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Molecules (Basel, Switzerland) Feb 2020Protonated rare gas clusters have previously been shown to display markably different structures than their pure, cationic counterparts. Here we have performed high...
Protonated rare gas clusters have previously been shown to display markably different structures than their pure, cationic counterparts. Here we have performed high resolution mass spectrometry measurements of protonated and pristine clusters of He containing up to 50 atoms. We identify notable differences between the magic numbers present in the two types of clusters, but in contrast to heavier rare gas clusters, neither the protonated nor pure clusters exhibit signs of icosahedral symmetries. These findings are discussed in light of results from heavier rare gases and previous theoretical work on protonated helium.
Topics: Cations; Helium; Mass Spectrometry; Protons
PubMed: 32120989
DOI: 10.3390/molecules25051066 -
Biochemistry Jun 2015The main properties of the voltage-gated proton channel (HV1) are described in this review, along with what is known about how the channel protein structure accomplishes... (Review)
Review
The main properties of the voltage-gated proton channel (HV1) are described in this review, along with what is known about how the channel protein structure accomplishes its functions. Just as protons are unique among ions, proton channels are unique among ion channels. Their four transmembrane helices sense voltage and the pH gradient and conduct protons exclusively. Selectivity is achieved by the unique ability of H3O(+) to protonate an Asp-Arg salt bridge. Pathognomonic sensitivity of gating to the pH gradient ensures HV1 channel opening only when acid extrusion will result, which is crucial to most of its biological functions. An exception occurs in dinoflagellates in which influx of H(+) through HV1 triggers the bioluminescent flash. Pharmacological interventions that promise to ameliorate cancer, asthma, brain damage in ischemic stroke, Alzheimer's disease, autoimmune diseases, and numerous other conditions await future progress.
Topics: Animals; Drug Discovery; Humans; Hydrogen-Ion Concentration; Ion Channel Gating; Ion Channels; Models, Molecular; Protein Conformation; Protons
PubMed: 25964989
DOI: 10.1021/acs.biochem.5b00353 -
Biosensors Feb 2023Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca) concentrations with genetically...
Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca) concentrations with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities.
Topics: Green Fluorescent Proteins; Calcium; Luminescent Proteins; Protons; Red Fluorescent Protein
PubMed: 36831983
DOI: 10.3390/bios13020218 -
European Biophysics Journal : EBJ Oct 20238-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer...
8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.
Topics: Azaguanine; Spectrum Analysis; Protons; Proteins; Quantum Theory
PubMed: 37507591
DOI: 10.1007/s00249-023-01672-x -
Nature Structural & Molecular Biology May 2022Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and...
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
Topics: Hydrogen Bonding; Proteins; Protons
PubMed: 35484235
DOI: 10.1038/s41594-022-00762-2 -
Biophysical Journal Dec 2021Ionizable residues can release and take up protons and this has an influence on protein structure and function. The extent of protonation is linked to the overall pH of...
Ionizable residues can release and take up protons and this has an influence on protein structure and function. The extent of protonation is linked to the overall pH of the solution and the local environments of ionizable residues. Binding or unbinding of a single proton generates a distinct charge microstate defined by a specific pattern of charges. Accordingly, the overall partition function is a sum over all charge microstates and Boltzmann weights of all conformations associated with each of the charge microstates. This ensemble-of-ensembles description recast as a q-canonical ensemble allows us to analyze and interpret potentiometric titrations that provide information regarding net charge as a function of pH. In the q-canonical ensemble, charge microstates are grouped into mesostates where each mesostate is a collection of microstates of the same net charge. Here, we show that leveraging the structure of the q-canonical ensemble allows us to decouple contributions of net proton binding and release from proton arrangement and conformational considerations. Through application of the q-canonical formalism to analyze potentiometric measurements of net charge in proteins with repetitive patterns of Lys and Glu residues, we determine the underlying mesostate pK values and, more importantly, we estimate relative mesostate populations as a function of pH. This is a strength of using the q-canonical approach that cannot be replicated using purely site-specific analyses. Overall, our work shows how measurements of charge equilibria, decoupled from measurements of conformational equilibria, and analyzed using the framework of the q-canonical ensemble, provide protein-specific quantitative descriptions of pH-dependent populations of mesostates. This method is of direct relevance for measuring and understanding how different charge states contribute to conformational, binding, and phase equilibria of proteins.
Topics: Hydrogen-Ion Concentration; Protein Conformation; Proteins; Protons
PubMed: 34826385
DOI: 10.1016/j.bpj.2021.11.2886 -
Chemistry (Weinheim An Der Bergstrasse,... Feb 2022Nitrogenase is the only enzyme in nature that can fix N from the air. The active cofactor of the leading form of this enzyme contains seven irons and one molybdenum...
Nitrogenase is the only enzyme in nature that can fix N from the air. The active cofactor of the leading form of this enzyme contains seven irons and one molybdenum connected by sulfide bridges. In several recent experimental studies, it has been suggested that the cofactor is very flexible, and might lose one of its sulfides during catalysis. In this study, the possible loss of a sulfide has been investigated by model calculations. In previous studies, we have shown that there should be four activation steps before catalysis starts, and this study is based on that finding. It was found here that, after the four reductions in the activation steps, a sulfide will become very loosely bound and can be released in a quite exergonic step with a low barrier. The binding of N has no part in that release. In our previous studies, we suggested that the central carbide should be protonated three times after the four activation steps. With the new finding, there will instead be a loss of a sulfide, as the barrier for the loss is much lower than the ones for protonating the carbide. Still, it is suggested here that the carbide will be protonated anyway, but only with one proton, in the E to E step. A very complicated transition state for H formation involving a large structural change was obtained. The combined step, with a loss of H and binding of N , is calculated to be endergonic by +2.3 kcal mol ; this is in excellent agreement with experiments in which an easily reversible step has been found.
