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FEBS Letters May 2010Mitochondrial uncoupling proteins (UCPs) are pure anion uniporters, which mediate fatty acid (FA) uniport leading to FA cycling. Protonated FAs then flip-flop back... (Review)
Review
Mitochondrial uncoupling proteins (UCPs) are pure anion uniporters, which mediate fatty acid (FA) uniport leading to FA cycling. Protonated FAs then flip-flop back across the lipid bilayer. An existence of pure proton channel in UCPs is excluded by the equivalent flux-voltage dependencies for uniport of FAs and halide anions, which are best described by the Eyring barrier variant with a single energy well in the middle of two peaks. Experiments with FAs unable to flip and alkylsulfonates also support this view. Phylogenetically, UCPs took advantage of the common FA-uncoupling function of SLC25 family carriers and dropped their solute transport function.
Topics: Animals; Electrophoresis; Humans; Ion Channels; Mitochondrial Proteins; Models, Biological; Protons; Uncoupling Protein 1
PubMed: 20206627
DOI: 10.1016/j.febslet.2010.02.068 -
Journal of the American Society For... Jun 2022Ionization of organic compounds with different structural and energetic properties including benzene derivatives, polycyclic aromatic hydrocarbons (PAHs), ketones, and...
Ionization of organic compounds with different structural and energetic properties including benzene derivatives, polycyclic aromatic hydrocarbons (PAHs), ketones, and polyenes was studied using a commercial atmospheric pressure corona discharge (APCI) ion source on a drift tube ion mobility-quadrupole-time-of-flight mass spectrometer (IM-QTOFMS). It was found that the studied cohort of compounds can be experimentally ionized via protonation, charge transfer, and hydride abstraction leading to formation of [M + H], [M], and [M - H] species, respectively. By experimentally monitoring the product ions and comparing the thermodynamic data for different ionization paths, it was proposed that NO is one of the main reactant ions (RIs) in the ion source used. Of particular focus in this work were theoretical and experimental studies of the effect of solvents frequently used for analytical applications with this ion source (acetonitrile, methanol, and chloroform) on the ionization mechanisms. In methanol, the studied compounds were observed to be ionized mainly via proton transfer while acetonitrile suppressed the protonation of compounds and enhanced their ionization via charge transfer and hydride abstraction. Use of chloroform as a solvent led to formation of CHCl as an alternative reactant ion (RI) to ionize the analytes via electrophilic substitution. Density functional theory (DFT) was used to study the different paths of ionization. The theoretical and experimental results showed that by using only the absolute thermodynamic data, the real ionization path cannot be determined and the energies of all competing processes such as charge transfer, protonation, and hydride abstraction need to be compared.
Topics: Acetonitriles; Atmospheric Pressure; Chloroform; Humans; Ions; Methanol; Protons; Solvents
PubMed: 35562191
DOI: 10.1021/jasms.2c00034 -
Acta Crystallographica. Section D,... Jul 2015The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five-membered ring....
The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five-membered ring. Analysis of the imidazole moieties found in histidine residues of atomic resolution protein crystal structures in the Protein Data Bank (PDB), and in small-molecule structures retrieved from the Cambridge Structural Database (CSD), identified characteristic patterns of bond lengths and angles related to the protonation state of the imidazole moiety. Using discriminant analysis, two functions could be defined, corresponding to linear combinations of the four most sensitive stereochemical parameters, two bond lengths (ND1-CE1 and CE1-NE2) and two endocyclic angles (-ND1- and -NE2-), that uniquely identify the protonation states of all imidazole moieties in the CSD and can be used to predict which N atom(s) of the histidine side chains in protein structures are protonated. Updated geometrical restraint target values are proposed for differently protonated histidine side chains for use in macromolecular refinement.
Topics: Crystallography, X-Ray; Databases, Protein; Histidine; Hydrogen Bonding; Imidazoles; Protein Conformation; Proteins; Protons; Stereoisomerism
PubMed: 26143916
DOI: 10.1107/S1399004715007816 -
Inorganic Chemistry Dec 2023Nitrogenase is the only enzyme that can cleave the strong triple bond in N, making nitrogen available for biological life. There are three isozymes of nitrogenase,...
Nitrogenase is the only enzyme that can cleave the strong triple bond in N, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E state, we find that protonation of the S2B μ belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.
Topics: Nitrogenase; Tricarboxylic Acids; Protons; Catalytic Domain
PubMed: 37987624
DOI: 10.1021/acs.inorgchem.3c02329 -
Biophysical Journal Jun 2022Proton-coupled peptide transporters (POTs) are crucial for the uptake of di- and tripeptides as well as drug and prodrug molecules in prokaryotes and eukaryotic cells....
Proton-coupled peptide transporters (POTs) are crucial for the uptake of di- and tripeptides as well as drug and prodrug molecules in prokaryotes and eukaryotic cells. We illustrate from multiscale modeling how transmembrane proton flux couples within a POT protein to drive essential steps of the full functional cycle: 1) protonation of a glutamate on transmembrane helix 7 (TM7) opens the extracellular gate, allowing ligand entry; 2) inward proton flow induces the cytosolic release of ligand by varying the protonation state of a second conserved glutamate on TM10; 3) proton movement between TM7 and TM10 is thermodynamically driven and kinetically permissible via water proton shuttling without the participation of ligand. Our results, for the first time, give direct computational confirmation for the alternating access model of POTs, and point to a quantitative multiscale kinetic picture of the functioning protein mechanism.
