scholarly journals Mechanism of Tripeptide Trimming by γ-Secretase

2021 ◽  
Author(s):  
Apurba Bhattarai ◽  
Sujan Devkota ◽  
Hung Nguyen Do ◽  
Jinan Wang ◽  
Sanjay Bhattarai ◽  
...  
Keyword(s):  
Experimental Data ◽  
Structural Changes ◽  
Transmembrane Domain ◽  
Amyloid Β ◽  
Structural Rearrangements ◽  
Accelerated Molecular Dynamics ◽  
Endoproteolytic Cleavage ◽  
N Terminus ◽  
Conformational Rearrangements ◽  
Positively Charged

The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer's disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and western blotting were used to quantify the efficiency of the first tripeptide trimming step (Aβ49 to Aβ46) of wildtype (WT) and familial AD (FAD) mutant APP substrate. In comparison to WT APP, the efficiency of this first trimming step was slightly higher for the I45F, A42T and V46F APP FAD mutants, but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate tripeptide trimming of Aβ49 by γ-secretase. The starting structure was active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai et al., ACS Cent Sci, 2020, 6:969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming by γ-secretase.

scholarly journals The Extreme C Terminus of Presenilin 1 Is Essential for γ-Secretase Complex Assembly and Activity

2004 ◽  
Vol 279 (44) ◽  
pp. 45564-45572 ◽  
Author(s):  
Anna Bergman ◽  
Hanna Laudon ◽  
Bengt Winblad ◽  
Johan Lundkvist ◽  
Jan Näslund
Keyword(s):  
Transmembrane Domain ◽  
Amyloid Β ◽  
Presenilin 1 ◽  
Amyloid Β Peptide ◽  
Terminal Part ◽  
Complex Assembly ◽  
Terminal Fragment ◽  
C Terminus ◽  
Secretase Activity ◽  
Endoproteolytic Cleavage

The γ-secretase complex catalyzes the cleavage of the amyloid precursor protein in its transmembrane domain resulting in the formation of the amyloid β-peptide and the cytoplasmic APP intracellular domain. The active γ-secretase complex is composed of at least four subunits: presenilin (PS), nicastrin, Aph-1, and Pen-2, where the presence of all components is critically required for γ-cleavage to occur. The PS proteins are themselves subjected to endoproteolytic cleavage resulting in the generation of an N-terminal and a C-terminal fragment that remain stably associated as a heterodimer. Here we investigated the effects of modifications on the C terminus of PS1 on PS1 endoproteolysis, γ-secretase complex assembly, and activity in cells devoid of endogenous PS. We report that certain mutations and, in particular, deletions of the PS1 C terminus decrease γ-secretase activity, PS1 endoproteolysis, and γ-secretase complex formation. We demonstrate that the N- and C-terminal PS1 fragments can associate with each other in mutants having C-terminal truncations that cause loss of interaction with nicastrin and Aph-1. In addition, we show that the C-terminal fragment of PS1 alone can mediate interaction with nicastrin and Aph-1 in PS null cells expressing only the C-terminal fragment of PS1. Taken together, these data suggest that the PS1 N- and C-terminal fragment intermolecular interactions are independent of an association with nicastrin and Aph-1, and that nicastrin and Aph-1 interact with the C-terminal part of PS1 in the absence of an association with full-length PS1 or the N-terminal fragment.

scholarly journals The N-Terminal Transmembrane Domain of λ S Is Required for Holin but Not Antiholin Function

2009 ◽  
Vol 192 (3) ◽  
pp. 725-733 ◽  
Author(s):  
Rebecca White ◽  
Tram Anh T. Tran ◽  
Chelsey A. Dankenbring ◽  
John Deaton ◽  
Ry Young
Keyword(s):  
Cytoplasmic Membrane ◽  
Transmembrane Domain ◽  
Amino Group ◽  
Missense Mutations ◽  
Wild Type Allele ◽  
Wild Type ◽  
Basic Residue ◽  
N Terminus ◽  
Terminal Amino ◽  
Positively Charged

