scholarly journals Physiological Metals Can Induce Conformational Changes in Transthyretin Structure: Neuroprotection or Misfolding Induction?

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 354
Author(s):  
Lidia Ciccone ◽  
Nicolò Tonali ◽  
William Shepard ◽  
Susanna Nencetti ◽  
Elisabetta Orlandini
Keyword(s):  
Cerebrospinal Fluid ◽  
Metal Ions ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Proteins ◽  
Active Conformation ◽  
Pathological Conditions ◽  
High Concentrations ◽  
Partially Unfolded

Transthyretin (TTR) is a plasma homotetrameric protein that transports thyroxine and retinol. TTR itself, under pathological conditions, dissociates into partially unfolded monomers that aggregate and form fibrils. Metal ions such as Zn2+, Cu2+, Fe2+, Mn2+ and Ca2+ play a controversial role in the TTR amyloidogenic pathway. TTR is also present in cerebrospinal fluid (CSF), where it behaves as one of the major Aβ-binding-proteins. The interaction between TTR and Aβ is stronger in the presence of high concentrations of Cu2+. Crystals of TTR, soaked in solutions of physiological metals such as Cu2+ and Fe2+, but not Mn2+, Zn2+, Fe3+, Al3+, Ni2+, revealed an unusual conformational change. Here, we investigate the effects that physiological metals have on TTR, in order to understand if metals can induce a specific and active conformation of TTR that guides its Aβ-scavenging role. The capability of certain metals to induce and accelerate its amyloidogenic process is also discussed.

Hairpin and hammerhead ribozymes: how different are they?

2002 ◽  
Vol 30 (6) ◽  
pp. 1116-1119 ◽  
Author(s):  
J. M. Burke
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Experimental Work ◽  
Hammerhead Ribozyme ◽  
Active Conformation ◽  
Hairpin Ribozyme ◽  
Hammerhead Ribozymes ◽  
Active Structure ◽  
Catalytic Function ◽  
Recent Experimental Work

Recent experimental work on the hairpin and hammerhead ribozymes suggests that they have more similarities than previously suspected. Notably, each is now known to function as a true RNA catalyst, not requiring metal ions for folding or catalytic function. The active conformation of the hairpin ribozyme has been established by crystallography, and is well supported by biochemical and biophysical evidence that has identified conformational changes and key nucleotides required for catalysis. Analogous work is under way to establish the active structure of the hammerhead ribozyme.

Local conformational changes in the 8–17 deoxyribozyme core induced by activating and inactivating divalent metal ions

2017 ◽  
Vol 15 (41) ◽  
pp. 8802-8809 ◽  
Author(s):  
Alessio Peracchi ◽  
Maria Bonaccio ◽  
Alfredo Credali
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Conformational Changes ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Specific Metal

Placing 2-aminopurine at position 15 of the 8–17 DNAzyme allows the detection of a specific metal-induced conformational change, apparently coupled to the activation of catalysis.

Ratcheting between Two Distinct Conformations of Substrate Drives the Sequential Cleavage of Prothrombin by Prothrombinase.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1717-1717
Author(s):  
Elsa Bianchini ◽  
Steven J. Orcutt ◽  
Sriram Krishnaswamy
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Conformational Transition ◽  
Salt Bridge ◽  
Single Type ◽  
Thrombin Inhibitor ◽  
Short Delay ◽  
Bridge Formation ◽  
Initial Cleavage ◽  
High Concentrations

