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European Journal of Biochemistry Jul 1983The dynamics of proton transfer between a surface-attached acidic moiety and the bulk of the solution was measured using the laser-induced proton pulse technique....
The dynamics of proton transfer between a surface-attached acidic moiety and the bulk of the solution was measured using the laser-induced proton pulse technique. [Gutman, M., Huppert, D. and Pines, E. (1981) J. Am. Chem. Soc. 103, 3709-3713]. The model system for this study consists of pH indicators (either neutral red or bromcresol green) adsorbed on Brij 58 micelles, as defined targets for protonation and a non-adsorbed proton emitter (2-naphthol-3,6-disulfonate) for generation of protons in bulk. The reaction was measured with 50-ns time resolution over a time period of about 200 microseconds. The results were analyzed by a numerical solution of the coupled nonlinear differential equation corresponding with the reaction system. [Gutman, M., et al. (1983) J. Am. Chem. Soc. 105, 2210-2216]. Quantitative analysis reveals two independent reactions which govern the observed dynamics: (a) a diffusion-controlled reaction between the proton and the surface targets; (b) translocation of the protonated target between the hydration layer of the interface and a more hydrophobic one. The contribution of the translocation reaction to the dynamics of surface protonation is more pronounced for compounds like carboxylates or phenolates which increase their hydrophobicity upon protonation. Amines and azoaromatic structures are more hydrophilic in their protonated states, the dynamics of their protonation is less affected by post-protonation distribution within the microenvironments of the interface. The interrelation between the partial rate constants and the macroscopic time constants and equilibrium parameters is analyzed.
Topics: Bromcresol Green; Energy Transfer; Kinetics; Macromolecular Substances; Mathematics; Micelles; Models, Chemical; Neutral Red; Protons; Surface Properties
PubMed: 6305658
DOI: 10.1111/j.1432-1033.1983.tb07531.x -
The Journal of Physical Chemistry. B Jun 2016IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers...
IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H](+) and [Cyd+H](+) is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H](+) is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H](+). O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ∼25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers.
Topics: Cytosine; Models, Molecular; Nitrogen; Oxygen; Protons; Thermodynamics
PubMed: 27159774
DOI: 10.1021/acs.jpcb.6b04388 -
Biopolymers Apr 2008All proteins, nucleic acids, and other biomolecules contain residues capable of exchanging protons with their environment. These proton transfer phenomena lead to pH...
All proteins, nucleic acids, and other biomolecules contain residues capable of exchanging protons with their environment. These proton transfer phenomena lead to pH sensitivity of many molecular processes underlying biological phenomena. In the course of biological evolution, Nature has invented some mechanisms to use pH gradients to regulate biomolecular processes inside cells or in interstitial fluids. Therefore, an ability to model protonation equilibria in molecular systems accurately would be of enormous value for our understanding of biological processes and for possible rational influence on them, like in developing pH dependent drugs to treat particular diseases. This work presents a derivation, by thermodynamic and statistical mechanical methods, of an expression for the free energy of a complex molecular system at arbitrary ionization state of its titratable residues. This constitutes one of the elements of modeling protonation equilibria. Starting from a consideration of a simple acid-base equilibrium of a model compound with a single tritratable group, we arrive at an expression which is of general validity for complex systems. The only approximation used in this derivation is the postulating that the interaction energy between any pair of titratable sites does not depend on the protonation states of all the remaining ionizable groups.
Topics: Hydrogen-Ion Concentration; Polymers; Protons; Thermodynamics; Titrimetry
PubMed: 17806123
DOI: 10.1002/bip.20837 -
Biophysical Chemistry Sep 2023The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic... (Review)
Review
The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, it is now better explained how the bacteriorhodopsin-purple membrane-ATPase system functions. The bacteriorhodopsin pumping of protons across the membrane results in the formation of TELP around the halobacterial extracellular membrane surface that is perfectly positioned to drive ATP synthase for the synthesis of ATP from ADP and Pi. The bacteriorhodopsin purple membrane sheet experiment of Heberle et al. 1994 is now better explained here as a transient "protonic capacitor". During the lifetime of a flashlight-induced protonic bacteriorhodopsin purple membrane capacitor activity, there is at least a transient non-zero membrane potential (Δψ ≠ 0). The experimental results demonstrated that "after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase" exactly as predicted by the TELP theory, which is fundamentally important to the science of bioenergetics.
