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  1 / 28009 MEDLINE  
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PMID:29311594
Autor:Nakanishi A; Kishikawa JI; Tamakoshi M; Mitsuoka K; Yokoyama K
Endereço:Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, 603-8555, Japan.
Título:Cryo EM structure of intact rotary H -ATPase/synthase from Thermus thermophilus.
Fonte:Nat Commun; 9(1):89, 2018 01 08.
ISSN:2041-1723
País de publicação:England
Idioma:eng
Resumo:Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H -rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (Bacterial Proteins); 0 (Protein Subunits); 0 (Protons); 8L70Q75FXE (Adenosine Triphosphate); EC 3.6.1.- (Vacuolar Proton-Translocating ATPases)


  2 / 28009 MEDLINE  
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PMID:28742053
Autor:Lehrack S; Assmann W; Bertrand D; Henrotin S; Herault J; Heymans V; Stappen FV; Thirolf PG; Vidal M; Van de Walle J; Parodi K
Endereço:Department of Medical Physics, Ludwig-Maximilians-Universität München, 85748 Garching b. München, Germany.
Título:Submillimeter ionoacoustic range determination for protons in water at a clinical synchrocyclotron.
Fonte:Phys Med Biol; 62(17):L20-L30, 2017 Aug 18.
ISSN:1361-6560
País de publicação:England
Idioma:eng
Resumo:Proton ranges in water between 145 MeV to 227 MeV initial energy have been measured at a clinical superconducting synchrocyclotron using the acoustic signal induced by the ion dose deposition (ionoacoustic effect). Detection of ultrasound waves was performed by a very sensitive hydrophone and signals were stored in a digital oscilloscope triggered by secondary prompt gammas. The ionoacoustic range measurements were compared to existing range data from a calibrated range detector setup on-site and agreement of better than 1 mm was found at a Bragg peak dose of about 10 Gy for 220 MeV initial proton energy, compatible with the experimental errors. Ionoacoustics has thus the potential to measure the Bragg peak position with submillimeter accuracy during proton therapy, possibly correlated with ultrasound tissue imaging.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Protons); 059QF0KO0R (Water)


  3 / 28009 MEDLINE  
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PMID:28470848
Autor:Camprubi E; Jordan SF; Vasiliadou R; Lane N
Endereço:Department of Genetics, Evolution and Environment, University College London, London, UK.
Título:Iron catalysis at the origin of life.
Fonte:IUBMB Life; 69(6):373-381, 2017 06.
ISSN:1521-6551
País de publicação:England
Idioma:eng
Resumo:Iron-sulphur proteins are ancient and drive fundamental processes in cells, notably electron transfer and CO fixation. Iron-sulphur minerals with equivalent structures could have played a key role in the origin of life. However, the 'iron-sulphur world' hypothesis has had a mixed reception, with questions raised especially about the feasibility of a pyrites-pulled reverse Krebs cycle. Phylogenetics suggests that the earliest cells drove carbon and energy metabolism via the acetyl CoA pathway, which is also replete in Fe(Ni)S proteins. Deep differences between bacteria and archaea in this pathway obscure the ancestral state. These differences make sense if early cells depended on natural proton gradients in alkaline hydrothermal vents. If so, the acetyl CoA pathway diverged with the origins of active ion pumping, and ancestral CO fixation might have been equivalent to methanogens, which depend on a membrane-bound NiFe hydrogenase, energy converting hydrogenase. This uses the proton-motive force to reduce ferredoxin, thence CO . The mechanism suggests that pH could modulate reduction potential at the active site of the enzyme, facilitating the difficult reduction of CO by H . This mechanism could be generalised under abiotic conditions so that steep pH differences across semi-conducting Fe(Ni)S barriers drives not just the first steps of CO fixation to C1 and C2 organics such as CO, CH SH and CH COSH, but a series of similar carbonylation and hydrogenation reactions to form longer chain carboxylic acids such as pyruvate, oxaloacetate and α-ketoglutarate, as in the incomplete reverse Krebs cycle found in methanogens. We suggest that the closure of a complete reverse Krebs cycle, by regenerating acetyl CoA directly, displaced the acetyl CoA pathway from many modern groups. A later reliance on acetyl CoA and ATP eliminated the need for the proton-motive force to drive most steps of the reverse Krebs cycle. © 2017 IUBMB Life, 69(6):373-381, 2017.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Ferredoxins); 0 (Iron-Sulfur Proteins); 0 (Ketoglutaric Acids); 0 (Protons); 142M471B3J (Carbon Dioxide); 2F399MM81J (Oxaloacetic Acid); 72-89-9 (Acetyl Coenzyme A); 8558G7RUTR (Pyruvic Acid); 8ID597Z82X (alpha-ketoglutaric acid); E1UOL152H7 (Iron)