ABSTRACT The λ S gene encodes a holin, S105, and an antiholin, S107, which differs by its Met-Lys N-terminal extension. The model for the lysis-defective character of S107 stipulates that the additional N-terminal basic residue keeps S107 from assuming the topology of S105, which is N-out, C-in, with three transmembrane domains (TMDs). Here we show that the N terminus of S105 retains its fMet residue but that the N terminus of S107 is fully deformylated. This supports the model that in S105, TMD1 inserts into the membrane very rapidly but that in S107, it is retained in the cytoplasm. Further, it reveals that, compared to S105, S107 has two extra positively charged moieties, Lys2 and the free N-terminal amino group, to hinder its penetration into an energized membrane. Moreover, an allele, S105ΔTMD1 , with TMD1 deleted, was found to be defective in lysis, insensitive to membrane depolarization, and dominant to the wild-type allele, indicating that the lysis-defective, antiholin character of S107 is due to the absence of TMD1 from the bilayer rather than to its ectopic localization at the inner face of the cytoplasmic membrane. Finally, the antiholin function of the deletion protein was compromised by the substitution of early-lysis missense mutations in either the deletion protein or parental S105 but restored when both S105ΔTMD1 and holin carried the substitution.

Characteristics of the Interaction between Thrombin Exosite1 and the Sequence 269-297 of Platelet Glycoprotein Ibα

1998 ◽  
Vol 80 (08) ◽  
pp. 310-315 ◽  
Author(s):  
Marie-Christine Bouton ◽  
Christophe Thurieau ◽  
Marie-Claude Guillin ◽  
Martine Jandrot-Perrus
Keyword(s):  
Platelet Activation ◽  
Electrostatic Interactions ◽  
Platelet Glycoprotein ◽  
Thrombin Receptor ◽  
Central Position ◽  
Amidolytic Activity ◽  
N Terminus ◽  
Hydrolysis Of ◽  
Chemical Cross Linking ◽  
Positively Charged

SummaryThe interaction between GPIb and thrombin promotes platelet activation elicited via the hydrolysis of the thrombin receptor and involves structures located on the segment 238-290 within the N-terminal domain of GPIbα and the positively charged exosite 1 on thrombin. We have investigated the ability of peptides derived from the 269-287 sequence of GPIbα to interact with thrombin. Three peptides were synthesized, including Ibα 269-287 and two scrambled peptides R1 and R2 which are comparable to Ibα 269-287 with regards to their content and distribution of anionic residues. However, R2 differs from both Ibα 269-287 and R1 by the shifting of one proline from a central position to the N-terminus. By chemical cross-linking, we observed the formation of a complex between 125I-Ibα 269-287 and α-thrombin that was inhibited by hirudin, the C-terminal peptide of hirudin, sodium pyrophosphate but not by heparin. The complex did not form when γ-thrombin was substituted for α-thrombin. Ibα 269-287 produced only slight changes in thrombin amidolytic activity and inhibited thrombin binding to fibrin. R1 and R2 also formed complexes with α-thrombin, modified slightly its catalytic activity and inhibited its binding to fibrin. Peptides Ibα 269-287 and R1 inhibited platelet aggregation and secretion induced by low thrombin concentrations whereas R2 was without effect. Our results indicate that Ibα 269-287 interacts with thrombin exosite 1 via mainly electrostatic interactions, which explains why the scrambled peptides also interact with exosite 1. Nevertheless, the lack of effect of R2 on thrombin-induced platelet activation suggests that proline 280 is important for thrombin interaction with GPIb.

Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution

2018 ◽  
Vol 28 (3) ◽  
pp. 265 ◽  
Author(s):  
Son Tung Ngo
Keyword(s):  
Structural Changes ◽  
Replica Exchange ◽  
Aβ Oligomers ◽  
Replica Exchange Molecular Dynamics ◽  
Charged Residue ◽  
Intermolecular Contacts ◽  
Structural Details ◽  
Positively Charged ◽  
Dynamic Fluctuation ◽  
Good Agreement

The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

scholarly journals Residues within the Transmembrane Domain of the Glucagon-Like Peptide-1 Receptor Involved in Ligand Binding and Receptor Activation: Modelling the Ligand-Bound Receptor

2011 ◽  
Vol 25 (10) ◽  
pp. 1804-1818 ◽  
Author(s):  
K. Coopman ◽  
R. Wallis ◽  
G. Robb ◽  
A. J. H. Brown ◽  
G. F. Wilkinson ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Structural Model ◽  
Transmembrane Domain ◽  
Transmembrane Helix ◽  
Receptor Activation ◽  
Agonist Affinity ◽  
Camp Generation ◽  
N Terminus ◽  
Glucagon Like Peptide ◽  
Glucagon Like Peptide 1