Topics: Protons; Bacteriorhodopsins; Membrane Potentials; Adenosine Triphosphate
PubMed: 37406610
DOI: 10.1016/j.bpc.2023.107072 -
Photochemical & Photobiological... Jun 2006Recently, reversible photoswitching in bulk samples or in individual molecules of Dronpa, a mutant of a green fluorescent protein (GFP)-like fluorescent protein, has...
Recently, reversible photoswitching in bulk samples or in individual molecules of Dronpa, a mutant of a green fluorescent protein (GFP)-like fluorescent protein, has been demonstrated. Intense irradiation at 488 nm changed Dronpa in a dim protonated form, and weak irradiation at 405 nm restored it to the bright deprotonated form. Here, we report on the mechanism of photoswitching of Dronpa by means of ensemble and single-molecule spectroscopy. Ensemble spectroscopy shows that the photoswitching can be described, in first approximation, by a three-state model including a deprotonated (B), a protonated (A1), and a photoswitched protonated (A2) forms of the chromophore. While the B and the A1 forms are in a ground state acid-base equilibrium, the B and the A2 forms are reversibly photoswitched upon irradiation with 488 and 405 nm light. At the single-molecule level, the on-times in fluorescence intensity trajectories excited at 488 nm decrease with increasing the excitation power, consistent with the photoswitching from the B to A2 form. The on-times agree well with expected values, which are calculated based on the ensemble spectroscopic properties of Dronpa. The fluorescence trajectory obtained with simultaneous dual-color excitation at 488 and 405 nm demonstrates reversible photoswitching between the B and the A2 forms at the single-molecule level. The efficiency of the photoswitching from the A2 to B form increased with increasing the excitation power of the 405 nm light. Our results demonstrate that Dronpa holds its outstanding photoswitching properties, based on a photo-induced protonation/deprotonation process, even at the single-molecule level.
Topics: Green Fluorescent Proteins; Photochemistry; Protons; Spectrometry, Fluorescence
PubMed: 16761085
DOI: 10.1039/b516339k -
Journal of Chemical Information and... Jun 2009In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two...
In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers.
Topics: Drug Evaluation, Preclinical; Humans; Ligands; Models, Molecular; Molecular Conformation; Proteins; Protons; Stereoisomerism; User-Computer Interface
PubMed: 19453150
DOI: 10.1021/ci800420z -
Proceedings of the National Academy of... Jun 2015The proton permeation process of the stator complex MotA/B in the flagellar motor of Escherichia coli was investigated. The atomic model structure of the transmembrane...
The proton permeation process of the stator complex MotA/B in the flagellar motor of Escherichia coli was investigated. The atomic model structure of the transmembrane part of MotA/B was constructed based on the previously published disulfide cross-linking and tryptophan scanning mutations. The dynamic permeation of hydronium/sodium ions and water molecule through the channel formed in MotA/B was observed using a steered molecular dynamics simulation. During the simulation, Leu46 of MotB acts as the gate for hydronium ion permeation, which induced the formation of water wire that may mediate the proton transfer to Asp32 on MotB. Free energy profiles for permeation were calculated by umbrella sampling. The free energy barrier for H3O(+) permeation was consistent with the proton transfer rate deduced from the flagellar rotational speed and number of protons per rotation, which suggests that the gating is the rate-limiting step. Structure and dynamics of the MotA/B with nonprotonated and protonated Asp32, Val43Met, and Val43Leu mutants in MotB were investigated using molecular dynamics simulation. A narrowing of the channel was observed in the mutants, which is consistent with the size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintained a kink whereas the protonation induced a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, which may be correlated to the motion of the flagellar rotor.
Topics: Bacterial Proteins; Cytoplasm; Escherichia coli Proteins; Ion Transport; Models, Molecular; Protein Conformation; Protons
PubMed: 26056313
DOI: 10.1073/pnas.1502991112 -
The Journal of Organic Chemistry May 2008In mass spectrometry of the alpha,beta-unsaturated aromatic ketones, Ph-CO-CH=CH-Ph', losses of a benzene from the two ends and elimination of a styrene are the three...
