scholarly journals Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

2021 ◽  
Vol 9 ◽  
Author(s):  
Divya Kaur ◽  
Umesh Khaniya ◽  
Yingying Zhang ◽  
M. R. Gunner
Keyword(s):  
Proton Transfer ◽  
Active Sites ◽  
Atp Synthesis ◽  
Signaling Cascades ◽  
Proton Pumps ◽  
High Concentration ◽  
Protein Motifs ◽  
Proton Transfers ◽  
Cellular Compartments ◽  
Multiple Charge

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

Catalytic Neutralization of Naphthenic Acid from Petroleum Crude Oil by Using Cerium Oxide Catalyst and 2- Methylimidazole in Polyethylene Glycol

2020 ◽  
Vol 13 ◽  
Author(s):  
Norshahidatul Akmar Mohd Shohaimi ◽  
Norfakhriah Jelani ◽  
Ahmad Zamani Ab Halim ◽  
Nor Hakimin Abdullah ◽  
Nurasmat Mohd Shukri
Keyword(s):  
Polyethylene Glycol ◽  
Crude Oil ◽  
Cerium Oxide ◽  
Active Sites ◽  
Naphthenic Acid ◽  
Naphthenic Acids ◽  
Catalyst Loading ◽  
High Concentration ◽  
Oil Refineries ◽  
Al2o3 Catalyst

: The presence of relatively high naphthenic acid in crude oil may contribute to the major corrosion in oil pipelines and distillation units in crude oil refineries. Thus, high concentration Naphthenic Acids crude oil is considered tobe of low quality and is marketed at lower prices. In order to overcome this problem, neutralization method had been developed to reduce the TAN value in crude oil. In this study, crude oil from Petronas Penapisan Melaka was investigated. The parameters studied were reagent concentration, catalyst loading, calcination temperature and reusability of the potential catalyst. Basic chemical used were 2- methylimidazole in polyethylene glycol (PEG 600) with concentration 100, 500 and 1000 ppm. Cerium oxide-based catalysts supported onto alumina prepared with different calcination temperatures. The catalyst was characterized by using Brunauer-Emmett-Teller (BET), Fourier Transform Infrared Spectroscopy (FTIR) and Thermogravimetry Analysis-Differential Thermal Gravity (TGA-DTG) to study physical properties of the catalyst. The Ce/Al2O3 catalyst calcined at 1000°C was the best catalyst due to larger surface area formation which lead to increment of active sites thus will boost the catalytic activity. The result showed that the Ce/Al2O3 catalyst meet Petronas requirement as the TAN value reduced to 0.6 mgKOH/g from original TAN value of 4.22 mgKOH/g. The best reduction of TAN was achieved by using catalyst loading of 0.39% and reagent of 1000 ppm.

Effect of Oxygen and Water in the CO Photocatalytic Oxidation with TiO2

2011 ◽  
Vol 324 ◽  
pp. 149-152
Author(s):  
Carlos Youssef ◽  
Eric Puzenat ◽  
Samir Najm ◽  
Nicole Jaffrezic-Renault ◽  
Chantal Guillard
Keyword(s):  
Water Vapor ◽  
Active Sites ◽  
Photocatalytic Oxidation ◽  
Low Oxygen ◽  
High Concentration ◽  
Co Concentration ◽  
Langmuir Hinshelwood Mechanism ◽  
Effect Of Oxygen ◽  
Two Parameters ◽  
Low Oxygen Concentration

TiO2P25 catalyst was used to study the photocatalytic oxidation of CO to CO2at 288K. Two parameters, O2and H2O were used to study its effect on the photocatalytic process. The dependency of the reaction rate on the CO concentration and water vapor was explained in terms of Langmuir-Hinshelwood mechanism. The presence of a high concentration of water vapor inhibits the CO photocatalytic oxidation at low oxygen concentration. We have noted an adsorption competition between CO and H2O on the TiO2active sites.