The C-terminal regions of glucagon-like peptide-1 (GLP-1) bind to the N terminus of the GLP-1 receptor (GLP-1R), facilitating interaction of the ligand N terminus with the receptor transmembrane domain. In contrast, the agonist exendin-4 relies less on the transmembrane domain, and truncated antagonist analogs (e.g. exendin 9–39) may interact solely with the receptor N terminus. Here we used mutagenesis to explore the role of residues highly conserved in the predicted transmembrane helices of mammalian GLP-1Rs and conserved in family B G protein coupled receptors in ligand binding and GLP-1R activation. By iteration using information from the mutagenesis, along with the available crystal structure of the receptor N terminus and a model of the active opsin transmembrane domain, we developed a structural receptor model with GLP-1 bound and used this to better understand consequences of mutations. Mutation at Y152 [transmembrane helix (TM) 1], R190 (TM2), Y235 (TM3), H363 (TM6), and E364 (TM6) produced similar reductions in affinity for GLP-1 and exendin 9–39. In contrast, other mutations either preferentially [K197 (TM2), Q234 (TM3), and W284 (extracellular loop 2)] or solely [D198 (TM2) and R310 (TM5)] reduced GLP-1 affinity. Reduced agonist affinity was always associated with reduced potency. However, reductions in potency exceeded reductions in agonist affinity for K197A, W284A, and R310A, while H363A was uncoupled from cAMP generation, highlighting critical roles of these residues in translating binding to activation. Data show important roles in ligand binding and receptor activation of conserved residues within the transmembrane domain of the GLP-1R. The receptor structural model provides insight into the roles of these residues.

scholarly journals Clusters of Charged Residues at the C Terminus of MotA and N Terminus of MotB Are Important for Function of the Escherichia coli Flagellar Motor

2008 ◽  
Vol 190 (15) ◽  
pp. 5517-5521 ◽  
Author(s):  
Edan R. Hosking ◽  
Michael D. Manson
Keyword(s):  
Escherichia Coli ◽  
Flagellar Motor ◽  
Protein Levels ◽  
Partner Protein ◽  
C Terminus ◽  
N Terminus ◽  
Charged Residues ◽  
Positively Charged ◽  
Terminal Cluster

ABSTRACT MotA contains a conserved C-terminal cluster of negatively charged residues, and MotB contains a conserved N-terminal cluster of positively charged residues. Charge-altering mutations affecting these residues impair motility but do not diminish Mot protein levels. The motility defects are reversed by second-site mutations targeting the same or partner protein.

scholarly journals Multi-Component Adsorption of Benzene, Toluene, Ethylbenzene, and Xylene from Aqueous Solutions by Montmorillonite Modified with Tetradecyl Trimethyl Ammonium Bromide

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
H. Nourmoradi ◽  
Mehdi Khiadani ◽  
M. Nikaeen
Keyword(s):  
Experimental Data ◽  
Aqueous Solutions ◽  
Structural Changes ◽  
Freundlich Isotherm ◽  
Isotherm Models ◽  
Ammonium Bromide ◽  
Order Kinetic ◽  
Multicomponent Adsorption ◽  
Benzene Toluene ◽  
Kinetic And Isotherm Models

Multicomponent adsorption of benzene, toluene, ethylbenzene, and xylene (BTEX) was assessed in aqueous solutions by montmorillonite modified with tetradecyl trimethyl ammonium bromide (TTAB-Mt). Batch experiments were conducted to determine the influences of parameters including loading rates of surfactant, contact time, pH, adsorbate concentration, and temperature on the adsorption efficiency. Scanning electron microscope (SEM) and X-ray diffractometer (XRD) were used to determine the adsorbent properties. Results showed that the modification of the adsorbent via the surfactant causes structural changes of the adsorbent. It was found that the optimum adsorption condition achieves with the surfactant loading rate of 200% of the cation exchange capacity (CEC) of the adsorbent for a period of 24 h. The sorption of BTEX by TTAB-Mt was in the order ofB<T<E<X. The experimental data were fitted by many kinetic and isotherm models. The results also showed that the pseudo-second-order kinetic model and Freundlich isotherm model could, respectively, be fitted to the experimental data better than other available kinetic and isotherm models. The thermodynamic study indicated that the sorption of BTEX with TTAB-Mt was achieved spontaneously and the adsorption process was endothermic as well as physical in nature. The regeneration results of the adsorbent also showed that the adsorption capacity of adsorbent after one use was 51% to 70% of original TTAB-Mt.

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