Journal articles: 'Protons'

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Abdallat, Mahmoud, Abdallah Barjas Qaswal, Majed Eftaiha, Abdel Rahman Qamar, Qusai Alnajjar, Rawand Sallam, Lara Kollab, et al. "A mathematical modeling of the mitochondrial proton leak via quantum tunneling." AIMS Biophysics 11, no. 2 (2024): 189–233. http://dx.doi.org/10.3934/biophy.2024012.

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<abstract> The mitochondrion is a vital intracellular organelle that is responsible for ATP production. It utilizes both the concentration gradient and the electrical potential of the inner mitochondrial membrane to drive the flow of protons from the intermembrane space to the matrix to generate ATP via ATP-synthase. However, the proton leak flow, which is mediated via the inner mitochondrial membrane and uncoupling proteins, can reduce the efficiency of ATP production. Protons can exhibit a quantum behavior within biological systems. However, the investigation of the quantum behavior of protons within the mitochondria is lacking particularly in the contribution to the proton leak. In the present study, we proposed a mathematical model of protons tunneling through the inner mitochondrial membrane and the mitochondrial carrier superfamily MCF including uncoupling proteins UCPs and the adenine nucleotide translocases ANTs. According to the model and its assumptions, the quantum tunneling of protons may contribute significantly to the proton leak if it is compared with the classical flow of protons. The quantum tunneling proton leak may depolarize the membrane potential, hence it may contribute to the physiological regulation of ATP synthesis and reactive oxygen species ROS production. In addition to that, the mathematical model of proton tunneling suggested that the proton-tunneling leak may depolarize the membrane potential to values beyond the physiological needs which in turn can harm the mitochondria and the cells. Moreover, we argued that the quantum proton leak might be more energetically favorable if it is compared with the classical proton leak. This may give the advantage for quantum tunneling of protons to occur since less energy is required to contribute significantly to the proton leak compared with the classical proton flow. </abstract>

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Akhmedov, Murodzhon, Bülent Çatay, and Mehmet Serkan Apaydın. "Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments." Journal of Bioinformatics and Computational Biology 13, no. 06 (December 2015): 1550020. http://dx.doi.org/10.1142/s0219720015500201.

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Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

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Pavković, Nemanja, Branislav Milovanović, Ana Stanojević, Mihajlo Etinski, and Milena Petković. "Proton leap: shuttling of protons onto benzonitrile." Physical Chemistry Chemical Physics 24, no. 6 (2022): 3958–69. http://dx.doi.org/10.1039/d1cp04338b.

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Gutta, Pradeep, and Dean J. Tantillo. "Proton Sandwiches: Nonclassical Carbocations with Tetracoordinate Protons." Angewandte Chemie International Edition 44, no. 18 (April 29, 2005): 2719–23. http://dx.doi.org/10.1002/anie.200461915.

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Gutta, Pradeep, and Dean J. Tantillo. "Proton Sandwiches: Nonclassical Carbocations with Tetracoordinate Protons." Angewandte Chemie 117, no. 18 (April 29, 2005): 2779–83. http://dx.doi.org/10.1002/ange.200461915.

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6

Weksler, Meir. "Protons." Medical Journal of Australia 199, no. 11 (December 2013): 801. http://dx.doi.org/10.5694/mja13.10908.

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Schiavilla, R., V. G. J. Stoks, W. Glöckle, H. Kamada, A. Nogga, J. Carlson, R. Machleidt, et al. "Weak capture of protons by protons." Physical Review C 58, no. 2 (August 1, 1998): 1263–77. http://dx.doi.org/10.1103/physrevc.58.1263.

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Lísal, Jiří, and Merritt Maduke. "Proton-coupled gating in chloride channels." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1514 (October 28, 2008): 181–87. http://dx.doi.org/10.1098/rstb.2008.0123.

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The physiologically indispensable chloride channel (CLC) family is split into two classes of membrane proteins: chloride channels and chloride/proton antiporters. In this article we focus on the relationship between these two groups and specifically review the role of protons in chloride-channel gating. Moreover, we discuss the evidence for proton transport through the chloride channels and explore the possible pathways that the protons could take through the chloride channels. We present results of a mutagenesis study, suggesting the feasibility of one of the pathways, which is closely related to the proton pathway proposed previously for the chloride/proton antiporters. We conclude that the two groups of CLC proteins, although in principle very different, employ similar mechanisms and pathways for ion transport.

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Ardalan, Afshan, Matthew D. Smith, and Masoud Jelokhani-Niaraki. "Uncoupling Proteins and Regulated Proton Leak in Mitochondria." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1528. http://dx.doi.org/10.3390/ijms23031528.

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Higher concentration of protons in the mitochondrial intermembrane space compared to the matrix results in an electrochemical potential causing the back flux of protons to the matrix. This proton transport can take place through ATP synthase complex (leading to formation of ATP) or can occur via proton transporters of the mitochondrial carrier superfamily and/or membrane lipids. Some mitochondrial proton transporters, such as uncoupling proteins (UCPs), transport protons as their general regulating function; while others are symporters or antiporters, which use the proton gradient as a driving force to co-transport other substrates across the mitochondrial inner membrane (such as phosphate carrier, a symporter; or aspartate/glutamate transporter, an antiporter). Passage (or leakage) of protons across the inner membrane to matrix from any route other than ATP synthase negatively impacts ATP synthesis. The focus of this review is on regulated proton transport by UCPs. Recent findings on the structure and function of UCPs, and the related research methodologies, are also critically reviewed. Due to structural similarity of members of the mitochondrial carrier superfamily, several of the known structural features are potentially expandable to all members. Overall, this report provides a brief, yet comprehensive, overview of the current knowledge in the field.

