Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme

2020 ◽  
Vol 124 (24) ◽  
pp. 4906-4918 ◽  
Author(s):  
Narendra Kumar ◽  
Dominik Marx
Keyword(s):  
Reaction Mechanism ◽  
The Self ◽  
Hairpin Ribozyme ◽  
Cleavage Reaction

Study of the reaction mechanism between electroless Ni–P and Sn and its effect on the crystallization of Ni–P

2003 ◽  
Vol 18 (1) ◽  
pp. 4-7 ◽  
Author(s):  
Y. C. Sohn ◽  
Jin Yu ◽  
S. K. Kang ◽  
W. K. Choi ◽  
D. Y. Shih
Keyword(s):  
Reaction Mechanism ◽  
Solid State ◽  
Solid State Reaction ◽  
Crystallization Temperature ◽  
Low Temperatures ◽  
Transformation Temperature ◽  
The Self ◽  
Heat Of Reaction ◽  
Solder Reaction ◽  
Electroless Ni

The reaction mechanism between electroless Ni–P and Sn was investigated to understand the effects of Sn on solder reaction-assisted crystallization at low temperatures as well as self-crystallization of Ni–P at high temperatures. Ni3Sn4 starts to form in a solid-state reaction well before Sn melts. Heat of reaction for Ni3Sn4 was measured during the Ni–P and Sn reaction (241.2 J/g). It was found that the solder reaction not only promotes crystallization at low temperatures by forming Ni3P in the P-rich layer but also facilitates self-crystallization of Ni–P by reducing the transformation temperature and heat of crystallization. The presence of Sn reduces the self-crystallization temperature of Ni–P by about 10 °C. The heat of crystallization also decreases with an increased Sn thickness.

Reaction mechanism of self-propagating high-temperature synthesis reaction in the Ni–Ti–B4C system

2008 ◽  
Vol 23 (9) ◽  
pp. 2519-2527 ◽  
Author(s):  
Y.F. Yang ◽  
H.Y. Wang ◽  
R.Y. Zhao ◽  
Y.H. Liang ◽  
Q.C. Jiang
Keyword(s):  
High Temperature ◽  
Reaction Mechanism ◽  
Intermetallic Compounds ◽  
Eutectic Point ◽  
The Self ◽  
Mutual Diffusion ◽  
Synthesis Reaction ◽  
Temperature Synthesis ◽  
Early Appearance ◽  
High Temperature Synthesis

The SHS reaction in the Ni–Ti–B4C system starts with the formation of Ni–Ti and Ni–B intermetallic compounds from the solid interacted reaction among the reactants and, subsequently, the formation of Ni–Ti and Ni–B liquid at the eutectic point. Meanwhile, some C atoms from the reaction between Ni and B4C can dissolve into Ni–Ti liquid to form TiC. The heat generated from these reactions can promote the mutual diffusion of Ni–Ti–C and Ni–B liquid and simultaneously accelerate the formation of Ni–Ti–C–B liquid. Finally the precipitation of TiC and TiB2 occur when the C and B atoms in the liquid become supersaturated. The addition of Ni not only promotes the occurrence of the self-propagating high temperature synthesis (SHS) reaction by forming Ni–Ti liquid, but also accelerates the SHS reaction by forming Ni–B liquid and dissociative C. The early appearance of dissociative C from the reaction between Ni and B4C causes the formation of TiC prior to that of TiB2.

scholarly journals Bicarbonate-dependent ATP cleavage catalysed by pyruvate carboxylase in the absence of pyruvate

1992 ◽  
Vol 287 (3) ◽  
pp. 1011-1017 ◽  
Author(s):  
P V Attwood ◽  
B D L A Graneri
Keyword(s):  
Reaction Mechanism ◽  
Atpase Activity ◽  
Active Site ◽  
Pyruvate Carboxylase ◽  
Substrate Inhibition ◽  
Cleavage Reaction ◽  
Acetyl Coa ◽  
Enzyme Preparations ◽  
Pyruvate Carboxylation ◽  
Rate Of Movement

Preparations of pyruvate carboxylase catalyse the cleavage of MgATP in the absence of pyruvate and acetyl-CoA. The rate of this cleavage is higher in the presence of HCO3- than in its absence. Incubation of the enzyme preparations with an excess of the pyruvate carboxylase inhibitor, avidin, completely abolishes the pyruvate carboxylating activity of the enzyme preparations but only abolishes the HCO3(-)-dependent MgATP cleaving activity, with no effect on the HCO3(-)-independent ATPase activity. The HCO3(-)-dependent MgATP cleavage is also sensitive to inhibition by a pyruvate carboxylase inhibitor, oxamate, and the dependence of the reaction on the free Mg2+ concentration is similar to that of the pyruvate-carboxylation reaction, whereas the HCO3(-)-independent MgATP cleavage is not dependent on the concentration of free Mg2+ in the range tested. This indicates that MgATP cleavage by pyruvate carboxylase is entirely dependent on the presence of HCO3- and that there may be a low level of ATPase contamination in the enzyme preparations. In addition, inhibition of the HCO3(-)-dependent MgATP cleavage by both avidin and oxamate indicate that although biotin does not directly participate in the reaction, its presence is required in that part of the active site of the enzyme. The rate of HCO3(-)-dependent MgATP cleavage is about 0.07% of that of the full pyruvate carboxylation reaction under similar conditions with saturating substrates. The reaction mechanism is sequential with respect to MgATP and HCO3- addition and Mg2+ adds at equilibrium before MgATP. Acetyl-CoA stimulates the HCO3(-)-dependent MgATP cleavage at low MgATP concentrations, with the stimulation being greater at low Mg2+ concentrations. At high levels of MgATP in the presence of acetyl-CoA, substrate inhibition is evident and is more pronounced at increasing concentrations of Mg2+. This inhibition appears to be, at least in part, caused by inhibition of decarboxylation of the enzyme-carboxybiotin complex by the binding to this complex of Mg2+ and MgATP, which probably act to reduce the rate of movement of carboxybiotin from the site of the MgATP cleavage reaction to that of the pyruvate carboxylation reaction where it is unstable and decarboxylates.