Topics: Glutamic Acid; Ligands; Membrane Transport Proteins; Peptides; Protons
PubMed: 35614850
DOI: 10.1016/j.bpj.2022.05.029 -
Biochimica Et Biophysica Acta.... Dec 2022Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in...
Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in proton transporters, deliver protons to an internal site. The protonation-coupled dynamics of bulk-exposed carboxylate clusters, also known as proton antennas, is poorly described. An essential open question is how water-mediated bridges between sidechains of the cluster respond to protonation change and facilitate transient proton storage. To address this question, here I studied the protonation-coupled dynamics at the proton-binding antenna of PsbO, a small extrinsinc subunit of the photosystem II complex, with atomistic molecular dynamics simulations and systematic graph-based analyses of dynamic protein and protein-water hydrogen-bond networks. The protonation of specific carboxylate groups is found to impact the dynamics of their local protein-water hydrogen-bond clusters. Regardless of the protonation state considered for PsbO, carboxylate pairs that can sample direct hydrogen bonding, or bridge via short hydrogen-bonded water chains, anchor to nearby basic or polar protein sidechains. As a result, carboxylic sidechains of the hypothesized antenna cluster are part of dynamic hydrogen bond networks that may rearrange rapidly when the protonation changes.
Topics: Carboxylic Acids; Histidine; Hydrogen Bonding; Photosystem II Protein Complex; Protons; Water
PubMed: 36116514
DOI: 10.1016/j.bbamem.2022.184052 -
ELife Oct 2021Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels,...
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
Topics: Animals; Ligand-Gated Ion Channels; Markov Chains; Nuclear Pore; Protons; Xenopus laevis
PubMed: 34652272
DOI: 10.7554/eLife.68369 -
BioTechniques Feb 2011Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate... (Review)
Review
Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate determination in biological and biomedical research. However, valid interpretation of results obtained with such probes requires careful consideration of numerous controls, as well as possible effects of non-protonic charges on dye behavior. In this context, we provide an overview of some of the important technical considerations, controls, and parallel complementary assays that can be employed to help ensure appropriate interpretation of results, thus providing a practical usage guide for monitoring mitochondrial membrane potentials with cationic probes. In total, this review will help illustrate both the strengths and potential pitfalls of common mitochondrial membrane potential dyes, and highlight best-usage approaches for their efficacious application in life sciences research.
Topics: Animals; Fluorescent Dyes; Humans; Membrane Potential, Mitochondrial; Mitochondria; Protons
PubMed: 21486251
DOI: 10.2144/000113610 -
International Journal of Molecular... Nov 2022Organic molecules with excited-state intramolecular proton transfer (ESIPT) and thermally activated delayed fluorescence (TADF) properties have great potential for...
Organic molecules with excited-state intramolecular proton transfer (ESIPT) and thermally activated delayed fluorescence (TADF) properties have great potential for realizing efficient organic light-emitting diodes (OLEDs). Furthermore, 2,2'-bipyridine-3,3'-diol (BP(OH)) is a typical molecule with ESIPT and TADF properties. Previously, the double ESIPT state was proved to be a luminescent state, and the T state plays a dominant role in TADF for the molecule. Nevertheless, whether BP(OH) undergoes a double or single ESIPT process is controversial. Since different ESIPT channels will bring different TADF mechanisms, the previously proposed TADF mechanism based on the double ESIPT structure for BP(OH) needs to be reconsidered. Herein, reduced density gradient, potential energy surface, IR spectra and exited-state hydrogen-bond dynamics computations confirm that BP(OH) undergoes the barrierless single ESIPT process rather than the double ESIPT process with a barrier. Moreover, based on the single ESIPT structure, we calculated spin-orbit coupling matrix elements, nonradiative rates and electron-hole distributions. These results disclose that the T state plays a predominant role in TADF. Our investigation provides a better understanding on the TADF mechanism in hydrogen-bonded molecular systems and the interaction between ESIPT and TADF, which further provides a reference for developing efficient OLEDs.
Topics: Protons; Alcohols; Proton Therapy; Hydrogen Bonding
PubMed: 36430447
DOI: 10.3390/ijms232213969 -
Protein Science : a Publication of the... Jan 2016The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to...
The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to investigate pKa values can provide general guidance for assigning proton locations, only static pictures of the chemical species are available. To obtain the overall protein dynamics for the interpretation of detailed enzyme catalysis in this study, guided by information from solid-state NMR, we performed molecular dynamics (MD) simulations for the PLP-dependent enzyme tryptophan synthase (TRPS), whose catalytic mechanism features multiple quasi-stable intermediates. The primary objective of this work is to elucidate how the position of a single proton on the reacting substrate affects local and global protein dynamics during the catalytic cycle. In general, proteins create a chemical environment and an ensemble of conformational motions to recognize different substrates with different protonations. The study of these interactions in TRPS shows that functional groups on the reacting substrate, such as the phosphoryl group, pyridine nitrogen, phenolic oxygen and carboxyl group, of each PLP-bound intermediate play a crucial role in constructing an appropriate molecular interface with TRPS. In particular, the protonation states of the ionizable groups on the PLP cofactor may enhance or weaken the attractions between the enzyme and substrate. In addition, remodulation of the charge distribution for the intermediates may help generate a suitable environment for chemical reactions. The results of our study enhance knowledge of protonation states for several PLP intermediates and help to elucidate their effects on protein dynamics in the function of TRPS and other PLP-dependent enzymes.
Topics: Biocatalysis; Crystallography, X-Ray; Molecular Dynamics Simulation; Molecular Structure; Protons; Pyridoxal Phosphate; Tryptophan Synthase
PubMed: 26013176
DOI: 10.1002/pro.2709