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Gary, S. Peter, Michelle F. Thomsen, Lin Yin, and Dan Winske. "Electromagnetic proton cyclotron instability: Interactions with magnetospheric protons." Journal of Geophysical Research: Space Physics 100, A11 (November 1, 1995): 21961–72. http://dx.doi.org/10.1029/95ja01403.

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11

Movellan, Kumar Tekwani, Eszter E. Najbauer, Supriya Pratihar, Michele Salvi, Karin Giller, Stefan Becker, and Loren B. Andreas. "Alpha protons as NMR probes in deuterated proteins." Journal of Biomolecular NMR 73, no. 1-2 (February 14, 2019): 81–91. http://dx.doi.org/10.1007/s10858-019-00230-y.

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Abstract We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli expression. We show that α-PET labeling is particularly useful in improving structural characterization of solid proteins by introduction of an additional proton reporter, while eliminating many strong dipolar couplings. The approach benefits from the high sensitivity associated with 1.3 mm samples, more abundant information including Hα resonances, and the narrow proton linewidths encountered for highly deuterated proteins. The labeling strategy solves amide proton exchange problems commonly encountered for membrane proteins when using perdeuteration and backexchange protocols, allowing access to alpha and all amide protons including those in exchange-protected regions. The incorporation of Hα protons provides new insights, as the close Hα–Hα and Hα–HN contacts present in β-sheets become accessible, improving the chance to determine the protein structure as compared with HN–HN contacts alone. Protonation of the Hα position higher than 90% is achieved for Ile, Leu, Phe, Tyr, Met, Val, Ala, Gln, Asn, Thr, Ser, Glu, Asp even though LAAO is only active at this degree for Ile, Leu, Phe, Tyr, Trp, Met. Additionally, the glycine methylene carbon is labeled preferentially with a single deuteron, allowing stereospecific assignment of glycine alpha protons. In solution, we show that the high deuteration level dramatically reduces R2 relaxation rates, which is beneficial for the study of large proteins and protein dynamics. We demonstrate the method using two model systems, as well as a 32 kDa membrane protein, hVDAC1, showing the applicability of the method to study membrane proteins.

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M., Ambaga, Tumen-Ulzii A., and Buyantushig T. "THE BUFFERING CAPACITY OF ERYTHROCYTE MEMBRANE SURROUNDINGS IN RELATION TO FREE PROTONS INSIGHTOF NEW ELUCIDATION OF EIGTH AND NINTH STAGES OF THE MEMBRANE REDOXY POTENTIAL THREE STATE DEPENDENT 9 STEPPED FULL CYCLE OF PROTON CONDUCTANCE IN THE HUMAN BODY." International Journal of Advanced Research 10, no. 11 (November 30, 2022): 29–33. http://dx.doi.org/10.21474/ijar01/15638.

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It was became clear that the flow-fate of all many many protons,generated in mitochondria of 50-80 trillion cells (now by us mitochondria flow of protons named as 1-7 stages of proton conductance) have been needed another special structures - another system needs to soak up the extra H+ activity generated as a result of process conducted in the 1-7 stages of proton conductance in order for true buffering to occur, that system consists of intracellular proteins, of which haemoglobin is the key player, concretely speaking,one of these are the erythrocyte membrane surroundings for packaging of protons and alsoHydrochloric acid formationby Gastric parietal cells,also H+/Na antiport in the membrane transports H+ out of cell and Na ion in the level of Peritubular capillary-Interstitial fluid-Tubule epithelial cells-Tubular fluid with accompanying maintaining of serum and cell pH-7,4.By our suggestion, the buffering capacity of erythrocyte membrane surroundings in relation to free protons, formed in the proton conductance have implemented within Ninth stage -located in the Respiratory membrane, Pulmonary circuit, where occurred oxygen uptake from alveolar air under effect of increased bicarbonate entry by bicarbonate/chloride ion shift mechanism, leading to increase of HbO2 formation, resulting to release of proton,electron from food substrates under the undirect action of oxygen released from membrane surroundings of erythrocyte in the 8-th stage of proton conductance.

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13

Szymonowicz, Klaudia, Adam Krysztofiak, Jansje van der Linden, Ajvar Kern, Simon Deycmar, Sebastian Oeck, Anthony Squire, et al. "Proton Irradiation Increases the Necessity for Homologous Recombination Repair Along with the Indispensability of Non-Homologous End Joining." Cells 9, no. 4 (April 5, 2020): 889. http://dx.doi.org/10.3390/cells9040889.

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Technical improvements in clinical radiotherapy for maximizing cytotoxicity to the tumor while limiting negative impact on co-irradiated healthy tissues include the increasing use of particle therapy (e.g., proton therapy) worldwide. Yet potential differences in the biology of DNA damage induction and repair between irradiation with X-ray photons and protons remain elusive. We compared the differences in DNA double strand break (DSB) repair and survival of cells compromised in non-homologous end joining (NHEJ), homologous recombination repair (HRR) or both, after irradiation with an equal dose of X-ray photons, entrance plateau (EP) protons, and mid spread-out Bragg peak (SOBP) protons. We used super-resolution microscopy to investigate potential differences in spatial distribution of DNA damage foci upon irradiation. While DNA damage foci were equally distributed throughout the nucleus after X-ray photon irradiation, we observed more clustered DNA damage foci upon proton irradiation. Furthermore, deficiency in essential NHEJ proteins delayed DNA repair kinetics and sensitized cells to both, X-ray photon and proton irradiation, whereas deficiency in HRR proteins sensitized cells only to proton irradiation. We assume that NHEJ is indispensable for processing DNA DSB independent of the irradiation source, whereas the importance of HRR rises with increasing energy of applied irradiation.