Abstract The conversion of human prothrombin to thrombin requires the cleavage of two peptide bonds. When catalyzed by prothrombinase, the reaction proceeds almost exclusively via initial cleavage at R320 followed by cleavage at R271 yielding meizothrombin (mIIa) as an intermediate. The scissile bonds are expected to be ~36 A apart in the zymogen. Yet, remarkably, evidence indicates that cleavage at these two sites is accomplished by a single type of exosite interaction that tethers the substrate to prothrombinase. The ability of prothrombinase to act on these spatially distinct sites, with such constraints, can be explained by a conformational change in the substrate following initial cleavage at R320. Cleavage at this site leads to internal salt bridge formation and a conformational transition to the proteinase. The role of the zymogen to proteinase transition in substrate cleavage was investigated by the use of a fully-carboxylated recombinant prothrombin derivative (IITAT) with the I-V-E sequence following R320 replaced with T-A-T. Thrombin produced by cleavage of IITAT exhibited ~0.2% of the catalytic activity observed with thrombin produced from wild type recombinant prothrombin (IIWT). IITAT can be cleaved at the R320 site but fails to undergo all subsequent conformational changes required for proteinase formation. SDS-PAGE and quantitative densitometry revealed that the action of prothrombinase on either IIWT or IITAT was consistent with ordered cleavage at R320 followed by cleavage at R271. The rates of consumption of IIWT and IITAT resulting from cleavage at R320 were equivalent. Cleavage at R320 in IITAT by prothrombinase is not detectably affected by the substituted P1′-P3′ sequence. The disappearance of IIWT was accompanied by a transient accumulation in mIIa that decreased to zero within 4 minutes while thrombin accumulated following a short delay. With IITAT, mIIa accumulated to higher levels and persisted for 45 minutes. Thrombin was produced with a lower rate and a longer delay phase. The findings imply a substantial decrease in the rate of the second cleavage reaction at R271 resulting from distant effects of the new P1′-P3′ residues following R320. The thrombin inhibitor, dansylarginine-N-(3-ethyl-1,5-pentanediyl)amide (DAPA) had no effect on the cleavage reactions in IIWT. However, increasing concentrations of DAPA as high as 400 μM were found to systematically enhance the rate of thrombin formation from IITAT by correcting defective cleavage at R271. The data are consistent with the interpretation that IITAT can be cleaved normally at R320 but subsequent accessibility and cleavage at R271 is reduced because of a defect in internal salt bridge formation and the conformational change associated with proteinase formation. Rescue of this defect by high concentrations of DAPA likely relates to the stabilization of a proteinase-like conformation in the intermediate produced by cleavage of IITAT at R320. Our findings suggest an important role for the zymogen to proteinase transition in determining the sequential action of prothrombinase on the two sites in prothrombin. We propose that exosite-dependent tethering of two distinct conformations of the substrate to prothrombinase drives the presentation of distantly positioned cleavage sites to the active site of the enzyme and accounts for the sequential cleavage of prothrombin.

Nanopore analysis of the interaction of metal ions with prion proteins and peptidesThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 347-358 ◽  
Author(s):  
Radu I. Stefureac ◽  
Claudia Avis Madampage ◽  
Olga Andrievskaia ◽  
Jeremy S. Lee
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Metal Ion ◽  
Prion Proteins ◽  
Peer Review Process ◽  
Cellular Biology ◽  
Divalent Metal Ions ◽  
High Concentrations ◽  
Individual Peptide ◽  
Selection Of

Nanopore analysis can be used to study conformational changes in individual peptide or protein molecules. Under an applied voltage there is a change in the event parameters of blockade current or time when a molecule bumps into or translocates through the pore. If a molecule undergoes a conformational change upon binding a ligand or metal ion the event parameters will be altered. The objective of this research was to demonstrate that the conformation of the prion protein (PrP) and prion peptides can be modulated by binding divalent metal ions. Peptides from the octarepeat region (Octa2, (PHGGGWGQ)2 and Octa 4, (PHGGGWGQ)4), residues 106–126 (PrP106–126), and the full-length Bovine recombinant prion (BrecPrP) were studied with an α-hemolysin pore. Octa2 readily translocated the pore but significant bumping events occurred on addition of Cu(II) and to a lesser extent Zn(II), demonstrating that complex formation was occurring with concomitant conformational changes. The binding of Cu(II) to Octa4 was more pronounced and at high concentrations only a small proportion of the complex could translocate. Addition of Zn(II) also caused significant changes to the event parameters but Mg(II) and Mn(II) were inert. Addition of Cu(II) to PrP106–126 caused the formation of a very tight complex, which could not translocate the pore. Small changes were observed with Zn(II), but not with Mg(II) or Mn(II). Analysis of BrecPrP showed that about 37% were translocation events, but on addition of Cu(II) or Zn(II) these disappeared and only bumping events were recorded. Suprisingly, addition of Mn(II) caused an increase in translocation events to about 64%. Thus, conformational changes to prions upon binding metal ions are readily observed by nanopore analysis.

