.07.001
更新日期：2020-08-07 00:00:00
abstract：:Vinculin is a key regulator of the actin cytoskeleton attachment to the cell membrane at cellular adhesion sites, which is crucial for processes such as cell motility and migration, development, survival, and wound healing. Vinculin loss results in embryonic lethality, cardiovascular diseases, and cancer. Its tail dom...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2012.06.015
更新日期：2012-10-05 00:00:00
abstract：:The transforms of a large number of models of deoxygenated sickle hemoglobin fibers, related to that derived from image reconstruction of electron micrographs, have been calculated and compared with X-ray diffraction data of 15 A resolution. The model of the fiber, determined from the reconstructed image, is a helix c...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(85)90172-x
更新日期：1985-06-25 00:00:00
abstract：:Proteolysis of rat liver chromatin by the Arg-C peptidase, clostripain, is characterized by a progressive fragmentation of the N-terminal segments of the four core histones H2A, H2B, H3 and H4, until a well-defined limit digest is reached. This work addresses the case of histone H4. Two intermediate proteolytic sites ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1629
更新日期：1994-10-14 00:00:00
abstract：:The late genes of bacteriophage P2 are clustered into four transcription units. We have reported the transcription initiation sites for two of the late messenger RNAs, encoding genes QP and ONMLKRS. We have now located the 5' ends of the two remaining late mRNAs. The first gene in the VJHG transcription unit has been ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(85)90226-8
更新日期：1985-02-05 00:00:00
abstract：:The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be r...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(83)80093-x
更新日期：1983-05-25 00:00:00
abstract：:Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule move together. Previous work has shown that this domain closure involves two hinges. Using the newly refined structure of the open form, the structural mechanism underlying this motion is analyzed here i...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1592
更新日期：1993-11-20 00:00:00
abstract：:ETV6 (or TEL), a transcriptional repressor belonging to the ETS family, is frequently involved in chromosomal translocations linked with human cancers. It displays a DNA-binding mode distinct from other ETS proteins due to the presence of a self-associating PNT domain. In this study, we used NMR spectroscopy to dissec...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2012.05.010
更新日期：2012-08-03 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：:Transverse sections (100 to 140 nm thick) of the flight muscles of the fleshfly Phormia terrae-novae and the housefly Musca domestica were studied. The images of 56 tubular myosin filaments of the fleshfly and 62 filaments of the housefly were digitized and computer processed by rotational averaging. The rotational po...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(88)90637-7
更新日期：1988-06-05 00:00:00
abstract：:The nuclear receptors peroxisome proliferator-activated receptors (PPARs) are known for their critical role in the metabolic syndrome. Here, we show that they are direct regulators of the family of pyruvate dehydrogenase kinase (PDK) genes, whose products act as metabolic homeostats in sensing hunger and satiety level...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.06.091
更新日期：2007-09-14 00:00:00
abstract：:We describe a selection procedure for construction of very high affinity variants of human growth hormone (hGH) for binding to the extra cellular domain of its receptor (called the hGHbp). Five different libraries of mutated hGH genes (each containing approximately 2 x 10(5) protein variants) were created by randomly ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1612
更新日期：1993-12-05 00:00:00
abstract：:We report a new vector, pEVOL, for the incorporation of unnatural amino acids into proteins in Escherichia coli using evolved Methanocaldococcus jannaschii aminoacyl-tRNA synthetase(s) (aaRS)/suppressor tRNA pairs. This new system affords higher yields of mutant proteins through the use of both constitutive and induci...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.10.030
更新日期：2010-01-15 00:00:00
abstract：:Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism. ...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2016.01.028
更新日期：2016-06-19 00:00:00
abstract：:Mutants of an archaeon Halobacterium halobium, resistant to the universal inhibitor of translation, pactamycin, were isolated. Pactamycin resistance correlated with the presence of mutations in the 16 S rRNA gene of H. halobium single rRNA operon. Three types of mutations were found in pactamycin resistant cells, A694...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1006/jmbi.1997.1387
更新日期：1997-11-21 00:00:00
abstract：:The amide proton exchange rates of Escherichia coli trp repressor have been measured through their effects on the longitudinal relaxation rates of the amide protons. Three types of exchange regimes have been observed: (1) slow exchange (on a minute/hour time-scale), measurable by isotope exchange, but not by relaxatio...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(05)80111-1
更新日期：1995-03-10 00:00:00
abstract：:A full length (25,000 base-pair) myosin heavy chain gene completely contained within a single cosmid clone was isolated from a Syrian hamster cosmid genomic library. Sequence comparison of the 3' untranslated region indicated the presence of a 75% homology with the rat embryonic myosin heavy chain gene. Extensive 5' f...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/0022-2836(91)90251-z
更新日期：1991-04-20 00:00:00
abstract：:In Xenopus somatic cells histone H1 effects the transcriptional repression of oocyte type 5 S RNA genes, without altering the transcription of the somatic type 5 S RNA genes. Using an unambiguous nucleosome mapping method we find substantial differences between the multiple in vitro nucleosome positions on the two typ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.2087
更新日期：1998-09-25 00:00:00
