scholarly journals Atomistic Insight into the Role of Threonine 127 in the Functional Mechanism of Channelrhodopsin-2

2019 ◽  
Vol 9 (22) ◽  
pp. 4905 ◽  
Author(s):  
David Ehrenberg ◽  
Nils Krause ◽  
Mattia Saita ◽  
Christian Bamann ◽  
Rajiv K. Kar ◽  
...  
Keyword(s):  
Schiff Base ◽  
Absorption Maximum ◽  
Light Adaptation ◽  
Resonance Raman Spectroscopy ◽  
Proton Pumping ◽  
Hydroxyl Group ◽  
Visible Absorption ◽  
Dark Light ◽  
Hydrogen Bonded

Channelrhodopsins (ChRs) belong to the unique class of light-gated ion channels. The structure of channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) has been resolved, but the mechanistic link between light-induced isomerization of the chromophore retinal and channel gating remains elusive. Replacements of residues C128 and D156 (DC gate) resulted in drastic effects in channel closure. T127 is localized close to the retinal Schiff base and links the DC gate to the Schiff base. The homologous residue in bacteriorhodopsin (T89) has been shown to be crucial for the visible absorption maximum and dark–light adaptation, suggesting an interaction with the retinylidene chromophore, but the replacement had little effect on photocycle kinetics and proton pumping activity. Here, we show that the T127A and T127S variants of CrChR2 leave the visible absorption maximum unaffected. We inferred from hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and resonance Raman spectroscopy that the hydroxylic side chain of T127 is hydrogen-bonded to E123 and the latter is hydrogen-bonded to the retinal Schiff base. The C=N–H vibration of the Schiff base in the T127A variant was 1674 cm−1, the highest among all rhodopsins reported to date. We also found heterogeneity in the Schiff base ground state vibrational properties due to different rotamer conformations of E123. The photoreaction of T127A is characterized by a long-lived P2380 state during which the Schiff base is deprotonated. The conservative replacement of T127S hardly affected the photocycle kinetics. Thus, we inferred that the hydroxyl group at position 127 is part of the proton transfer pathway from D156 to the Schiff base during rise of the P3530 intermediate. This finding provides molecular reasons for the evolutionary conservation of the chemically homologous residues threonine, serine, and cysteine at this position in all channelrhodopsins known so far.

Theoretical Analysis of Hydrogen Bonding in the Active Site of Bovine Rhodopsin

2008 ◽  
Vol 59 (11) ◽  
Author(s):  
Ana-Nicoleta Bondar ◽  
Minoru Sugihara
Keyword(s):  
Schiff Base ◽  
Proton Transfer ◽  
Protein Structures ◽  
Binding Pocket ◽  
Transfer Path ◽  
Bovine Rhodopsin ◽  
Protein Amino Acids ◽  
Retinal Binding Pocket ◽  
Hydrogen Bonded

The retinal binding pocket of bovine rhodopsin contains an extended hydrogen-bonded network that involves protein amino acids and water molecules. The protonation state and the role of Glu181, which is part of the hydrogen-bonded network, have been debated. According to the counterion switch model, Glu181 is protonated in the rhodopsin state and it becomes negatively charged (and a counterion for the protonated retinal Schiff base) in Meta II, upon proton transfer to Glu113[24, 25]. In contrast, in the complex counterion model Glu181 is negatively charged in rhodopsin, and the role of counterion is gradually shifted from Glu113 to Glu181 during activation [13]. Here we perform computer simulations to examine the energetics of a putative proton transfer path from Glu181 to the counterion of the retinal Schiff base, Glu113, in the rhodopsin and bathorhodopsin intermediates. The calculated energy barriers and reaction energies are significant. This suggests that proton transfer from Glu181 to Glu113 is very unlikely in the rhodopsin and bathorohodopsin protein structures.