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14

Epalle, Nathan Hugo, and Eric Beitz. "Local Attraction of Substrates and Co-Substrates Enhances Weak Acid and Base Transmembrane Transport." Biomolecules 12, no. 12 (November 30, 2022): 1794. http://dx.doi.org/10.3390/biom12121794.

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The transmembrane transport of weak acid and base metabolites depends on the local pH conditions that affect the protonation status of the substrates and the availability of co-substrates, typically protons. Different protein designs ensure the attraction of substrates and co-substrates to the transporter entry sites. These include electrostatic surface charges on the transport proteins and complexation with seemingly transport-unrelated proteins that provide substrate and/or proton antenna, or enzymatically generate substrates in place. Such protein assemblies affect transport rates and directionality. The lipid membrane surface also collects and transfers protons. The complexity in the various systems enables adjustability and regulation in a given physiological or pathophysiological situation. This review describes experimentally shown principles in the attraction and facilitation of weak acid and base transport substrates, including monocarboxylates, ammonium, bicarbonate, and arsenite, plus protons as a co-substrate.

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15

Wójcik, J., K. Ruszczyńska, I. Zhukov, and A. Ejchart. "NMR measurements of proton exchange between solvent and peptides and proteins." Acta Biochimica Polonica 46, no. 3 (September 30, 1999): 651–63. http://dx.doi.org/10.18388/abp.1999_4137.

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Scope and limitations of the NMR based methods, equilibration and magnetization transfer, for measuring proton exchange rates of amide protons in peptides and proteins with water protons are discussed. Equilibration is applied to very slow processes detected by hydrogen-deuterium exchange after a solute is dissolved in D2O. Magnetization transfer allows to study moderately rapid processes in H2O. A number of precautions should be undertaken in order to avoid systemic errors inherent in the magnetization transfer method.

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16

Goitein, Michael, and Gudrun Goitein. "Swedish protons." Acta Oncologica 44, no. 8 (January 2005): 793–97. http://dx.doi.org/10.1080/02841860500402207.

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17

BORMAN, STU. "SHUFFLING PROTONS." Chemical & Engineering News 79, no. 43 (October 22, 2001): 55. http://dx.doi.org/10.1021/cen-v079n043.p055.

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Goitein, Michael. "Magical Protons?" International Journal of Radiation Oncology*Biology*Physics 70, no. 3 (March 2008): 654–56. http://dx.doi.org/10.1016/j.ijrobp.2007.10.057.

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Alcaraz, J., B. Alpat, G. Ambrosi, H. Anderhub, L. Ao, A. Arefiev, P. Azzarello, et al. "Cosmic protons." Physics Letters B 490, no. 1-2 (September 2000): 27–35. http://dx.doi.org/10.1016/s0370-2693(00)00970-9.

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Bortfeld, T. "SP-0529 For the motion - Protons for Protons." Radiotherapy and Oncology 170 (May 2022): S465. http://dx.doi.org/10.1016/s0167-8140(22)03986-x.

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21

Keller, David, Seema Singh, Paola Turina, Roderick Capaldi, and Carlos Bustamante. "Structure of ATP synthase by SFM and single-particle image analysis." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 722–23. http://dx.doi.org/10.1017/s0424820100139986.

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F1Fo ATP synthases are the proteins responsible for the synthesis of ATP in oxidative phosphorylation, and are present in some form in all aerobic organisms, both prokaryotic and eukaryotic. They use the energy stored in a transmembrane proton gradient (which is generated by other members of the oxidative phosphorylation pathway) to synthesize ATP from ADP and Pi or, working in reverse, to pump protons across the membrane using the energy of ATP hydrolysis. The full protein has two sectors, F1 and Fo. F1 is normally bound to Fo (which is membrane integrated), but is water soluble when dissociated. The F1 sector contains the sites which bind ADP and catalyze its conversion to ATP. The Fo sector contains a channel which allows protons to to cross the membrane, dissipating the transmembrane chemical potential. By an unknown mechanism this translocation of protons through Fo is coupled to the hydrolysis or synthesis of ATP in F1, so that the energy released in hydrolysis of ATP can drive the motion of protons against an electrochemical potential, or the energy of translocating protons can be used to form high energy ADP-Pi bonds.

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Wobig, Lea, Thérèse Wolfenstetter, Sylvia Fechner, Wolfgang Bönigk, Heinz G. Körschen, Jan F. Jikeli, Christian Trötschel, et al. "A family of hyperpolarization-activated channels selective for protons." Proceedings of the National Academy of Sciences 117, no. 24 (May 28, 2020): 13783–91. http://dx.doi.org/10.1073/pnas.2001214117.

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Proton (H+) channels are special: They select protons against other ions that are up to a millionfold more abundant. Only a few proton channels have been identified so far. Here, we identify a family of voltage-gated “pacemaker” channels, HCNL1, that are exquisitely selective for protons. HCNL1 activates during hyperpolarization and conducts protons into the cytosol. Surprisingly, protons permeate through the channel’s voltage-sensing domain, whereas the pore domain is nonfunctional. Key to proton permeation is a methionine residue that interrupts the series of regularly spaced arginine residues in the S4 voltage sensor. HCNL1 forms a tetramer and thus contains four proton pores. Unlike classic HCN channels, HCNL1 is not gated by cyclic nucleotides. The channel is present in zebrafish sperm and carries a proton inward current that acidifies the cytosol. Our results suggest that protons rather than cyclic nucleotides serve as cellular messengers in zebrafish sperm. Through small modifications in two key functional domains, HCNL1 evolutionarily adapted to a low-Na+freshwater environment to conserve sperm’s ability to depolarize.