  4 / 28009 MEDLINE  
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PMID:29193978
Autor:Balestri D; Roux Y; Mattarozzi M; Mucchino C; Heux L; Brazzolotto D; Artero V; Duboc C; Pelagatti P; Marchiò L; Gennari M
Endereço:Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma , Parco Area delle Scienze 17A, 43124 Parma, Italy.
Título:Heterogenization of a [NiFe] Hydrogenase Mimic through Simple and Efficient Encapsulation into a Mesoporous MOF.
Fonte:Inorg Chem; 56(24):14801-14808, 2017 Dec 18.
ISSN:1520-510X
País de publicação:United States
Idioma:eng
Resumo:In the quest for new, efficient, and noble-metal-free H -evolution catalysts, hydrogenase enzymes are a source of inspiration. Here, we describe the development of a new hybrid material based on a structural and functional [NiFe]-hydrogenase model complex (NiFe) incorporated into the Zr-based MOF PCN-777. The bulk NiFe@PCN-777 material was synthesized by simple encapsulation. Characterization by solid-state NMR and IR spectroscopy, SEM-EDX, ICP-OES, and gas adsorption confirmed the inclusion of the guest. FTO-supported thin films of the NiFe@PCN-777 composite were obtained by electrophoretic deposition of the bulk material and characterized by SEM-EDX, ICP-OES, and cyclic voltammetry. The average surface concentration of electroactive NiFe catalyst in the film was found to be ∼9.6 × 10 mol cm , implying that a surprisingly high fraction (37%) of NiFe units incorporated in the MOF are electroactive. By cyclic voltammetry, we showed that NiFe maintains its electrocatalytic capabilities for H reduction inside the MOF cavities, even if under controlled-potential electrolysis conditions the activity of NiFe cannot be discerned from that of free PCN-777 and FTO.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Metal-Organic Frameworks); 0 (Protons); 7OV03QG267 (Nickel); C6V6S92N3C (Zirconium); E1UOL152H7 (Iron); EC 1.12.- (nickel-iron hydrogenase); EC 1.12.7.2 (Hydrogenase)


