Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain11Edited by P. E. Wright

2001 ◽  
Vol 306 (1) ◽  
pp. 97-108 ◽  
Author(s):  
Jing-Song Fan ◽  
Qiang Zhang ◽  
Hidehito Tochio ◽  
Ming Li ◽  
Mingjie Zhang
Keyword(s):  
Target Recognition ◽  
Structural Basis ◽  
Sequence Dependent

scholarly journals Crystal Structure of GRIP1 PDZ6-Peptide Complex Reveals the Structural Basis for Class II PDZ Target Recognition and PDZ Domain-mediated Multimerization

2002 ◽  
Vol 278 (10) ◽  
pp. 8501-8507 ◽  
Author(s):  
Young Jun Im ◽  
Seong Ho Park ◽  
Seong-Hwan Rho ◽  
Jun Hyuck Lee ◽  
Gil Bu Kang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Target Recognition ◽  
Pdz Domain ◽  
Class Ii ◽  
Structural Basis ◽  
Peptide Complex

scholarly journals Structural basis for the sequence-dependent effects of platinum–DNA adducts

2009 ◽  
Vol 37 (8) ◽  
pp. 2434-2448 ◽  
Author(s):  
Srinivas Ramachandran ◽  
Brenda R. Temple ◽  
Stephen G. Chaney ◽  
Nikolay V. Dokholyan
Keyword(s):  
Dna Adducts ◽  
Structural Basis ◽  
Sequence Dependent

scholarly journals Structural basis for piRNA-targeting

2020 ◽  
Author(s):  
Todd A. Anzelon ◽  
Saikat Chowdhury ◽  
Siobhan M. Hughes ◽  
Yao Xiao ◽  
Gabriel C. Lander ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Target Recognition ◽  
Structural Basis ◽  
Seed Region ◽  
Active Conformation ◽  
Argonaute Proteins ◽  
Cellular Mrnas ◽  
Target Association ◽  
Animal Genomes

SummaryPiwi proteins use PIWI-interacting RNAs (piRNAs) to identify and silence the transposable elements (TEs) pervasively found in animal genomes. The Piwi targeting mechanism is proposed to be similar to targeting by Argonaute proteins, which employ microRNA (miRNA) guides to repress cellular mRNAs, but has not been characterized in detail. We present cryo-EM structures of a Piwi-piRNA complex with and without target RNAs and analysis of target recognition. Resembling Argonaute, Piwi identifies targets using the piRNA seed-region. However, Piwi creates a much weaker seed so that prolonged target association requires further piRNA-target pairing. Beyond the seed, Piwi creates wide central cleft wide for unencumbered piRNA-target pairing, enabling long-lived Piwi-piRNA-target interactions that are tolerant of mismatches. Piwi ensures targeting fidelity by blocking propagation of the piRNA-target duplex in the absence of faithful seed pairing, and by requiring extended piRNA-target pairing to reach an endonucleolytically active conformation. This mechanism allows Piwi to minimize off-targeting cellular mRNAs and adapt piRNA sequences to evolving genomic threats.

scholarly journals Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

2018 ◽  
Vol 46 (8) ◽  
pp. 4316-4324 ◽  
Author(s):  
Giedrius Sasnauskas ◽  
Kotryna Kauneckaitė ◽  
Virginijus Siksnys
Keyword(s):  
Target Recognition ◽  
Structural Basis ◽  
B3 Domain

Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition

1998 ◽  
Vol 5 (4) ◽  
pp. 317-325 ◽  
Author(s):  
Danette L. Daniels ◽  
Alexandra R. Cohen ◽  
James M. Anderson ◽  
Axel T. Brünger
Keyword(s):  
Crystal Structure ◽  
Target Recognition ◽  
Pdz Domain ◽  
Class Ii ◽  
Structural Basis

scholarly journals Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases

2006 ◽  
Vol 35 (2) ◽  
pp. 584-594 ◽  
Author(s):  
Y.-T. Wang ◽  
W.-J. Yang ◽  
C.-L. Li ◽  
L. G. Doudeva ◽  
H. S. Yuan
Keyword(s):  
Dna Cleavage ◽  
Structural Basis ◽  
Sequence Dependent

scholarly journals Beyond the seed: structural basis for supplementary microRNA targeting

2018 ◽  
Author(s):  
Jessica Sheu-Gruttadauria ◽  
Yao Xiao ◽  
Luca F. R. Gebert ◽  
Ian J. MacRae
Keyword(s):  
Mirna Target ◽  
Target Recognition ◽  
Structural Basis ◽  
Seed Region ◽  
Base Pairs ◽  
Argonaute Proteins ◽  
Target Rna ◽  
Mirna Seed ◽  
Mirna Targeting

AbstractmicroRNAs (miRNA) guide Argonaute proteins to mRNAs targeted for repression. Target recognition occurs primarily through the miRNA seed region, composed of guide (g) nucleotides g2–g8. However, nucleotides beyond the seed are also important for some known miRNA-target interactions. Here, we report the structure of human Argonaute2 (Ago2) engaged with a target RNA recognized through both miRNA seed and supplementary (g13–g16) regions. Ago2 creates a “supplementary chamber” that accommodates up to 5 miRNA-target base pairs. Seed and supplementary chambers are adjacent to each other, and can be bridged by an unstructured target loop of 1–15 nucleotides. Opening of the supplementary chamber may be constrained by tension in the miRNA 3' tail as increases in miRNA length stabilize supplementary interactions. Contrary to previous reports, we demonstrate optimal supplementary interactions can increase target affinity >20-fold. These results provide a mechanism for extended miRNA-targeting, suggest a function for 3' isomiRs in tuning miRNA targeting specificity, and indicate that supplementary interactions may contribute more to target recognition than is widely appreciated.

scholarly journals Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Zhu Liu ◽  
Zhou Gong ◽  
Wen-Xue Jiang ◽  
Ju Yang ◽  
Wen-Kai Zhu ◽  
...  
Keyword(s):  
Target Recognition ◽  
Conformational Space ◽  
Paramagnetic Nmr ◽  
Structural Basis ◽  
Binding Affinities ◽  
Recognition Mechanism ◽  
Ubiquitin Chain ◽  
Conformational Selection ◽  
Nmr Data ◽  
Covalently Linked

A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

scholarly journals Structural basis of target recognition by Atg8/LC3 during selective autophagy

2008 ◽  
Vol 13 (12) ◽  
pp. 1211-1218 ◽  
Author(s):  
Nobuo N. Noda ◽  
Hiroyuki Kumeta ◽  
Hitoshi Nakatogawa ◽  
Kenji Satoo ◽  
Wakana Adachi ◽  
...  
Keyword(s):  
Target Recognition ◽  
Structural Basis ◽  
Selective Autophagy
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