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Förtsch, S. V., A. A. Cowley, J. J. Lawrie, J. V. Pilcher, F. D. Smit, and D. M. Whittal. "Coincident proton emission induced by 200 MeV protons onAu197." Physical Review C 48, no. 2 (August 1, 1993): 743–55. http://dx.doi.org/10.1103/physrevc.48.743.

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Buch-Pedersen, M. J., B. P. Pedersen, B. Veierskov, P. Nissen, and M. G. Palmgren. "Protons and how they are transported by proton pumps." Pflügers Archiv - European Journal of Physiology 457, no. 3 (May 6, 2008): 573–79. http://dx.doi.org/10.1007/s00424-008-0503-8.

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Schober, T. "Effective diffusivity of protons in high-temperature proton conductors." Ionics 1, no. 2 (March 1995): 97–100. http://dx.doi.org/10.1007/bf02388664.

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Denker, A., and J. Opitz-Coutureau. "Proton-induced x-ray emission using 68 MeV Protons." X-Ray Spectrometry 33, no. 1 (January 2004): 61–66. http://dx.doi.org/10.1002/xrs.706.

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Potgieter, Marius S., O. P. M. Aslam, Driaan Bisschoff, and Donald Ngobeni. "A Perspective on the Solar Modulation of Cosmic Anti-Matter." Physics 3, no. 4 (December 7, 2021): 1190–225. http://dx.doi.org/10.3390/physics3040076.

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Global modulation studies with comprehensive numerical models contribute meaningfully to the refinement of very local interstellar spectra (VLISs) for cosmic rays. Modulation of positrons and anti-protons are investigated to establish how the ratio of their intensity, and with respect to electrons and protons, are changing with solar activity. This includes the polarity reversal of the solar magnetic field which creates a 22-year modulation cycle. Modeling illustrates how they are modulated over time and the particle drift they experience which is significant at lower kinetic energy. The VLIS for anti-protons has a peculiar spectral shape in contrast to protons so that the total modulation of anti-protons is awkwardly different to that for protons. We find that the proton-to-anti-proton ratio between 1–2 GeV may change by a factor of 1.5 over a solar cycle and that the intensity for anti-protons may decrease by a factor of ~2 at 100 MeV during this cycle. A composition is presented of VLIS for protons, deuteron, helium isotopes, electrons, and particularly for positrons and anti-protons. Gaining knowledge of their respective 11 and 22 year modulation is useful to interpret observations of low-energy anti-nuclei at the Earth as tests of dark matter annihilation.

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Schlegel, Andreas, Adames Omar, Pia Jentsch, Andreas Morell, and Christoph Kempf. "Semliki Forest virus envelope proteins function as proton channels." Bioscience Reports 11, no. 5 (October 1, 1991): 243–55. http://dx.doi.org/10.1007/bf01127500.

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It has been shown that isolated nucleocapsids of Semliki Forest virus (SFV) contract upon low pH exposure (Soederlund et al., 1972). This contraction of the nucleocapsids has been used as an indicator to demonstrate that the spike proteins of SFV can translocate protons into the interior of the virus particle upon low pH (5.8) exposure. Spikeless virus particles obtained after bromelain digestion, which were used as a control, did not translocate protons. This implies that the ectodomain of the spike plays a crucial role for the proton translocation.

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Patyal, Baldev. "Dosimetry Aspects of Proton Therapy." Technology in Cancer Research & Treatment 6, no. 4_suppl (August 2007): 17–23. http://dx.doi.org/10.1177/15330346070060s403.

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High-energy photons and high-energy protons are very different in the ways they interact with matter. These differences lead to distinct advantages of protons over photons for treatment of cancer. Some aspects of proton interactions with tissue that make this modality superior for treating cancer are: (i) Initially, the protons lose energy very slowly as they enter the body; this results in a low entrance dose and low doses to the normal tissues proximal to the tumor. (ii) Near the end of range, protons lose energy very rapidly and deposit all their energy over a very small volume before they come to rest. This is the Bragg peak, a property that results in delivery of the maximum dose to the tumor. (iii) Beyond the Bragg peak, the energy deposited by the protons is zero; no dose is received by normal tissues distal to the tumor. Therefore, protons deliver their maximum dose to the tumor, a low dose to normal structures proximal to the tumor, and no dose to the normal structures beyond the tumor, ideal properties of a radiation modality to treat cancer. One distinct advantage of protons over photons is the ease with which the tumor target can be irradiated conformably to a high dose, and at the same time the normal structures in the vicinity of the tumor can be protected conformably from that high dose. Given the same dose to the tumor via photons and protons, protons inherently deliver less integral dose and, thus, lead to fewer normal-tissue complications. In addition, proton interactions also offer distinct radiobiological advantages over photons. Superior physical and radiobiological proton interactions lead naturally to the concepts of dose escalation and hypofractionation. The superiority of treatment delivery with protons as contrasted with photons is demonstrated by treatment plans.

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Bellomo, Giovanni, Enrico Ravera, Vito Calderone, Mauro Botta, Marco Fragai, Giacomo Parigi, and Claudio Luchinat. "Revisiting paramagnetic relaxation enhancements in slowly rotating systems: how long is the long range?" Magnetic Resonance 2, no. 1 (January 29, 2021): 25–31. http://dx.doi.org/10.5194/mr-2-25-2021.

