scholarly journals Exploring the Early Stages of the Amyloid Aβ(1–42) Peptide Aggregation Process: An NMR Study

2021 ◽  
Vol 14 (8) ◽  
pp. 732
Author(s):  
Angelo Santoro ◽  
Manuela Grimaldi ◽  
Michela Buonocore ◽  
Ilaria Stillitano ◽  
Anna Maria D’Ursi
Keyword(s):  
Conformational Changes ◽  
Amyloid Fibrils ◽  
Structural Model ◽  
Conformational Transition ◽  
Helical Structure ◽  
Aggregation Process ◽  
Nmr Study ◽  
Aβ Aggregation ◽  
Dynamics Simulations ◽  
Β Sheet

Alzheimer’s disease (AD) is a neurodegenerative pathology characterized by the presence of neurofibrillary tangles and amyloid plaques, the latter mainly composed of Aβ(1–40) and Aβ(1–42) peptides. The control of the Aβ aggregation process as a therapeutic strategy for AD has prompted the interest to investigate the conformation of the Aβ peptides, taking advantage of computational and experimental techniques. Mixtures composed of systematically different proportions of HFIP and water have been used to monitor, by NMR, the conformational transition of the Aβ(1–42) from soluble α-helical structure to β-sheet aggregates. In the previous studies, 50/50 HFIP/water proportion emerged as the solution condition where the first evident Aβ(1–42) conformational changes occur. In the hypothesis that this solvent reproduces the best condition to catch transitional helical-β-sheet Aβ(1–42) conformations, in this study, we report an extensive NMR conformational analysis of Aβ(1–42) in 50/50 HFIP/water v/v. Aβ(1–42) structure was solved by us, giving evidence that the evolution of Aβ(1–42) peptide from helical to the β-sheet may follow unexpected routes. Molecular dynamics simulations confirm that the structural model we calculated represents a starting condition for amyloid fibrils formation.

Conformational Changes of the Wild-Type hIAPP and the S20P Mutant in Water Revealed by Molecular Dynamics Simulations

2011 ◽  
Vol 396-398 ◽  
pp. 1554-1557
Author(s):  
Mian Wang ◽  
Jian Yi Wang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Conformational Changes ◽  
Amyloid Fibrils ◽  
Helical Structure ◽  
Wild Type ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Networks ◽  
Α Helix ◽  
Dynamics Simulations

Conformational changes of wild-type (WT) hIAPP and the S20P mutant in explicit water are investigated using molecular dynamics. In the whole simulation, WT shows compacter structure and has more hydrogen-bond networks than S20P. The residues 14-18 in WT is always maintained as a helical structure which is stabilized by the hydrogen bond between Ser20 and NH group of His18, and the other regions in WT partially loosen from α-helix structures into the coil structures. The S20P mutant in a shortage of hydrogen-bond interaction unfolds faster than WT. This work provides insight into the specific conformation of IAPP which is associated with the generation of amyloid fibrils.

scholarly journals Computational modeling reveals a hydrophobic force-induced pore-forming mechanism for cholesterol-dependent cytolysins

2019 ◽  
Author(s):  
Shichao Pang ◽  
Junchen Yang ◽  
Jingfang Wang
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Structural Model ◽  
Hydrophobic Interactions ◽  
Free Energy Calculations ◽  
Forming Process ◽  
Hydrophobic Force ◽  
Forming Mechanism ◽  
Hydrophobic Pore ◽  
Dynamics Simulations

ABSTRACTDuring the pore-forming process, cholesterol-dependent cytolysins (CDCs) bind to cholesterol-rich membranes and subsequently undergo a series of conformational changes, predominantly involving in the collapse of the protein and the transformation from α helices to β-hairpins to form a large hydrophobic pore. In the current study, we reconstructed a structural model for both the prepore and pore-forming complexes of PFO based on the cryo-EM data of pneumolysin and performed molecular dynamics simulations and free energy calculations to study the conformational changes in the PFO prepore-to-pore conversion. Our simulations indicate that D2 cannot collapse spontaneously due to the hydrogen bonding and pi-pi interactions between domains D2 and D3, which are partially weakened by binding to cell membranes and oligomerization. The free energy landscape for the prepore-to-pore conversion reveals that an additional force is required for the collapse of D2 to overcome an energy barrier of ∼ 24 kcal/mol. Based on these computational results, we proposed a hydrophobic force-induced pore-forming mechanism to explain the pore-forming process of CDCs. In this mechanism, the hydrophobic interactions between the TMHs and membranes are essential for the prepore-to-pore conversion. The hydrophobic force generated by the TMHs-membrane interactions drives the conformational changes in domains D2 and D3. These findings well explain how the conformational changes within two distant domains synergistically occur, and fits well for the previous biophysical and biochemical data.