A mathematical model of the carbon metabolism in photosynthesis. Difficulties in explaining oscillations by fructose 2, 6-bisphosphate regulation

1989 ◽  
Vol 237 (1289) ◽  
pp. 389-415 ◽  
Keyword(s):  
Mathematical Model ◽  
Active Sites ◽  
Starch Synthesis ◽  
Standard Free Energy ◽  
Atp Synthesis ◽  
Rate Equations ◽  
Standard Free Energy Change ◽  
Sucrose Synthesis ◽  
Carbon Reduction ◽  
Fructose 2

A mathematical model of the pentosephosphate carbon reduction (PCR) cycle is presented. The internal structure of the model is consistent with and complements the known biochemical pathways in the PCR cycle, together with starch and sucrose synthesis. Individual enzymes are described by maximum rate ( V m ), standard free energy change (Δ G´ 0 ) and Michaelis constant ( K m ) values as parameters and rate-equations, sym­metrical for the direct and reverse reactions. Enzymic control is included in the starch synthesis pathway (activation by phosphoglycerate (PGA)), inhibition by inorganic phosphate) and in the reactions of sucrose synthesis based on fructose 2, 6-bisphosphate (F2, 6BP) as a metabolite con­trolling the cytosolic fructose bisphosphatase (FBPase) activity. The phosphate translocator carries out the exchange of triose phosphates, orthophosphate and PGA. Ionic forms of metabolites are calculated in relation to pH and assumed to be the actual reacting substances. The significant concentration of the active sites of ribulose 1, 5-bisphosphate (RuBP) carboxylase is taken into account. Light reactions are included only in the form of an ATPase the Δ G´ 0 of which is shifted towards ATP synthesis by the existing proton gradient. The behaviour of the model was studied with the aim of reproducing oscillations in photosynthesis. It is concluded that oscillations in photosynthesis cannot be caused by the fructose 2, 6-bisphosphate control of sucrose synthesis alone, but that an additional control of photosynthetic rate must also be involved.

Cellular metabolism

2021 ◽  
pp. 105-194
Keyword(s):  
Electron Transport Chain ◽  
Inborn Errors Of Metabolism ◽  
Krebs Cycle ◽  
Cellular Metabolism ◽  
Atp Synthesis ◽  
The Body ◽  
Clinical Aspects ◽  
Inborn Errors ◽  
Transport Chain ◽  
Cellular Compartments

‘Cellular metabolism’ addresses the major biochemical pathways and processes of the cells of the body. These include the central metabolic pathways involved in energy production: the tricarboxylic acid or Krebs cycle, and ATP synthesis through the electron transport chain and oxidative phosphorylation (chemiosmotic theory). Metabolism of each of the major fuel sources is considered: lipids, carbohydrates, and proteins, including energy storage as fat and glycogen, and excretion of nitrogen via the urea cycle. The different cellular compartments for metabolism are explored, as is the integration and regulation of the metabolic processes in a number of conditions such as fasting and starvation, exercise, pregnancy, and diabetes. Finally in this chapter the clinical aspects of metabolism are discussed, including energy balance and nutrition, obesity, and inborn errors of metabolism.

Pathway of Proton Transfer in Bacterial Reaction Centers: Role of Aspartate-L213 in Proton Transfers Associated with Reduction of Quinone to Dihydroquinone

Biochemistry ◽  
1994 ◽  
Vol 33 (3) ◽  
pp. 734-745 ◽  
Author(s):  
M. L. Paddock ◽  
S. H. Rongey ◽  
P. H. McPherson ◽  
A. Juth ◽  
G. Feher ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Reaction Centers ◽  
Bacterial Reaction Centers ◽  
Proton Transfers

SIMULATION OF CO CHEMISORPTION ON Pt SUPPORTED ON FRACTAL SURFACES

2005 ◽  
Vol 04 (03) ◽  
pp. 769-785 ◽  
Author(s):  
GIANINA DOBRESCU ◽  
IUDIT FANGLI ◽  
MIRCEA RUSU
Keyword(s):  
Active Sites ◽  
Energy Surface ◽  
Weak Interactions ◽  
Fractal Surface ◽  
High Concentration ◽  
Co Chemisorption ◽  
Fractal Surfaces ◽  
Lennard Jones ◽  
Planar Surfaces ◽  
Co Chemisorption On Pt