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Abstract. Cross-relaxation terms in paramagnetic systems that reorient rigidly with slow tumbling times can increase the effective longitudinal relaxation rates of protons of more than 1 order of magnitude. This is evaluated by simulating the time evolution of the nuclear magnetization using a complete relaxation rate-matrix approach. The calculations show that the Solomon dependence of the paramagnetic relaxation rates on the metal–proton distance (as r−6) can be incorrect for protons farther than 15 Å from the metal and thus can cause sizable errors in R1-derived distance restraints used, for instance, for protein structure determination. Furthermore, the chemical exchange of these protons with bulk water protons can enhance the relaxation rate of the solvent protons by far more than expected from the paramagnetic Solomon equation. Therefore, it may contribute significantly to the water proton relaxation rates measured at magnetic resonance imaging (MRI) magnetic fields in the presence of slow-rotating nanoparticles containing paramagnetic ions and a large number of exchangeable surface protons.

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Parker, J. C. "Interactions of lithium and protons with the sodium-proton exchanger of dog red blood cells." Journal of General Physiology 87, no. 2 (February 1, 1986): 189–200. http://dx.doi.org/10.1085/jgp.87.2.189.

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Passive movements of Li in dog red blood cells (RBC) ar like those of Na and protons in being stimulated by osmotic cell shrinkage and inhibited by amiloride. Li and protons have similar asymmetrical effects on Na-H exchange. When the intracellular fluid is made rich in Li or protons, Na-H exchange is stimulated. When the extracellular fluid is enriched in Li or protons, Na-H exchange is inhibited. In the case of protons, these effects can override alterations in driving force that are created by the experimental conditions. For example, acidification of the cytoplasm stimulates outward Na movements, while acidification of the medium inhibits Na efflux. Thus, protons (and, by analogy, Li) can interact with the Na-H exchanger not only as substrates but also as modulators. In previous experiments, the only way to activate the Na-H exchanger in dog RBC was to shrink the cells in hypertonic media. The influences of Li or protons, however, are so strong as to preempt the volume effects, so that the pathway can be activated even in swollen cells and deactivated in shrunken ones.

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Hoang, Ngoc H., Vera Strogolova, Jaramys J. Mosley, Rosemary A. Stuart, and Jonathan Hosler. "Hypoxia-inducible gene domain 1 proteins in yeast mitochondria protect against proton leak through complex IV." Journal of Biological Chemistry 294, no. 46 (October 7, 2019): 17669–77. http://dx.doi.org/10.1074/jbc.ra119.010317.

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Hypoxia-inducible gene domain 1 (HIGD1) proteins are small integral membrane proteins, conserved from bacteria to humans, that associate with oxidative phosphorylation supercomplexes. Using yeast as a model organism, we have shown previously that its two HIGD1 proteins, Rcf1 and Rcf2, are required for the generation and maintenance of a normal membrane potential (ΔΨ) across the inner mitochondrial membrane (IMM). We postulated that the lower ΔΨ observed in the absence of the HIGD1 proteins may be due to decreased proton pumping by complex IV (CIV) or enhanced leak of protons across the IMM. Here we measured the ΔΨ generated by complex III (CIII) to discriminate between these possibilities. First, we found that the decreased ΔΨ observed in the absence of the HIGD1 proteins cannot be due to decreased proton pumping by CIV because CIII, operating alone, also exhibited a decreased ΔΨ when HIGD1 proteins were absent. Because CIII can neither lower its pumping stoichiometry nor transfer protons completely across the IMM, this result indicates that HIGD1 protein ablation enhances proton leak across the IMM. Second, we demonstrate that this proton leak occurs through CIV because ΔΨ generation by CIII is restored when CIV is removed from the cell. Third, the proton leak appeared to take place through an inactive population of CIV that accumulates when HIGD1 proteins are absent. We conclude that HIGD1 proteins in yeast prevent CIV inactivation, likely by preventing the loss of lipids bound within the Cox3 protein of CIV.

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Giovannini, Daniela, Cinzia De Angelis, Maria Denise Astorino, Emiliano Fratini, Evaristo Cisbani, Giulia Bazzano, Alessandro Ampollini, et al. "In Vivo Radiobiological Investigations with the TOP-IMPLART Proton Beam on a Medulloblastoma Mouse Model." International Journal of Molecular Sciences 24, no. 9 (May 5, 2023): 8281. http://dx.doi.org/10.3390/ijms24098281.

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Protons are now increasingly used to treat pediatric medulloblastoma (MB) patients. We designed and characterized a setup to deliver proton beams for in vivo radiobiology experiments at a TOP-IMPLART facility, a prototype of a proton-therapy linear accelerator developed at the ENEA Frascati Research Center, with the goal of assessing the feasibility of TOP-IMPLART for small animal proton therapy research. Mice bearing Sonic-Hedgehog (Shh)-dependent MB in the flank were irradiated with protons to test whether irradiation could be restricted to a specific depth in the tumor tissue and to compare apoptosis induced by the same dose of protons or photons. In addition, the brains of neonatal mice at postnatal day 5 (P5), representing a very small target, were irradiated with 6 Gy of protons with two different collimated Spread-Out Bragg Peaks (SOBPs). Apoptosis was visualized by immunohistochemistry for the apoptotic marker caspase-3-activated, and quantified by Western blot. Our findings proved that protons could be delivered to the upper part while sparing the deepest part of MB. In addition, a comparison of the effectiveness of protons and photons revealed a very similar increase in the expression of cleaved caspase-3. Finally, by using a very small target, the brain of P5-neonatal mice, we demonstrated that the proton irradiation field reached the desired depth in brain tissue. Using the TOP-IMPLART accelerator we established setup and procedures for proton irradiation, suitable for translational preclinical studies. This is the first example of in vivo experiments performed with a “full-linac” proton-therapy accelerator.