scholarly journals Inhibition of peptide aggregation by means of enzymatic phosphorylation

2016 ◽  
Vol 12 ◽  
pp. 2462-2470 ◽  
Author(s):  
Kristin Folmert ◽  
Malgorzata Broncel ◽  
Hans v. Berlepsch ◽  
Christopher Hans Ullrich ◽  
Mary-Ann Siegert ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Conformational Transition ◽  
Structural Characteristics ◽  
Random Coil ◽  
Amyloid Formation ◽  
Initial Growth ◽  
Amyloid Fibril Formation ◽  
Dependent Protein ◽  
Enzymatic Phosphorylation ◽  
Β Sheet

As is the case in numerous natural processes, enzymatic phosphorylation can be used in the laboratory to influence the conformational populations of proteins. In nature, this information is used for signal transduction or energy transfer, but has also been shown to play an important role in many diseases like tauopathies or diabetes. With the goal of determining the effect of phosphorylation on amyloid fibril formation, we designed a model peptide which combines structural characteristics of α-helical coiled-coils and β-sheets in one sequence. This peptide undergoes a conformational transition from soluble structures into insoluble amyloid fibrils over time and under physiological conditions and contains a recognition motif for PKA (cAMP-dependent protein kinase) that enables enzymatic phosphorylation. We have analyzed the pathway of amyloid formation and the influence of enzymatic phosphorylation on the different states along the conformational transition from random-coil to β-sheet-rich oligomers to protofilaments and on to insoluble amyloid fibrils, and we found a remarkable directing effect from β-sheet-rich structures to unfolded structures in the initial growth phase, in which small oligomers and protofilaments prevail if the peptide is phosphorylated.

scholarly journals Hairpin RNA-induced conformational change of a eukaryotic-specific lysyl-tRNA synthetase extension and role of adjacent anticodon-binding domain

2020 ◽  
Vol 295 (34) ◽  
pp. 12071-12085
Author(s):  
Sheng Liu ◽  
Maryanne Refaei ◽  
Shuohui Liu ◽  
Aaron Decker ◽  
Jennifer M. Hinerman ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Conformational Transition ◽  
Critical Role ◽  
Helical Structure ◽  
Trna Synthetase ◽  
Binding Domain ◽  
Covalent Attachment ◽  
Intrinsically Disordered ◽  
High Affinity ◽  
Rna Hairpins

Human lysyl-tRNA synthetase (hLysRS) is essential for aminoacylation of tRNALys. Higher eukaryotic LysRSs possess an N-terminal extension (Nterm) previously shown to facilitate high-affinity tRNA binding and aminoacylation. This eukaryote-specific appended domain also plays a critical role in hLysRS nuclear localization, thus facilitating noncanonical functions of hLysRS. The structure is intrinsically disordered and therefore remains poorly characterized. Findings of previous studies are consistent with the Nterm domain undergoing a conformational transition to an ordered structure upon nucleic acid binding. In this study, we used NMR to investigate how the type of RNA, as well as the presence of the adjacent anticodon-binding domain (ACB), influences the Nterm conformation. To explore the latter, we used sortase A ligation to produce a segmentally labeled tandem-domain protein, Nterm–ACB. In the absence of RNA, Nterm remained disordered regardless of ACB attachment. Both alone and when attached to ACB, Nterm structure remained unaffected by titration with single-stranded RNAs. The central region of the Nterm domain adopted α-helical structure upon titration of Nterm and Nterm–ACB with RNA hairpins containing double-stranded regions. Nterm binding to the RNA hairpins resulted in CD spectral shifts consistent with an induced helical structure. NMR and fluorescence anisotropy revealed that Nterm binding to hairpin RNAs is weak but that the binding affinity increases significantly upon covalent attachment to ACB. We conclude that the ACB domain facilitates induced-fit conformational changes and confers high-affinity RNA hairpin binding, which may be advantageous for functional interactions of LysRS with a variety of different binding partners.