scholarly journals Conformational changes and the role of metals in the mechanism of type II dehydroquinase from Aspergillus nidulans

1996 ◽  
Vol 319 (1) ◽  
pp. 269-278 ◽  
Author(s):  
Joanna R BOTTOMLEY ◽  
Alastair R. HAWKINS ◽  
Colin KLEANTHOUS
Keyword(s):  
Metal Ions ◽  
Aspergillus Nidulans ◽  
Conformational Change ◽  
Conformational Changes ◽  
Proteinase K ◽  
Type Ii ◽  
Affinity Labelling ◽  
Arginine Residues ◽  
Limited Digestion ◽  
Type Ii Dehydroquinase

We have investigated the involvement of metal ions and conformational changes in the elimination reaction catalysed by type II dehydroquinase from Aspergillus nidulans. Mechanistic comparisons between dehydroquinases and aldolases raised the possibility that, by analogy with type II aldolases, type II dehydroquinases may require bivalent metal ions for activity. This hypothesis was tested by a combination of metal analysis, effects of metal chelators and denaturation/renaturation experiments, all of which failed to show any evidence that type II dehydroquinases are metal-dependent dehydratases. Analysis of native and refolded enzyme by electron microscopy showed that the dodecameric type II enzyme from A. nidulans adopts a ring-like structure similar to that of glutamine synthase, suggesting an arrangement of two hexameric rings stacked on top of one another. Evidence for a ligand-induced conformational change came from both chemical modification and proteolysis experiments. Inactivation data with the arginine-specific reagent phenylglyoxal indicated that, at pH 7.5, two arginine residues are modified: one modification displays affinity-labelling kinetics and has a 1:1 stoichiometry, while the other displays simple bimolecular kinetics and a stoichiometry of 2:1. The labelling at the affinity site is markedly enhanced by the addition of ligand, implying that this active-site residue is further exposed to modification by phenylglyoxal as a result of a ligand-induced conformational change. A combination of proteolysis and electrospray MS experiments identified the site of affinity labelling as Arg-19. The highly conserved N-terminal region encompassing Arg-19 of type II dehydroquinase was found to be particularly susceptible to proteolytic cleavage. Limited digestion with proteinase K inactivates the enzyme, although the type II oligomeric structure is retained, and ligand binding partially protects against this inactivation.

Efficient Preconcentration of Cu2+, Zn2+ and Fe3+ with an Agarose-Schiff Base Sorbent

2007 ◽  
Vol 72 (7) ◽  
pp. 908-916 ◽  
Author(s):  
Payman Hashemi ◽  
Hatam Hassanvand ◽  
Hossain Naeimi
Keyword(s):  
Schiff Base ◽  
Metal Ions ◽  
Metal Ion ◽  
Good Accuracy ◽  
Kinetic Studies ◽  
Sample Volume ◽  
Effects Of Ph ◽  
Glass Column ◽  
High Concentrations ◽  
Ph Range