  5 / 28009 MEDLINE  
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PMID:29188999
Autor:Song LC; Zhu L; Hu FQ; Wang YX
Endereço:Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, and ‡Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China.
Título:Studies on Chemical Reactivity and Electrocatalysis of Two Acylmethyl(hydroxymethyl)pyridine Ligand-Containing [Fe]-Hydrogenase Models (2-COCH -6-HOCH C H N)Fe(CO) L (L = η -SCOMe, η -2-SC H N).
Fonte:Inorg Chem; 56(24):15216-15230, 2017 Dec 18.
ISSN:1520-510X
País de publicação:United States
Idioma:eng
Resumo:On the basis of preparation and characterization of [Fe]-H ase models (2-COCH -6-HOCH C H N)Fe(CO) L (A, L = η -SCOMe; B, L = η -2-SC H N), the chemical reactivities of A and B with various electrophilic and nucleophilic reagents have been investigated, systematically. Thus, when A reacted with 1 equiv of MeCOCl in the presence of Et N in MeCN to give the η -SCOMe-coordinated acylation product (2-COCH -6-MeCO CH C H N)Fe(CO) (η -SCOMe) (1), treatment of A with excess HBF ·Et O in MeCN gave the cationic MeCN-coordinated complex [(2-COCH -6-HOCH C H N)Fe(CO) (MeCN)](BF ) (2). In addition, when 2 was treated with 1 equiv of 2,6-(p-4-MeC H ) C H SK or PPh in CH Cl to give the thiophenolato- and PPh -substituted derivatives (2-COCH -6-HOCH C H N)Fe(CO) [2,6-(p-MeC H ) C H S] (3) and [(2-COCH -6-HOCH C H N)Fe(CO) (PPh )](BF ) (4), treatment of B with 1 equiv of PMe or P(OMe) in THF afforded the phosphine- and phosphite-substituted complexes (2-COCH -6-HOCH C H N)(η -2-SC H N)Fe(CO) L (5, L = PMe ; 6, L = P(OMe) ). Interestingly, in contrast to A, when B reacted with excess HBF ·Et O in MeCN to afford the BF adduct [2-COCH -6-HO(BF )CH C H N]Fe(CO) (η -2-SC H N) (7), reaction of B with 1 equiv of p-MeC H COCl in the presence of Et N in MeCN gave not only the expected 2-acylmethyl-6-p-toluoyloxomethylpyridine-containing complex (2-COCH -6-p-MeC H CO CH C H N)Fe(CO) (η -2-SC H N) (8), but also gave the unexpected 2-toluoyloxovinyl-6-toluoyloxomethylpyridine-containing complex (2-p-MeC H CO C H-6-p-MeC H CO CH C H N)Fe(CO) (η -2-SC H N) (9). While the possible pathways for the novel reactions leading to complexes 1, 2, and 7-9 are suggested, the structures of complexes B, 1-4, and 6-9 were unambiguously confirmed by X-ray crystallography. In addition, model complexes A and B have been found to be catalysts for proton reduction to H from TFA under CV conditions.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Iron Compounds); 0 (Iron-Sulfur Proteins); 0 (Ligands); 0 (Protons); 0 (Pyridines); 0 (acylmethyl(hydroxymethyl)pyridine); EC 1.12.- (iron hydrogenase); EC 1.12.7.2 (Hydrogenase)


  6 / 28009 MEDLINE  
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PMID:29354835
Autor:Avilés-Moreno JR; Berden G; Oomens J; Martínez-Haya B
Endereço:Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain. bmarhay@upo.es.
Título:Guanidinium/ammonium competition and proton transfer in the interaction of the amino acid arginine with the tetracarboxylic 18-crown-6 ionophore.
Fonte:Phys Chem Chem Phys; 20(6):4067-4073, 2018 Feb 07.
ISSN:1463-9084
País de publicação:England
Idioma:eng
Resumo:The recognition of arginine plays a central role in modern proteomics and genomics. Arginine is unique among natural amino acids due to the high basicity of its guanidinium side chain, which sustains specific interactions and proton exchange biochemical processes. The search for suitable macrocyclic ionophores constitutes a promising route towards the development of arginine receptors. This study evaluates the conformational features involved in the binding of free arginine by the polyether macrocycle (18-crown-6)-tetracarboxylic acid. Infrared action vibrational spectroscopy and quantum-chemical computations are combined to characterize the complexes with net charges +1 and +2. The spectrum of the +1 complex can be explained in terms of a configuration predominantly stabilized by a robust bidentate coordination of guanidinium with a carboxylate group formed from the deprotonation of one side group of the crown ether. The released proton is transferred to the amino terminus of arginine, which then coordinates with the crown ether ring. In an alternative type of conformation, partly consistent with experiment, the amino terminus is neutral and the guanidinium group inserts into the crown ether cavity. In the +2 complexes, arginine is always doubly protonated and the most stable conformations are characterized by a tripodal coordination of the ammonium -NH group of arginine with the oxygen atoms of the macrocycle ring, while the interactions of the amino acid with the side carboxylic acid groups of the crown ether acquire a remarkable lesser role.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Ammonium Compounds); 0 (Crown Ethers); 0 (Protons); 63J177NC5B (18-crown-6); 94ZLA3W45F (Arginine); JU58VJ6Y3B (Guanidine)