scholarly journals Recent Insights into the Pathogenesis of Type AA Amyloidosis

2011 ◽  
Vol 11 ◽  
pp. 641-650 ◽  
Author(s):  
J. C. H. van der Hilst
Keyword(s):  
Amino Acids ◽  
Amyloid Fibrils ◽  
Rare Event ◽  
Helical Structure ◽  
Amyloid A ◽  
Acid Protein ◽  
Life Threatening ◽  
Shock Proteins ◽  
Β Sheet

The amyloidoses are a group of life-threatening diseases in which fibrils made of misfolded proteins are deposited in organs and tissues. The fibrils are stable, insoluble aggregates of precursor proteins that have adopted an antiparallel β-sheet structure. In type AA, or reactive, amyloidosis, the precursor protein of the fibrils is serum amyloid A (SAA). SAA is a 104-amino-acid protein that is produced in the liver in response to proinflammatory cytokines. Although the protein that is produced by the liver contains 104 amino acids, only the N-terminal 66–76 amino acids are found in amyloid fibrils. Furthermore, SAA has been shown to have an α-helical structure primarily. Thus, for SAA to be incorporated into an amyloid fibril, two processes have to occur: C-terminal cleavage and conversion into a β-sheet. Only a minority of patients with elevated SAA levels develop amyloidosis. Factors that contribute to the risk of amyloidosis include the duration and degree of SAA elevation, polymorphisms in SAA, and the type of autoinflammatory syndrome. In the Hyper-IgD syndrome, amyloidosis is less prevalent than in the other autoinflammatory diseases.In vitrowork has shown that the isoprenoid pathway influences amyloidogenesis by farnesylated proteins. Although many proteins contain domains that have a potential for self-aggregation, amyloidosis is only a very rare event. Heat shock proteins (HSPs) are chaperones that assist other proteins to attain, maintain, and regain a functional conformation. In this review, recent insights into the pathogenesis of amyloidosis are discussed, in addition to a new hypothesis for a role of HSPs in the pathogenesis of type AA.

scholarly journals The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

2017 ◽  
Vol 13 ◽  
pp. 2842-2853 ◽  
Author(s):  
Yaochun Xu ◽  
Isabelle Correia ◽  
Tap Ha-Duong ◽  
Nadjib Kihal ◽  
Jean-Louis Soulier ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Amyloid Peptide ◽  
Central Position ◽  
Aggregation Process ◽  
Proof Of Concept ◽  
Protein Protein Interactions ◽  
Conformational Studies ◽  
Dynamics Simulations ◽  
Β Sheet ◽  
Central Residue

Pentapeptides having the sequence R-HN-Ala-Val-X-Val-Leu-OMe, where the central residue X is L-serine, L-threonine, (2S,3R)-L-CF3-threonine and (2S,3S)-L-CF3-threonine were prepared. The capacity of (2S,3S)- and (2S,3R)-CF3-threonine analogues to stabilize an extended structure when introduced in the central position of pentapeptides is demonstrated by NMR conformational studies and molecular dynamics simulations. CF3-threonine containing pentapeptides are more prone to mimic β-strands than their natural Ser and Thr pentapeptide analogues. The proof of concept that these fluorinated β-strand mimics are able to disrupt protein–protein interactions involving β-sheet structures is provided. The CF3-threonine containing pentapeptides interact with the amyloid peptide Aβ1-42 in order to reduce the protein–protein interactions mediating its aggregation process.

scholarly journals Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks

2020 ◽  
Author(s):  
Suman Samantray ◽  
Wibke Schumann ◽  
Alexander-Maurice Illig ◽  
Martin Carballo-Pacheco ◽  
Arghadwip Paul ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Aggregation ◽  
Amyloid Fibrils ◽  
Md Simulations ◽  
Aggregation Process ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Dynamics Simulations ◽  
Transition Networks