Sorption and preconcentration of Cu2+, Zn2+ and Fe3+ on a salen-type Schiff base, 2,2'- [ethane-1,2-diylbis(nitrilomethylidyne)]bis(2-methylphenol), chemically immobilized on a highly crosslinked agarose support, were studied. Kinetic studies showed higher sorption rates of Cu2+ and Fe3+ in comparison with Zn2+. Half-times (t1/2) of 31, 106 and 58 s were obtained for sorption of Cu2+, Zn2+ and Fe3+ by the sorbent, respectively. Effects of pH, eluent concentration and volume, ionic strength, buffer concentration, sample volume and interferences on the recovery of the metal ions were investigated. A 5-ml portion of 0.4 M HCl solution was sufficient for quantitative elution of the metal ions from 0.5 ml of the sorbent packed in a 6.5 mm i.d. glass column. Quantitative recoveries were obtained in a pH range 5.5-6.5 for all the analytes. The volumes to be concentrated exceeding 500 ml, ionic strengths as high as 0.5 mol l-1, and acetate buffer concentrations up to 0.3 mol l-1 for Zn2+ and 0.4 mol l-1 for Cu2+ and Fe3+ did not have any significant effect on the recoveries. The system tolerated relatively high concentrations of diverse ions. Preconcentration factors up to 100 and detection limits of 0.31, 0.16 and 1.73 μg l-1 were obtained for Cu2+, Zn2+ and Fe3+, respectively, for their determination by a flame AAS instrument. The method was successfully applied to the metal ion determinations in several river water samples with good accuracy.

scholarly journals Shear-Induced Amyloid Aggregation in the Brain: V. Are Alzheimer’s and Other Amyloid Diseases Initiated in the Lower Brain and Brainstem by Cerebrospinal Fluid Flow Stresses?

2020 ◽  
pp. 1-24
Author(s):  
Conrad N. Trumbore
Keyword(s):  
Cerebrospinal Fluid ◽  
Conformational Changes ◽  
Extensional Flow ◽  
Amyloid Β ◽  
High Energy ◽  
Mechanical Agitation ◽  
Cerebrospinal Fluid Flow ◽  
Pulse Waves ◽  
Amyloid Diseases ◽  
The Brain

Amyloid-β (Aβ) and tau oligomers have been identified as neurotoxic agents responsible for causing Alzheimer’s disease (AD). Clinical trials using Aβ and tau as targets have failed, giving rise to calls for new research approaches to combat AD. This paper provides such an approach. Most basic AD research has involved quiescent Aβ and tau solutions. However, studies involving laminar and extensional flow of proteins have demonstrated that mechanical agitation of proteins induces or accelerates protein aggregation. Recent MRI brain studies have revealed high energy, chaotic motion of cerebrospinal fluid (CSF) in lower brain and brainstem regions. These and studies showing CSF flow within the brain have shown that there are two energetic hot spots. These are within the third and fourth brain ventricles and in the neighborhood of the circle of Willis blood vessel region. These two regions are also the same locations as those of the earliest Aβ and tau AD pathology. In this paper, it is proposed that cardiac systolic pulse waves that emanate from the major brain arteries in the lower brain and brainstem regions and whose pulse waves drive CSF flows within the brain are responsible for initiating AD and possibly other amyloid diseases. It is further proposed that the triggering of these diseases comes about because of the strengthening of systolic pulses due to major artery hardening that generates intense CSF extensional flow stress. Such stress provides the activation energy needed to induce conformational changes of both Aβ and tau within the lower brain and brainstem region, producing unique neurotoxic oligomer molecule conformations that induce AD.

Blood–brain barrier and blood–cerebrospinal fluid barrier in normal and pathological conditions

2016 ◽  
Vol 33 (2) ◽  
pp. 89-96 ◽  
Author(s):  
Masaki Ueno ◽  
Yoichi Chiba ◽  
Ryuta Murakami ◽  
Koichi Matsumoto ◽  
Machi Kawauchi ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Blood Brain Barrier ◽  
Brain Barrier ◽  
Pathological Conditions ◽  
Blood Brain
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