Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis

2017 ◽  
Vol 12 (5) ◽  
pp. 1397-1415 ◽  
Author(s):  
Chris Rechlin ◽  
Frithjof Scheer ◽  
Felix Terwesten ◽  
Tobias Wulsdorf ◽  
Ewa Pol ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Aldose Reductase ◽  
Computational Analysis

scholarly journals Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis

2019 ◽  
Vol 63 (4) ◽  
pp. 1528-1543 ◽  
Author(s):  
Mathieu Rappas ◽  
Ammar A. E. Ali ◽  
Kirstie A. Bennett ◽  
Jason D. Brown ◽  
Sarah J. Bucknell ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Computational Analysis ◽  
Binding Modes ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0161894 ◽  
Author(s):  
Cuong The Nguyen ◽  
Kiwamu Tanaka ◽  
Yangrong Cao ◽  
Sung-Hwan Cho ◽  
Dong Xu ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Computational Analysis ◽  
Extracellular Atp ◽  
Ligand Binding Site

scholarly journals Crystal packing modifies ligand binding affinity: The case of aldose reductase

2012 ◽  
Vol 80 (11) ◽  
pp. 2552-2561 ◽  
Author(s):  
Alexandra Cousido-Siah ◽  
Tatiana Petrova ◽  
Isabelle Hazemann ◽  
André Mitschler ◽  
Francesc X. Ruiz ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Aldose Reductase ◽  
Crystal Packing

Computational analysis of the structural basis of ligand binding to the crustacean retinoid X receptor

2010 ◽  
Vol 5 (4) ◽  
pp. 317-324 ◽  
Author(s):  
G. Purna Chandra Nagaraju ◽  
G.L.V. Prasad ◽  
L. Taliaferro-Smith ◽  
B.V. Aruna ◽  
B. Reddya Naik ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Computational Analysis ◽  
Retinoid X Receptor ◽  
Structural Basis

scholarly journals Selective Phenome Growth Adapted NK Model: A Novel Landscape to Represent Aptamer Ligand Binding

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Andrew Brian Kinghorn ◽  
Julian Alexander Tanner
Keyword(s):  
Ligand Binding ◽  
Microarray Data ◽  
Computational Analysis ◽  
Selection Process ◽  
Theoretical Models ◽  
Fitness Landscapes ◽  
New Approach ◽  
Aptamer Selection ◽  
Interaction Map ◽  
Target Binding

Aptamers are single-stranded oligonucleotides selected by evolutionary approaches from massive libraries with significant potential for specific molecular recognition in diagnostics and therapeutics. A complete empirical characterisation of an aptamer selection experiment is not feasible due to the vast complexity of aptamer selection. Simulation of aptamer selection has been used to characterise and optimise the selection process; however, the absence of a good model for aptamer-target binding limits this field of study. Here, we generate theoretical fitness landscapes which appear to more accurately represent aptamer-target binding. The method used to generate these landscapes, selective phenome growth, is a new approach in which phenotypic contributors are added to a genotype/phenotype interaction map sequentially in such a way so as to increase the fitness of a selected fit sequence. In this way, a landscape is built around the selected fittest sequences. Comparison to empirical aptamer microarray data shows that our theoretical fitness landscapes more accurately represent aptamer ligand binding than other theoretical models. These improved fitness landscapes have potential for the computational analysis and optimisation of other complex systems.

An Integrated Computational Analysis of the Structure, Dynamics, and Ligand Binding Interactions of the Human Galectin Network

2011 ◽  
Vol 51 (8) ◽  
pp. 1918-1930 ◽  
Author(s):  
Carlos M. A. Guardia ◽  
Diego F. Gauto ◽  
Santiago Di Lella ◽  
Gabriel A. Rabinovich ◽  
Marcelo A. Martí ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Computational Analysis ◽  
Binding Interactions ◽  
Structure Dynamics

scholarly journals Structural basis for Na+-sensitivity in dopamine D2 and D3 receptors

2015 ◽  
Vol 51 (41) ◽  
pp. 8618-8621 ◽  
Author(s):  
Mayako Michino ◽  
R. Benjamin Free ◽  
Trevor B. Doyle ◽  
David R. Sibley ◽  
Lei Shi
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Computational Analysis ◽  
Structural Basis ◽  
Ligand Binding Site ◽  
Binding Assays ◽  
D3 Receptors ◽  
Dopamine D2 ◽  
The Impact

To understand the structural basis for the Na+-sensitivity of ligand binding to dopamine D2-like receptors, using computational analysis in combination with binding assays, we identified interactions critical in propagating the impact of Na+on receptor conformations and on the ligand-binding site.

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