CO chemisorption on Pt supported on fractal surfaces was simulated in order to compute chemisorption dimension and active sites fractal dimension. Pt deposition was simulated using different models on both fractal and planar surfaces. The potential energy surface with two adsorption positions model was used to compute Pt–CO interaction and a Lennard–Jones 6–12 potential was used to simulate CO–CO interaction. Two Pt phases on fractal surface, one at low concentration — the dispersed phase and the second at high concentration — the aggregated phase characterized by weak interactions with support are obtained. The results are in accord with experimental data of CO chemisorption on Pt supported on γ-alumina. Computed data obtained for planar support are compared with those obtained on fractal support. The effect of fractal support on chemisorption data is underlined.

scholarly journals Systematic analysis of Ca2+homeostasis inSaccharomyces cerevisiaebased on chemical-genetic interaction profiles

2017 ◽  
Vol 28 (23) ◽  
pp. 3415-3427 ◽  
Author(s):  
Farzan Ghanegolmohammadi ◽  
Mitsunori Yoshida ◽  
Shinsuke Ohnuki ◽  
Yuko Sukegawa ◽  
Hiroki Okada ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Principal Component ◽  
Analysis Of Covariance ◽  
High Dimensional ◽  
High Concentration ◽  
Systematic Analysis ◽  
Chemical Genetic ◽  
Cellular Processes ◽  
Cellular Compartments

We investigated the global landscape of Ca2+homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+. After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+–cls interactions. We found that high-dimensional, morphological Ca2+–cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+–cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+–cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+homeostasis.

Application of Fragment Molecular Orbital Method to investigate dopamine receptors

2019 ◽  
Vol 6 (3) ◽  
pp. 24-32 ◽  
Author(s):  
Jokūbas Preikša ◽  
Paweł Śliwa
Keyword(s):  
Ligand Binding ◽  
Dopamine Receptors ◽  
Molecular Orbital ◽  
Active Sites ◽  
Signaling Cascades ◽  
Orbital Method ◽  
Amino Acid Residues ◽  
Molecular Orbital Method ◽  
Fragment Molecular Orbital ◽  
Multiple Signaling

GPCRs are a vast family of seven-domain transmembrane proteins. This family includes dopamine receptors (D1, D2, D3, D4, and D5), which mediate the variety of dopamine-controlled physiological functions in the brain and periphery. Ligands of dopamine receptors are used for managing several neuropsychiatric disorders, including bipolar disorder, schizophrenia, anxiety, and Parkinson’s disease. Recent studies have revealed that dopamine receptors could be part of multiple signaling cascades, rather than of a single signaling pathway. For these targets, a variety of experimental and computational drug design techniques are utilized. In this work, dopamine receptors D2, D3, and D4 were investigated using molecular dynamic method as well as computational ab initio Fragment Molecular Orbital method (FMO), which can reveal atomistic details about ligand binding. The results provided useful insights into the significances of amino acid residues in ligand binding sites. Moreover, similarities and differences between active-sites of three studied types of receptors were examined.

scholarly journals A critical appraisal of evidence for localized energy coupling. Kinetic studies on liposomes containing bacteriorhodopsin and ATP synthase

1985 ◽  
Vol 230 (2) ◽  
pp. 543-549 ◽  
Author(s):  
R L Van der Bend ◽  
J Petersen ◽  
J A Berden ◽  
K Van Dam ◽  
H V Westerhoff
Keyword(s):  
Electron Transfer ◽  
Atp Synthase ◽  
Critical Appraisal ◽  
Atp Synthesis ◽  
Kinetic Studies ◽  
Energy Coupling ◽  
Proton Pumps ◽  
Specific Interactions ◽  
Mitochondrial Atp Synthase ◽  
Different Levels

In intact systems (chloroplasts, mitochondria and bacteria) many experiments have been reported which are indicative of localized coupling between ATP synthase and electron transfer complexes. We have carried out similar experiments with a system in which we may assume that specific interactions between the proton pumps are absent: reconstituted vesicles containing bacteriorhodopsin and yeast mitochondrial ATP synthase. The only experiment that gives results which differ from those previously published for intact systems concerns the effect of uncouplers on the rate of ATP synthesis at different levels of inhibition of the ATP synthase. We propose that this type of experiment may discriminate between localized and delocalized coupling.

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