Inhibition of the Self-cleavage Reaction of the Human Hepatitis Delta Virus Ribozyme by Antibiotics

1996 ◽  
Vol 259 (5) ◽  
pp. 916-925 ◽  
Author(s):  
Jeff Rogers ◽  
Alex H. Chang ◽  
Uwe von Ahsen ◽  
Renée Schroeder ◽  
Julian Davies
Keyword(s):  
Hepatitis Delta Virus ◽  
The Self ◽  
Cleavage Reaction ◽  
Hepatitis Delta ◽  
Hepatitis Delta Virus Ribozyme ◽  
Human Hepatitis ◽  
Delta Virus

Exploring the self-redox reaction mechanism of Mn-doped Mg2(Ti/Sn)O4 with its precise dopant position

2019 ◽  
Vol 110 ◽  
pp. 112-119 ◽  
Author(s):  
Hongwei Xu ◽  
Lili Wang ◽  
Chao Lv ◽  
Fuqiang Li ◽  
Qi Wang ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Redox Reaction ◽  
The Self ◽  
Mn Doped

scholarly journals The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations

2015 ◽  
Vol 17 (1) ◽  
pp. 670-679 ◽  
Author(s):  
Vojtěch Mlýnský ◽  
Nils G. Walter ◽  
Jiří Šponer ◽  
Michal Otyepka ◽  
Pavel Banáš
Keyword(s):  
Active Site ◽  
The Self ◽  
Direct Impact ◽  
Cleavage Reaction ◽  
Hdv Ribozyme ◽  
Specific Position

The specific position and coordination of active site Mg2+ ion have a significant direct impact on the self-cleavage reaction in HDV ribozyme.

scholarly journals Pressure modulates the self-cleavage step of the hairpin ribozyme

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Caroline Schuabb ◽  
Narendra Kumar ◽  
Salome Pataraia ◽  
Dominik Marx ◽  
Roland Winter
Keyword(s):  
The Self ◽  
Hairpin Ribozyme ◽  
Cleavage Step

Catalysis by the nucleolytic ribozymes

2011 ◽  
Vol 39 (2) ◽  
pp. 641-646 ◽  
Author(s):  
David M.J. Lilley
Keyword(s):  
Base Catalysis ◽  
Hairpin Ribozyme ◽  
Cleavage Reaction ◽  
Acid Base ◽  
Rate Enhancement ◽  
General Base ◽  
General Acid ◽  
Varkud Satellite Ribozyme

The nucleolytic ribozymes use general acid–base catalysis to contribute significantly to their rate enhancement. The VS (Varkud satellite) ribozyme uses a guanine and an adenine nucleobase as general base and acid respectively in the cleavage reaction. The hairpin ribozyme is probably closely similar, while the remaining nucleolytic ribozymes provide some interesting contrasts.

Recombinant expression of antimicrobial peptides using a novel self-cleaving aggregation tag in Escherichia coli

2014 ◽  
Vol 60 (3) ◽  
pp. 113-120 ◽  
Author(s):  
Chao Luan ◽  
Yong Gang Xie ◽  
Yu Tian Pu ◽  
Hai Wen Zhang ◽  
Fei Fei Han ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Peptides ◽  
Recombinant Expression ◽  
Expression System ◽  
Effective Means ◽  
Protein Aggregates ◽  
The Self ◽  
Active Protein ◽  
Cleavage Reaction ◽  
Amphipathic Peptide

Antimicrobial peptides (AMPs) are part of the innate immune system of complex multicellular organisms. Despite the fact that AMPs show great potential as a novel class of antibiotics, the lack of a cost-effective means for their mass production limits both basic research and clinical use. In this work, we describe a novel expression system for the production of antimicrobial peptides in Escherichia coli by combining ΔI-CM mini-intein with the self-assembling amphipathic peptide 18A to drive the formation of active aggregates. Two AMPs, human β-defensin 2 and LL-37, were fused to the self-cleaving tag and expressed as active protein aggregates. The active aggregates were recovered by centrifugation and the intact antimicrobial peptides were released into solution by an intein-mediated cleavage reaction in cleaving buffer (phosphate-buffered saline supplemented with 40 mmol/L Bis–Tris, 2 mmol/L EDTA, pH 6.2). The peptides were further purified by cation-exchange chromatography. Peptides yields of 0.82 ± 0.24 and 0.59 ± 0.11 mg/L were achieved for human β-defensin 2 and LL-37, respectively, with demonstrated antimicrobial activity. Using our expression system, intact antimicrobial peptides were recovered by simple centrifugation from active protein aggregates after the intein-mediated cleavage reaction. Thus, we provide an economical and efficient way to produce intact antimicrobial peptides in E. coli.

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