Topics: Molybdenum; Nitrogen; Nitrogenase; Oxidation-Reduction; Protons; Sulfides
PubMed: 35098591
DOI: 10.1002/chem.202103745 -
The Journal of General Physiology Jan 2021The functionally diverse cyclic nucleotide binding domain (CNBD) superfamily of cation channels contains both depolarization-gated (e.g., metazoan EAG family K+...
The functionally diverse cyclic nucleotide binding domain (CNBD) superfamily of cation channels contains both depolarization-gated (e.g., metazoan EAG family K+ channels) and hyperpolarization-gated channels (e.g., metazoan HCN pacemaker cation channels and the plant K+ channel KAT1). In both types of CNBD channels, the S4 transmembrane helix of the voltage sensor domain (VSD) moves outward in response to depolarization. This movement opens depolarization-gated channels and closes hyperpolarization-gated channels. External divalent cations and protons prevent or slow movement of S4 by binding to a cluster of acidic charges on the S2 and S3 transmembrane domains of the VSD and therefore inhibit activation of EAG family channels. However, a similar divalent ion/proton binding pocket has not been described for hyperpolarization-gated CNBD family channels. We examined the effects of external Cd2+ and protons on Arabidopsisthaliana KAT1 expressed in Xenopus oocytes and found that these ions strongly potentiate voltage activation. Cd2+ at 300 µM depolarizes the V50 of KAT1 by 150 mV, while acidification from pH 7.0 to 4.0 depolarizes the V50 by 49 mV. Regulation of KAT1 by Cd2+ is state dependent and consistent with Cd2+ binding to an S4-down state of the VSD. Neutralization of a conserved acidic charge in the S2 helix in KAT1 (D95N) eliminates Cd2+ and pH sensitivity. Conversely, introduction of acidic residues into KAT1 at additional S2 and S3 cluster positions that are charged in EAG family channels (N99D and Q149E in KAT1) decreases Cd2+ sensitivity and increases proton potentiation. These results suggest that KAT1, and presumably other hyperpolarization-gated plant CNBD channels, can open from an S4-down VSD conformation homologous to the divalent/proton-inhibited conformation of EAG family K+ channels.
Topics: Animals; Ions; Oocytes; Protons
PubMed: 33275659
DOI: 10.1085/jgp.202012647 -
Scientific Reports Aug 2018The H, K-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K from the lumen....
The H, K-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K from the lumen. The mechanism of release of a proton into a highly acidic stomach environment, and the subsequent binding of a K ion necessitates a network of protonable residues and dynamically changing protonation states in the cation binding pocket dominated by five acidic amino acid residues E343, E795, E820, D824, and D942. We perform molecular dynamics simulations of spontaneous K binding to all possible protonation combinations of the acidic amino acids and carry out free energy calculations to determine the optimal protonation state of the luminal-open EP state of the pump which is ready to bind luminal K. A dynamic pK correlation analysis reveals the likelihood of proton transfer events within the cation binding pocket. In agreement with in-vitro measurements, we find that E795 is likely to be protonated, and that E820 is at the center of the proton transfer network in the luminal-open EP state. The acidic residues D942 and D824 are likely to remain protonated, and the proton redistribution occurs predominantly amongst the glutamate residues exposed to the lumen. The analysis also shows that a lower number of K ions bind at lower pH, modeled by a higher number of protons in the cation binding pocket, in agreement with the 'transport stoichiometry variation' hypothesis.
Topics: Animals; Binding Sites; H(+)-K(+)-Exchanging ATPase; HEK293 Cells; Humans; Models, Molecular; Mutant Proteins; Potassium; Protein Conformation; Protons; Swine; Thermodynamics
PubMed: 30143663
DOI: 10.1038/s41598-018-30885-w -
Nature Communications Jan 2023Pseudocapacitive charge storage in TiCT MXenes in acid electrolytes is typically described as involving proton intercalation/deintercalation accompanied by redox...
Pseudocapacitive charge storage in TiCT MXenes in acid electrolytes is typically described as involving proton intercalation/deintercalation accompanied by redox switching of the Ti centres and protonation/deprotonation of oxygen functional groups. Here we conduct nanoscale electrochemical measurements in a unique experimental configuration, restricting the electrochemical contact area to a small subregion (0.3 µm) of a monolayer TiCT flake. In this unique configuration, proton intercalation into interlayer spaces is not possible, and surface processes are isolated from the bulk processes, characteristic of macroscale electrodes. Analysis of the pseudocapacitive response of differently sized MXene flakes indicates that entire MXene flakes are charged through electrochemical contact of only a small basal plane subregion, corresponding to as little as 3% of the flake surface area. Our observation of pseudocapacitive charging outside the electrochemical contact area is suggestive of a fast transport of protons mechanism across the MXene surface.
Topics: Protons; Electrodes; Oxygen
PubMed: 36690615
DOI: 10.1038/s41467-023-35950-1