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Troost, E. "SP-0532 Against the motion (rebuttal) - Protons against Protons." Radiotherapy and Oncology 170 (May 2022): S465. http://dx.doi.org/10.1016/s0167-8140(22)03989-5.

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Fan, Jieqing, Qun Tan, and Jianhong Hao. "Analysis of displacement damage mechanism and simulation proton irradiation on GaAs." AIP Advances 12, no. 9 (September 1, 2022): 095304. http://dx.doi.org/10.1063/5.0104457.

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GaAs is an important material for preparing power supply for space vehicles, satellites, and space systems. To study the displacement damage of GaAs material caused by protons in the space environment, in this article, the Monte Carlo software Geant4 was used to simulate the transport process of space protons in GaAs; calculate the non-ionizing energy loss (NIEL) of protons with different energies; and obtain the species, energy range, and proportion of primary knock-on atom produced by proton irradiation with different energies. The results show that with the increase in the incident proton energy, the probability of elastic collision decreases and the probability of inelastic collision increases. The main source of displacement damage changes from elastic collision to inelastic collision. The radiation damage of low energy protons is serious at the end of the range, while that of high energy protons is serious at the beginning and end of the range. With the increase in the proton energy, the number of displaced atoms increases and the NIEL changes slowly. This provides a theoretical reference for the reliable operation of spacecraft.

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Trzebiński, M., R. Staszewski, and J. Chwastowski. "LHC High- Runs: Transport and Unfolding Methods." ISRN High Energy Physics 2012 (September 25, 2012): 1–10. http://dx.doi.org/10.5402/2012/491460.

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The paper describes the transport of the elastically and diffractively scattered protons in the proton-proton interactions at the LHC for the high- runs. A parametrisation of the scattered proton transport through the LHC magnetic lattice is presented. The accuracy of the unfolding of the kinematic variables of the scattered protons is discussed.

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Sakai, Jun-ichi, and Ryo Sugihara. "Non-Stochastic Acceleration of Protons in the Magnetic Neutral Sheet." Symposium - International Astronomical Union 107 (1985): 513–18. http://dx.doi.org/10.1017/s007418090007604x.

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A rapid non-stochastic proton acceleration mechanism by electrostatic waves during the substorm activity in the magnetospheric tail is presented to explain the origin of energetic protons (up to MeV). The protons are accelerated normal to the neutral sheet. Near a reconnection point, however, the protons are also accelerated along the sheet by a second process.

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Sokolov, Valerij S., Vsevolod Yu Tashkin, Darya D. Zykova, Yulia V. Kharitonova, Timur R. Galimzyanov, and Oleg V. Batishchev. "Electrostatic Potentials Caused by the Release of Protons from Photoactivated Compound Sodium 2-Methoxy-5-nitrophenyl Sulfate at the Surface of Bilayer Lipid Membrane." Membranes 13, no. 8 (August 8, 2023): 722. http://dx.doi.org/10.3390/membranes13080722.

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Lateral transport and release of protons at the water–membrane interface play crucial roles in cell bioenergetics. Therefore, versatile techniques need to be developed for investigating as well as clarifying the main features of these processes at the molecular level. Here, we experimentally measured the kinetics of binding of protons released from the photoactivated compound sodium 2-methoxy-5-nitrophenyl sulfate (MNPS) at the surface of a bilayer lipid membrane (BLM). We developed a theoretical model of this process describing the damage of MNPS coupled with the release of the protons at the membrane surface, as well as the exchange of MNPS molecules and protons between the membrane and solution. We found that the total change in the boundary potential difference across the membrane, ∆ϕb, is the sum of opposing effects of adsorption of MNPS anions and release of protons at the membrane–water interface. Steady-state change in the ∆ϕb due to protons decreased with the concentration of the buffer and increased with the pH of the solution. The change in the concentration of protons evaluated from measurements of ∆ϕb was close to that in the unstirred water layer near the BLM. This result, as well as rate constants of the proton exchange between the membrane and the bulk solution, indicated that the rate-limiting step of the proton surface to bulk release is the change in the concentration of protons in the unstirred layer. This means that the protons released from MNPS remain in equilibrium between the BLM surface and an adjacent water layer.

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Liu, Huiya, Anle Lei, Ning Kang, Honghai An, Zhiyong Xie, Yao Zhao, Shenlei Zhou, et al. "Characterization of Energetic Protons Generated in the ShenGuang-II UP Petawatt Laser Interactions with Foil Targets." Laser and Particle Beams 2021 (August 17, 2021): 1–7. http://dx.doi.org/10.1155/2021/7205383.

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The characterization of energetic protons generated in the ShenGuang-II UP petawatt laser interactions with foil targets has been systematically studied. The proton energy spectra and angular distributions are measured with a radiochromic film stack. It shows that the proton energy spectra have a Boltzmann distribution with temperature of about 2.8 MeV and cutoff energy of about 20 MeV. The divergence angles of protons vary from 10° to 60°, dependent on the proton energy. The proton source size and location are investigated via the proton point-projection mesh imaging. The proton virtual sources are found to locate tens to hundreds of microns in front of the foil target, depending on the proton energies. A Monte Carlo simulation estimates the diameter of the virtual proton source to be about 12 μm for the protons with energy of 16.8 MeV, which is much smaller than the laser focus size of about 50 μm. The spatial resolution of the 16.8 MeV proton imaging is quantified with the point spread function to be about 15 μm, which is consistent with the proton virtual source size. These results will be important for the users conducting experiments with the protons as a backlighting source on the ShenGuang-II UP petawatt laser.

