scholarly journals The binding site for ribosomal protein S8 in 16S rRNA andspcmRNA fromEscherichia coli: minimum structural requirements and the effects of single bulged bases on S8 — RNA interaction

1994 ◽  
Vol 22 (9) ◽  
pp. 1687-1695 ◽  
Author(s):  
Herren Wu ◽  
Lihong Jiang ◽  
Robert A. Zimmermann
Keyword(s):  
16S Rrna ◽  
Ribosomal Protein ◽  
Binding Site ◽  
Structural Requirements ◽  
Fromescherichia Coli ◽  
Rna Interaction

Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition

1993 ◽  
Vol 215 (3) ◽  
pp. 787-792 ◽  
Author(s):  
Marylene MOUGEL ◽  
Christine ALLMANG ◽  
Flore EYERMANN ◽  
Claire CACHIA ◽  
Bernard EHRESMANN ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Ribosomal Protein ◽  
Binding Site

Dissection of the 16S rRNA binding site for ribosomal protein S4

1990 ◽  
Vol 1050 (1-3) ◽  
pp. 34-37 ◽  
Author(s):  
Amalia Sapag ◽  
Jailaxmi V. Vartikar ◽  
David E. Draper
Keyword(s):  
16S Rrna ◽  
Ribosomal Protein ◽  
Binding Site ◽  
Ribosomal Protein S4

Mutational and Structural Analysis of the RNA Binding Site for Escherichia coli Ribosomal Protein S7

1994 ◽  
Vol 244 (1) ◽  
pp. 74-85 ◽  
Author(s):  
François Dragon ◽  
Catherine Payant ◽  
Léa Brakier-Gingras
Keyword(s):  
Escherichia Coli ◽  
Structural Analysis ◽  
Ribosomal Protein ◽  
Binding Site ◽  
Rna Binding

scholarly journals Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Noa Katz ◽  
Eitamar Tripto ◽  
Naor Granik ◽  
Sarah Goldberg ◽  
Orna Atar ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Coat Proteins ◽  
Structural Determinants ◽  
Design Build ◽  
Machine Learning Approach ◽  
Successful Design ◽  
Experimental Findings ◽  
Rna Interaction

AbstractWe apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP. To verify our model and experimental findings, we design several non-repetitive binding site cassettes and validate their functionality in mammalian cells. We find that the binding of each CP to RNA is characterized by a unique space of sequence and structural determinants, thus providing a more complete description of CP-RNA interaction as compared with previous low-throughput findings. Finally, based on the binding spaces we demonstrate a computational tool for the successful design and rapid synthesis of functional non-repetitive binding-site cassettes.

Mutant Ribosomal Protein with Defective RNA Binding Site

1971 ◽  
Vol 234 (52) ◽  
pp. 273-275 ◽  
Author(s):  
M. GREEN ◽  
C. G. KURLAND
Keyword(s):  
Ribosomal Protein ◽  
Binding Site ◽  
Rna Binding ◽  
Defective Rna
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