AbstractProtein disorder and aggregation play significant roles in the pathogenesis of numerous neuro-degenerative diseases, such as Alzheimer’s and Parkinson’s disease. The end products of the aggregation process in these diseases are β-sheet rich amyloid fibrils. Though in most cases small, soluble oligomers formed during amyloid aggregation are the toxic species. A full understanding of the physicochemical forces behind the protein aggregation process is required if one aims to reveal the molecular basis of the various amyloid diseases. Among a multitude of biophysical and biochemical techniques that are employed for studying protein aggregation, molecular dynamics (MD) simulations at the atomic level provide the highest temporal and spatial resolution of this process, capturing key steps during the formation of amyloid oligomers. Here we provide a step-by-step guide for setting up, running, and analyzing MD simulations of aggregating peptides using GROMACS. For the analysis we provide the scripts that were developed in our lab, which allow to determine the oligomer size and inter-peptide contacts that drive the aggregation process. Moreover, we explain and provide the tools to derive Markov state models and transition networks from MD data of peptide aggregation.

scholarly journals Far-Off Resonance: Multiwavelength Raman Spectroscopy Probing Amide Bands of Amyloid-β-(37–42) Peptide

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3556
Author(s):  
Martynas Talaikis ◽  
Simona Strazdaitė ◽  
Mantas Žiaunys ◽  
Gediminas Niaura
Keyword(s):  
Raman Spectroscopy ◽  
Conformational Changes ◽  
Relative Intensity ◽  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Intensity Increase ◽  
Amyloid Β Peptide ◽  
Peptide Backbone ◽  
Sheet Structure ◽  
Β Sheet

Several neurodegenerative diseases, like Alzheimer’s and Parkinson’s are linked with protein aggregation into amyloid fibrils. Conformational changes of native protein into the β-sheet structure are associated with a significant change in the vibrational spectrum. This is especially true for amide bands which are inherently sensitive to the secondary structure of a protein. Raman amide bands are greatly intensified under resonance conditions, in the UV spectral range, allowing for the selective probing of the peptide backbone. In this work, we examine parallel β-sheet forming GGVVIA, the C-terminus segment of amyloid-β peptide, using UV–Vis, FTIR, and multiwavelength Raman spectroscopy. We find that amide bands are enhanced far from the expected UV range, i.e., at 442 nm. A reasonable two-fold relative intensity increase is observed for amide II mode (normalized according to the δCH2/δCH3 vibration) while comparing 442 and 633 nm excitations; an increase in relative intensity of other amide bands was also visible. The observed relative intensification of amide II, amide S, and amide III modes in the Raman spectrum recorded at 442 nm comparing with longer wavelength (633/785/830 nm) excited spectra allows unambiguous identification of amide bands in the complex Raman spectra of peptides and proteins containing the β-sheet structure.

scholarly journals A structural model of the human serotonin transporter in an outward-occluded state

2019 ◽  
Author(s):  
Eva Hellsberg ◽  
Gerhard F. Ecker ◽  
Anna Stary-Weinzinger ◽  
Lucy R. Forrest
Keyword(s):  
Serotonin Transporter ◽  
Conformational Changes ◽  
Structural Model ◽  
Antidepressant Drugs ◽  
Homology Model ◽  
Synaptic Cleft ◽  
Open Conformation ◽  
Starting Point ◽  
Ligand Interactions ◽  
Dynamics Simulations

AbstractThe human serotonin transporter hSERT facilitates the reuptake of its endogenous substrate serotonin from the synaptic cleft into presynaptic neurons after signaling. Reuptake regulates the availability of this neurotransmitter and therefore hSERT plays an important role in balancing human mood conditions. In 2016, the first 3D structures of this membrane transporter were reported in an inhibitor-bound, outward-open conformation. These structures revealed valuable information about interactions of hSERT with antidepressant drugs. Nevertheless, the question remains how serotonin facilitates the specific conformational changes that open and close pathways from the synapse and to the cytoplasm as required for transport. Here, we present a serotonin-bound homology model of hSERT in an outward-occluded state, a key intermediate in the physiological cycle, in which the interactions with the substrate are likely to be optimal. Our approach uses two template structures and includes careful refinement and comprehensive computational validation. According to microsecond-long molecular dynamics simulations, this model exhibits interactions between the gating residues in the extracellular pathway, and these interactions differ from those in an outward-open conformation of hSERT bound to serotonin. Moreover, we predict several features of this state by monitoring the intracellular gating residues, the extent of hydration, and, most importantly, protein-ligand interactions in the central binding site. The results illustrate common and distinct characteristics of these two transporter states and provide a starting point for future investigations of the transport mechanism in hSERT.

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