Insights into the Role of Hydroxyl Group on Carboxyl-modified MWCNTs in Accelerating Atenolol Removal by Fe(III)/H2O2 System

2021 ◽  
pp. 130581
Author(s):  
Shuai Shao ◽  
Gaobo Wang ◽  
Zhimin Gong ◽  
Mengjie Wang ◽  
Jianhua Hu ◽  
...  
Keyword(s):  
Hydroxyl Group ◽  
H2o2 System

scholarly journals The role of acid in the formation of hydrogen-bonded networks featuring 4,4′-dicarboxy-2,2′-bipyridine (H2dcbp): Synthesis, structural and magnetic characterisation of {[Cu(H2dcbp)Cl2]·H2O}2and [Cu(H2dcbp)(NO3)2(H2O)]

CrystEngComm ◽  
2005 ◽  
Vol 7 (13) ◽  
pp. 90-95 ◽  
Author(s):  
Eithne Tynan ◽  
Paul Jensen ◽  
Anthea C. Lees ◽  
Boujemaa Moubaraki ◽  
Keith S. Murray ◽  
...  
Keyword(s):  
Hydrogen Bonded

The Role of Hydroxyl Group Acidity on the Activity of Silica-Supported Secondary Amines for the Self-Condensation ofn-Butanal

ChemSusChem ◽  
2014 ◽  
Vol 8 (3) ◽  
pp. 466-472 ◽  
Author(s):  
Sankaranarayanapillai Shylesh ◽  
David Hanna ◽  
Joseph Gomes ◽  
Christian G. Canlas ◽  
Martin Head-Gordon ◽  
...  
Keyword(s):  
The Self ◽  
Secondary Amines ◽  
Hydroxyl Group

Synthesis and Characterizations of Nanocubes, Monodispersed Nanocrystals and Nanospheres of Au

2007 ◽  
Vol 353-358 ◽  
pp. 2163-2166
Author(s):  
Ming Yang ◽  
Guo Qing Zhou ◽  
Jiang Guo Zhao ◽  
Zhan Jun Li
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Powder Diffraction ◽  
Visible Absorption ◽  
X Ray ◽  
Transmission Electron ◽  
Uv Visible ◽  
Scherrer Formula ◽  
Visible Absorption Spectroscopy

Nanocubes, monodispersed nanocrystals and nanospheres of Au have been prepared by a simple reaction between HAuCl4·4H2O, NaOH and NH2OH·HCl in the presence of gelatin. The role of gelatin and the affection of pH in producing the nanoparticles of Au were discussed. The products were characterized by X-ray powder diffraction, transmission electron microscopy, and UV-visible absorption spectroscopy. The sizes of the monodispersed nanocrystals of Au were estimated by Debye-Scherrer formula according to XRD spectrum.

scholarly journals The Mechanism of the Tyrosine Transporter TyrP Supports a Proton Motive Tyrosine Decarboxylation Pathway in Lactobacillus brevis

2006 ◽  
Vol 188 (6) ◽  
pp. 2198-2206 ◽  
Author(s):  
Wout A. M. Wolken ◽  
Patrick M. Lucas ◽  
Aline Lonvaud-Funel ◽  
Juke S. Lolkema
Keyword(s):  
Phenyl Ring ◽  
Lactobacillus Brevis ◽  
Proton Motive Force ◽  
Proton Pumping ◽  
Hydroxyl Group ◽  
Transporter Gene ◽  
Tyrosine Decarboxylase ◽  
Rate Analysis ◽  
Substrate Analogues ◽  
Decarboxylation Reaction

ABSTRACT The tyrosine decarboxylase operon of Lactobacillus brevis IOEB9809 contains, adjacent to the tyrosine decarboxylase gene, a gene for TyrP, a putative tyrosine transporter. The two genes potentially form a proton motive tyrosine decarboxylation pathway. The putative tyrosine transporter gene of L. brevis was expressed in Lactococcus lactis and functionally characterized using right-side-out membranes. The transporter very efficiently catalyzes homologous tyrosine-tyrosine exchange and heterologous exchange between tyrosine and its decarboxylation product tyramine. Tyrosine-tyramine exchange was shown to be electrogenic. In addition to the exchange mode, the transporter catalyzes tyrosine uniport but at a much lower rate. Analysis of the substrate specificity of the transporter by use of a set of 19 different tyrosine substrate analogues showed that the main interactions between the protein and the substrates involve the amino group and the phenyl ring with the para hydroxyl group. The carboxylate group that is removed in the decarboxylation reaction does not seem to contribute to the affinity of the protein for the substrates significantly. The properties of the TyrP protein are those typical for precursor-product exchangers that operate in proton motive decarboxylation pathways. It is proposed that tyrosine decarboxylation in L. brevis results in proton motive force generation by an indirect proton pumping mechanism.

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