  7 / 28009 MEDLINE  
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PMID:27770745
Autor:Kocak A; Erol I; Yildiz M; Can H
Endereço:Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey. Electronic address: kocak@gtu.edu.tr.
Título:Computational insights into the protonation states of catalytic dyad in BACE1-acyl guanidine based inhibitor complex.
Fonte:J Mol Graph Model; 70:226-235, 2016 11.
ISSN:1873-4243
País de publicação:United States
Idioma:eng
Resumo:Developing small compound based drugs targeting the ß-secretase (BACE) enzyme is one of the most promising strategies in treatment of the Alzheimer's disease. As the enzyme shows the activity based on the acid-base reaction at a very narrow pH range, the protonation state of aspartic acids with the residue number 32 and 228 (Asp32 and Asp228), which forms the active site dyad, along with the protonation state of the ligand (substrate or inhibitor) play very critical role in interactions between the ligand and enzyme. Thus, understanding the nature of the protonation state of both enzyme's active site dyad and ligand is crucial for drug design in Alzheimer's disease field. Here we have investigated the protonation state of the Asp32 and Asp228 residues in the presence of a highly potent beta secretase inhibitor, containing acyl guanidine warhead that have recently been devised but not extensively studied. Our Quantum Mechanical, Molecular Dynamics and Docking studies on all the possible protonation states have suggested that the dyad residues are in di-deprotonated states in the presence of protonated inhibitor.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Ligands); 0 (Protease Inhibitors); 0 (Protons); EC 3.4.- (Amyloid Precursor Protein Secretases); JU58VJ6Y3B (Guanidine)


  8 / 28009 MEDLINE  
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PMID:28470253
Autor:Sladek V; Kóna J; Tokiwa H
Endereço:Institute of Chemistry - Centre for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia. vladimir.sladek86@gmail.com sladek.vladimir@savba.sk.
Título:In silico analysis of interaction pattern switching in ligandreceptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors.
Fonte:Phys Chem Chem Phys; 19(19):12527-12537, 2017 May 21.
ISSN:1463-9084
País de publicação:England
Idioma:eng
Resumo:Golgi α-mannosidase II (GM) is a pharmaceutical target for the design of inhibitors with anticancer activity. The known potent GM inhibitors undergo complex interactions with Zn ions and the active-site amino acids, many of which contain ionisable functional groups. Herein, the physical insight into the ligandreceptor interactions has been provided based on energy decomposition techniques: SAPT (symmetry adapted perturbation theory) and FMO-PIEDA (fragment molecular orbital-pair interaction energy decomposition analysis) for a large GM active-site cluster. Protonation-dependent molecular recognition in Golgi α-mannosidase was demonstrated for five inhibitors, mannose, and its transition state. Zn ion and Asp472 induce the key interactions with the deprotonated inhibitors (bearing an amino group in the neutral state), followed by Asp92 and Asp341. This interaction pattern is consistent for all the studied inhibitors and is similar to the interaction pattern of the enzyme native substrate - mannose. The interactions with Zn ion become repulsive for the protonated states of the inhibitors (bearing an amino group with +1 charge) and the mannosyl transition state. The importance of Asp92 and Asp204 considerably increases, while the interactions with Asp472 and Asp341 are slightly modified. The interaction pattern for the protonated ligands seems to have an oxocarbenium transition state-like character, rather than a Michaelis complex of GM. The electrostatic interactions with amino acids coordinating zinc ion are of key importance for both the neutral and protonated states of the inhibitors. The ligand's diol group has a dual role as an electron donor, coordinating zinc ion, and as an electron acceptor, interacting with Asp92 and Asp472 via strong hydrogen bonds. This interaction pattern is an essential structural feature of the potent GM inhibitors, which is consistent with the experimental findings. Based on the calculations, either the protonated or deprotonated state of the ligand may be the active form of the GM inhibitor, exhibiting different interacting patterns.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Antineoplastic Agents); 0 (Enzyme Inhibitors); 0 (Ligands); 0 (Protons); EC 3.2.1.- (Mannosidases); EC 3.2.1.114 (mannosyl-oligosaccharide 1,3 - 1,6-alpha-mannosidase); J41CSQ7QDS (Zinc)


