scholarly journals Identifying Structural Determinants of High-Potency MDPV Binding at the Human Dopamine Transporter S1 Binding Site

2019 ◽  
Vol 116 (3) ◽  
pp. 557a-558a
Author(s):  
Tyler W.E. Steele ◽  
Brian Ruiz ◽  
Zachary Spires ◽  
Jose M. Eltit
1999 ◽  
Vol 42 (20) ◽  
pp. 4122-4128 ◽  
Author(s):  
Adam Q. Siddiqui ◽  
Christopher McGuigan ◽  
Carlo Ballatore ◽  
Fabio Zuccotto ◽  
Ian H. Gilbert ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Noa Katz ◽  
Eitamar Tripto ◽  
Naor Granik ◽  
Sarah Goldberg ◽  
Orna Atar ◽  
...  

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.


2013 ◽  
Vol 84 (1) ◽  
pp. 114-127 ◽  
Author(s):  
Kasper B. Hansen ◽  
Nami Tajima ◽  
Rune Risgaard ◽  
Riley E. Perszyk ◽  
Lars Jørgensen ◽  
...  

2002 ◽  
Vol 45 (19) ◽  
pp. 4110-4118 ◽  
Author(s):  
William J. Houlihan ◽  
Umer F. Ahmad ◽  
Judith Koletar ◽  
Lawrence Kelly ◽  
Leonard Brand ◽  
...  

2017 ◽  
Vol 292 (17) ◽  
pp. 7161-7161
Author(s):  
Yang Li ◽  
Felix P. Mayer ◽  
Peter S. Hasenhuetl ◽  
Verena Burtscher ◽  
Klaus Schicker ◽  
...  

2010 ◽  
Vol 16 (25) ◽  
pp. 2818-2836 ◽  
Author(s):  
Carles Galdeano ◽  
Elisabet Viayna ◽  
Pau Arroyo ◽  
Axel Bidon-Chanal ◽  
J. Ramon Blas ◽  
...  

2002 ◽  
Vol 45 (19) ◽  
pp. 4097-4109 ◽  
Author(s):  
William J. Houlihan ◽  
Lawrence Kelly ◽  
Jessica Pankuch ◽  
Judith Koletar ◽  
Leonard Brand ◽  
...  

1998 ◽  
Vol 37 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Antonio V Ferrer-Montiel ◽  
Jaime M Merino ◽  
Rosa Planells-Cases ◽  
William Sun ◽  
Mauricio Montal

2020 ◽  
Author(s):  
Shabareesh Pidathala ◽  
Aditya Kumar Mallela ◽  
Deepthi Joseph ◽  
Aravind Penmatsa

AbstractNorepinephrine is a biogenic amine neurotransmitter that has widespread effects on cardiovascular tone, alertness and sensation of pain. As a consequence, blockers of norepinephrine uptake have served as vital tools to treat depression and chronic pain. Here, we employ a modified Drosophila melanogaster dopamine transporter as a surrogate for the human norepinephrine transporter and determine the X-ray structures of the transporter in its substrate-free and norepinephrine-bound forms. We also report structures of the transporter in complex with inhibitors of chronic pain including duloxetine, milnacipran and a synthetic opioid, tramadol. When compared to dopamine, we observe that norepinephrine binds in a different pose, in the vicinity of subsite C within the primary binding site. Our experiments reveal that this region is the binding site for chronic pain inhibitors and a determinant for norepinephrine-specific reuptake inhibition, thereby providing a paradigm for the design of specific inhibitors for catecholamine neurotransmitter transporters.HighlightsX-ray structures of the Drosophila dopamine transporter in substrate-free and norepinephrine bound forms.Norepinephrine and dopamine bind in distinct conformations within the binding pocket.Chronic pain inhibitors S-duloxetine, milnacipran and tramadol bind in the primary binding site and overlap with the norepinephrine-binding pose.Selective norepinephrine reuptake inhibition occurs through specific interactions at the subsite C in the primary binding pocket.


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