In mass spectrometry of the alpha,beta-unsaturated aromatic ketones, Ph-CO-CH=CH-Ph', losses of a benzene from the two ends and elimination of a styrene are the three major fragmentation reactions of the protonated molecules. When the ketones are substituted on the right phenyl ring, the electron-donating groups are in favor of losing a styrene to form the benzoyl cation, PhCO(+), whereas the electron-withdrawing groups strongly favor loss of benzene of the left side to form a cinnamoyl cation, Ph'CH=CHCO(+). When the ketones are substituted on the left phenyl ring, the substituent effects on the reactions are reversed. In both cases, the ratios of the two competitive product ions are well-correlated with the sigma p(+) substituent constants. Theoretical calculations indicate that the carbonyl oxygen is the most favorable site for protonation, and the olefinic carbon adjacent to the carbonyl is also favorable especially when a strong electron-releasing group is present on the right phenyl ring. The energy barrier to the interconversion between the ions formed from protonation at these two sites regulates the overall reactions. Transfer of a proton from the carbonyl oxygen to the ipso position on either phenyl ring, which is dissociative, triggers loss of benzene.
Topics: Ketones; Mass Spectrometry; Models, Molecular; Molecular Structure; Protons
PubMed: 18370421
DOI: 10.1021/jo702464b -
Critical Reviews in Analytical Chemistry 2023In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS).... (Review)
Review
In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Since 2003, when the term "reactive matrices" was suggested and the dignity of compounds, possessing dualistic properties as matrices and derivatization agents was demonstrated, corresponding approach has found application in various fields and, in particular, in bioanalysis (metabolomics, lipidomics, etc.). The main advantage of this methodology is that it reduces sample treatment time, simplifies the procedure of sample handling, improves the sensitivity of analysis, enhances the molecular identification and profiling. Within the framework of this review, the main attention is paid to "true" reactive matrices that interact with analyte molecules through an exchange or addition reactions. A special section discusses practical application of reactive matrices in the determination of the distribution of targeted and non-targeted organic substances on the surface of biological tissue sections by MALDI-MS imaging. In this critical review, a controversial proposal is made to consider protonating and deprotonating matrices as reactive, because they can undergo a chemical reaction such as proton transfer that occurs in both target solution and MALDI plume. In this respect, special attention is paid to "proton sponge" matrices that have found a wide application in the analysis of various acidic compounds by MALDI-MS in the negative mode. Historical data on the formation of ions and the fate of matrices in MALDI are considered at the beginning of this article.
Topics: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Protons; Metabolomics; Specimen Handling; Lasers
PubMed: 34969337
DOI: 10.1080/10408347.2021.2001309 -
International Journal of Radiation... Nov 2013The purpose of this article is to review briefly the nature of protons: creation at the Big Bang, abundance, physical characteristics, internal components, and life...
The purpose of this article is to review briefly the nature of protons: creation at the Big Bang, abundance, physical characteristics, internal components, and life span. Several particle discoveries by proton as the experimental tool are considered. Protons play important roles in science, medicine, and industry. This article was prompted by my experience in the curative treatment of cancer patients by protons and my interest in the nature of protons as particles. The latter has been stimulated by many discussions with particle physicists and reading related books and journals. Protons in our universe number ≈10(80). Protons were created at 10(-6) -1 second after the Big Bang at ≈1.37 × 10(10) years beforethe present. Proton life span has been experimentally determined to be ≥10(34) years; that is, the age of the universe is 10(-24)th of the minimum life span of a proton. The abundance of the elements is hydrogen, ≈74%; helium, ≈24%; and heavier atoms, ≈2%. Accordingly, protons are the dominant baryonic subatomic particle in the universe because ≈87% are protons. They are in each atom in our universe and thus involved in virtually every activity of matter in the visible universe, including life on our planet. Protons were discovered in 1919. In 1968, they were determined to be composed of even smaller particles, principally quarks and gluons. Protons have been the experimental tool in the discoveries of quarks (charm, bottom, and top), bosons (W(+), W(-), Z(0), and Higgs), antiprotons, and antineutrons. Industrial applications of protons are numerous and important. Additionally, protons are well appreciated in medicine for their role in radiation oncology and in magnetic resonance imaging. Protons are the dominant baryonic subatomic particle in the visible universe, comprising ≈87% of the particle mass. They are present in each atom of our universe and thus a participant in every activity involving matter.
Topics: Astronomical Phenomena; Elementary Particle Interactions; Elementary Particles; History, 19th Century; History, 20th Century; History, 21st Century; History, Ancient; Protons
PubMed: 24074929
DOI: 10.1016/j.ijrobp.2013.06.2033