  9 / 28009 MEDLINE  
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PMID:28467902
Autor:Furukawa A; Yoshikaie K; Mori T; Mori H; Morimoto YV; Sugano Y; Iwaki S; Minamino T; Sugita Y; Tanaka Y; Tsukazaki T
Endereço:Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.
Título:Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF.
Fonte:Cell Rep; 19(5):895-901, 2017 May 02.
ISSN:2211-1247
País de publicação:United States
Idioma:eng
Resumo:Protein secretion mediated by SecYEG translocon and SecA ATPase is enhanced by membrane-embedded SecDF by using proton motive force. A previous structural study of SecDF indicated that it comprises 12 transmembrane helices that can conduct protons and three periplasmic domains, which form at least two characterized transition states, termed the F and I forms. We report the structures of full-length SecDF in I form at 2.6- to 2.8-Å resolution. The structures revealed that SecDF in I form can generate a tunnel that penetrates the transmembrane region and functions as a proton pathway regulated by a conserved Asp residue of the transmembrane region. In one crystal structure, periplasmic cavity interacts with a molecule, potentially polyethylene glycol, which may mimic a substrate peptide. This study provides structural insights into the Sec protein translocation that allows future analyses to develop a more detailed working model for SecDF.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Bacterial Proteins); 0 (Glycolipids); 0 (Peptides); 0 (Protons); 0 (SEC Translocation Channels); 0 (deinococcucin A)


  10 / 28009 MEDLINE  
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PMID:28464743
Autor:Dahle TJ; Rykkelid AM; Stokkevåg CH; Mairani A; Görgen A; Edin NJ; Rørvik E; Fjæra LF; Malinen E; Ytre-Hauge KS
Endereço:a Department of Physics and Technology , University of Bergen , Bergen , Norway.
Título:Monte Carlo simulations of a low energy proton beamline for radiobiological experiments.
Fonte:Acta Oncol; 56(6):779-786, 2017 Jun.
ISSN:1651-226X
País de publicação:England
Idioma:eng
Resumo:BACKGROUND: In order to determine the relative biological effectiveness (RBE) of protons with high accuracy, radiobiological experiments with detailed knowledge of the linear energy transfer (LET) are needed. Cell survival data from high LET protons are sparse and experiments with low energy protons to achieve high LET values are therefore required. The aim of this study was to quantify LET distributions from a low energy proton beam by using Monte Carlo (MC) simulations, and to further compare to a proton beam representing a typical minimum energy available at clinical facilities. MATERIALS AND METHODS: A Markus ionization chamber and Gafchromic films were employed in dose measurements in the proton beam at Oslo Cyclotron Laboratory. Dose profiles were also calculated using the FLUKA MC code, with the MC beam parameters optimized based on comparisons with the measurements. LET spectra and dose-averaged LET (LET ) were then estimated in FLUKA, and compared with LET calculated from an 80 MeV proton beam. RESULTS: The initial proton energy was determined to be 15.5 MeV, with a Gaussian energy distribution of 0.2% full width at half maximum (FWHM) and a Gaussian lateral spread of 2 mm FWHM. The LET increased with depth, from approximately 5 keV/µm in the entrance to approximately 40 keV/µm in the distal dose fall-off. The LET values were considerably higher and the LET spectra were much narrower than the corresponding spectra from the 80 MeV beam. CONCLUSIONS: MC simulations accurately modeled the dose distribution from the proton beam and could be used to estimate the LET at any position in the setup. The setup can be used to study the RBE for protons at high LET , which is not achievable in clinical proton therapy facilities.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Protons)



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