Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pKa calculations

2001 ◽  
Vol 43 (4) ◽  
pp. 403-412 ◽  
Author(s):  
Jens E. Nielsen ◽  
Gerrit Vriend
Keyword(s):  
Hydrogen Bond ◽  
Boltzmann Equation ◽  
Hydrogen Bond Network ◽  
Pka Calculations ◽  
Poisson Boltzmann ◽  
Bond Network ◽  
Poisson Boltzmann Equation

scholarly journals Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel

2018 ◽  
Vol 115 (52) ◽  
pp. E12172-E12181 ◽  
Author(s):  
Haidai Hu ◽  
Kenichi Ataka ◽  
Anaïs Menny ◽  
Zaineb Fourati ◽  
Ludovic Sauguet ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Ion Channel ◽  
Transmembrane Domain ◽  
Hydrogen Bond Network ◽  
Transmembrane Region ◽  
Allosteric Site ◽  
Closed Channel ◽  
Open Conformation ◽  
Poisson Boltzmann ◽  
Bond Network

The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure–function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking. We used an electrostatics-based (finite difference Poisson–Boltzmann/Debye–Hückel) method to predict the acidities of all aspartic and glutamic residues in GLIC, both in its active and closed-channel states. Those residues with a predicted pKa close to the experimental pH50 were individually replaced by alanine and the resulting variant receptors were titrated by ATR/FTIR spectroscopy. E35, located in front of loop F far away from the orthosteric site, appears as the key proton sensor with a measured individual pKa at 5.8. In the GLIC open conformation, E35 is connected through a water-mediated hydrogen-bond network first to the highly conserved electrostatic triad R192-D122-D32 and then to Y197-Y119-K248, both located at the extracellular domain–transmembrane domain interface. The second triad controls a cluster of hydrophobic side chains from the M2-M3 loop that is remodeled during the gating transition. We solved 12 crystal structures of GLIC mutants, 6 of them being trapped in an agonist-bound but nonconductive conformation. Combined with previous data, this reveals two branches of a continuous network originating from E35 that reach, independently, the middle transmembrane region of two adjacent subunits. We conclude that GLIC’s gating proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site.

Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

2021 ◽  
pp. 120431
Author(s):  
Akinori Honda ◽  
Shunta Kakihara ◽  
Shuhei Ichimura ◽  
Kazuaki Tomono ◽  
Mina Matsushita ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Kinetics ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Kinetics Of

scholarly journals Hydrogen‐Bond Network Determines the Early Photoisomerization of Cph1 and AnPixJ Phytochromes

2021 ◽  
Author(s):  
Xiang-Yang Liu ◽  
Teng-Shuo Zhang ◽  
Qiu Fang ◽  
Wei-Hai Fang ◽  
Leticia González ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Monte Carlo methods for linear and non-linear Poisson-Boltzmann equation

2015 ◽  
Vol 48 ◽  
pp. 420-446 ◽  
Author(s):  
Mireille Bossy ◽  
Nicolas Champagnat ◽  
Hélène Leman ◽  
Sylvain Maire ◽  
Laurent Violeau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Boltzmann Equation ◽  
Monte Carlo Methods ◽  
Non Linear ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation
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