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Wan, Q., R. K. Xu, and X. H. Li. "Proton release by tea plant (Camellia sinensis L.) roots as affected by nutrient solution concentration and pH." Plant, Soil and Environment 58, No. 9 (October 2, 2012): 429–34. http://dx.doi.org/10.17221/326/2012-pse.

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Solution culture experiments were conducted and the protons released were measured with an automatic titration system to determine the main factors affecting proton release by tea roots. Results indicated that the higher were the cation concentrations, the more protons were released from the roots, suggesting that tea roots took up a large amount of cations during growth, and then released protons to maintain charge balance of the plant body. The amount of protons released from tea roots at controlled pH was much higher than that in the treatments with uncontrolled pH. Stepwise multiple linear regression analysis showed that both NH4+ and Al(III) played distinct roles in proton release by tea plant roots. The uptake of Al(III) and NH4+ and subsequent release of protons may be an important mechanism for soil acidification in tea gardens.

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Nishino, M. N., M. Fujimoto, T. Terasawa, G. Ueno, K. Maezawa, T. Mukai, and Y. Saito. "Temperature anisotropies of electrons and two-component protons in the dusk plasma sheet." Annales Geophysicae 25, no. 6 (June 29, 2007): 1417–32. http://dx.doi.org/10.5194/angeo-25-1417-2007.

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Abstract. To investigate the cold plasma sheet formation under northward IMF, we study the temperature anisotropies of electrons and two-component protons observed by the Geotail spacecraft. The two-component protons, which are occasionally observed in the dusk plasma sheet near the low-latitude boundary, are the result of spatial mixing of the hot protons of the magnetosphere proper and the cold protons from the solar wind. Recent research focusing on the two-component protons reported that the cold proton component at times has a strong anisotropy, and that the sense of the anisotropy depends on the observed locations. Since electrons have been known to possess a strong parallel anisotropy around the low-latitude boundary layer, we compare anisotropies of electrons and protons to find that the strengths of parallel anisotropies of electrons and the cold proton component are in good correlation in the tail flank. The parallel anisotropy of electrons is stronger than that of the cold proton component, which is attributed to selective heating of electrons. We further find that the strengths of the parallel anisotropies in the tail flank depend on the latitudinal angle of the IMF; strong parallel anisotropies occur under strongly northward IMF. We discuss that the Kelvin-Helmholtz vortices, which developed under strongly northward IMF, and the resultant magnetic reconnection therein may lead to the strong parallel anisotropies observed in the tail flank.

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Kwon, Hanna, Jaswir Basran, Juliette M. Devos, Reynier Suardíaz, Marc W. van der Kamp, Adrian J. Mulholland, Tobias E. Schrader, et al. "Visualizing the protons in a metalloenzyme electron proton transfer pathway." Proceedings of the National Academy of Sciences 117, no. 12 (March 9, 2020): 6484–90. http://dx.doi.org/10.1073/pnas.1918936117.

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In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.

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Glerup, M. "Vibrational spectroscopy on protons and deuterons in proton conducting perovskites." Solid State Ionics 148, no. 1-2 (May 1, 2002): 83–92. http://dx.doi.org/10.1016/s0167-2738(02)00048-6.

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Cowley, A. A., J. V. Pilcher, J. J. Lawrie, and D. M. Whittal. "Protons of 200 MeV incident onC12. II. Quasifree proton knockout." Physical Review C 40, no. 5 (November 1, 1989): 1950–58. http://dx.doi.org/10.1103/physrevc.40.1950.

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Grigorieva, I. Yu, A. B. Struminsky, Yu I. Logachev, and A. M. Sadovskii. "Coronal Propagation of Solar Protons during and after Their Stochastic Acceleration." Космические исследования 61, no. 3 (May 1, 2023): 230–41. http://dx.doi.org/10.31857/s0023420622600246.

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Solar protons in eruptive flares are stochastically accelerated in a wide spatial angle, and then they are effectively kept behind the expanding coronal mass ejection (CME) front, which can either bring protons to the magnetic-field line going to a remote observer or carry them away. We consider 13 solar proton events of cycle 24 in which protons with energy E 100 MeV were recorded and were accompanied by the detection of solar hard X-ray (HXR) radiation with E 100 keV by an ACS SPI detector and γ-radiation with E 100 MeV by the FermiLAT telescope with a source in the western hemisphere of the Sun. The first arrival of solar protons into the Earth’s orbit was determined in each event by a significant “proton” excess over the ACS SPI background during or after the HXR burst. All events were considered relative to our chosen zero time (0 min) of parent flares. The “early” arrival of protons to the Earth’s orbit (+20 min), which was observed in four events, corresponds to the “fast” acceleration of electrons (10 MeV/s). The “late” arrival of protons (+20 min) corresponds to the “slow” acceleration of electrons (1 MeV/s) and was observed in six events. In three events, a “delayed” arrival of protons (+30 min) was observed, when the CME propagation hindered the magnetic connection of the source with the observer. The direction of CME propagation is characterized in the catalog (SOHO LASCO CME Catalog) by the position angle (PA). The observed PA systematizes the times of the first arrival of protons and the growth rate of their intensity. The PA parameter should be taken into account in the analysis of proton events.

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DeCoursey, Thomas E. "Voltage and pH sensing by the voltage-gated proton channel, H V 1." Journal of The Royal Society Interface 15, no. 141 (April 2018): 20180108. http://dx.doi.org/10.1098/rsif.2018.0108.

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Voltage-gated proton channels are unique ion channels, membrane proteins that allow protons but no other ions to cross cell membranes. They are found in diverse species, from unicellular marine life to humans. In all cells, their function requires that they open and conduct current only under certain conditions, typically when the electrochemical gradient for protons is outwards. Consequently, these proteins behave like rectifiers, conducting protons out of cells. Their activity has electrical consequences and also changes the pH on both sides of the membrane. Here we summarize what is known about the way these proteins sense the membrane potential and the pH inside and outside the cell. Currently, it is hypothesized that membrane potential is sensed by permanently charged arginines (with very high p K a ) within the protein, which results in parts of the protein moving to produce a conduction pathway. The mechanism of pH sensing appears to involve titratable side chains of particular amino acids. For this purpose their p K a needs to be within the operational pH range. We propose a ‘counter-charge’ model for pH sensing in which electrostatic interactions within the protein are selectively disrupted by protonation of internally or externally accessible groups.

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OELERT, WALTER. "ELENA: AN UPGRADE TO THE ANTI-PROTON DECELERATOR AT CERN." International Journal of Modern Physics A 26, no. 03n04 (February 10, 2011): 390–95. http://dx.doi.org/10.1142/s0217751x11051718.

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CERN has a long tradition of pursuing fundamental physics on a variety of energy scales. For anti-protons CERN famously produced the high-energy SPS beam but also the world's only and unique sources of low-energy anti-protons – first the Low Energy Anti-proton Ring (LEAR) and thereafter the Anti-proton Decelerator (AD). The scientific demand for low-energy anti-protons at the AD continues to grow. More rapid progress and much higher measurement precision might be possible by upgrading the AD to increase and optimize the number of cold anti-protons that can be trapped and accumulated. To achieve this the construction of an Extra Low ENergy Antiproton (ELENA) ring is proposed which involves both the addition of a small storage ring and electrostatic beam lines to the experiments. The design parameters have been carefully studied and agreed upon over several years. At least during the next decade there is no alternative low-energy anti-proton source for physics to be done now.

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Mashiko, Misaki, Aya Kurosawa, Yuki Tani, Takashi Tsuji, and Shigeki Takeda. "GPR31 and GPR151 are activated under acidic conditions." Journal of Biochemistry 166, no. 4 (May 23, 2019): 317–22. http://dx.doi.org/10.1093/jb/mvz042.

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Abstract Recent studies have revealed that not only proton-sensing channels, but also one family of G protein-coupled receptors (GPCRs) comprising OGR1, GPR4, G2A and TDAG8 are responsible for the sensing of extracellular protons, or pH. Here, we report that two other GPCRs, GPR31 and GPR151, were also activated in acidic condition. Elevated pH of assay mixtures resulted in a remarkable increase in [35S]GTPγS binding by GPR31–Giα and GPR151–Giα fusion proteins in a narrow range between pH 6 and 5. Our reporter gene assays with CHO cells expressing recombinant GPR31 or GPR151 also showed that activation was maximal at pH ∼5.8. Although these results from in vitro and cellular assays revealed slightly different pH sensitivities, all of our results indicated that GPR31 and GPR151 sensed extracellular protons equally well as other proton-sensing GPCRs.

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Sladkov, K. D., and S. S. Kolesnikov. "Model of a Molecular Proton Sensor in Taste Cells." Биологические мембраны Журнал мембранной и клеточной биологии 40, no. 3 (May 1, 2023): 188–93. http://dx.doi.org/10.31857/s023347552303009x.

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Otopetrins represents a group of membrane proteins that function as proton-selective ion channels. Existing evidence indicates that Otop1, the eponym of the family, is a likely molecular sensor of protons involved in detecting acid stimuli in taste cells of type III. Acid stimuli is believed to initiate an inward current carried by protons through receptive apical membrane to depolarize a type III cell and trigger a train of action potentials driving afferent neurotransmission. While many details of this rather complicated process have not been uncovered yet, mathematical modelling could provide a sufficient insight into sour transduction. Here we present a mathematical model for describing dynamic and transport properties of Otop1 channel. The elaborated model appropriately describes proton currents through Otop1 under different conditions, and it could be employed for further modeling of sour responses of taste cells.

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Jones, S. B., T. S. Nonnenmacher, E. Atkin, G. J. Barker, A. Basharina-Freshville, C. Betancourt, S. B. Boyd, et al. "Off-Axis Characterisation of the CERN T10 Beam for low Momentum Proton Measurements with a High Pressure Gas Time Projection Chamber." Instruments 4, no. 3 (July 28, 2020): 21. http://dx.doi.org/10.3390/instruments4030021.

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We present studies of proton fluxes in the T10 beamline at CERN. A prototype high pressure gas time projection chamber (TPC) was exposed to the beam of protons and other particles, using the 0.8 GeV/c momentum setting in T10, in order to make cross section measurements of low energy protons in argon. To explore the energy region comparable to hadrons produced by GeV-scale neutrino interactions at oscillation experiments, i.e., near 0.1 GeV of kinetic energy, methods of moderating the T10 beam were employed: the dual technique of moderating the beam with acrylic blocks and measuring scattered protons off the beam axis was used to decrease the kinetic energy of incident protons, as well as change the proton/minimum ionising particle (MIP) composition of the incident flux. Measurements of the beam properties were made using time of flight systems upstream and downstream of the TPC. The kinetic energy of protons reaching the TPC was successfully changed from ∼0.3 GeV without moderator blocks to less than 0.1 GeV with four moderator blocks (40 cm path length). The flux of both protons and MIPs off the beam axis was increased. The ratio of protons to MIPs vary as a function of the off-axis angle allowing for possible optimisation of the detector to select the type of required particles. Simulation informed by the time of flight measurements show that with four moderator blocks placed in the beamline, (5.6 ± 0.1) protons with energies below 0.1 GeV per spill traversed the active TPC region. Measurements of the beam composition and energy are presented.

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Journal articles on the topic 'Protons'

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