scholarly journals The structural transformation comparison of the human Prion protein mutants V176G, E196A, and I215V by using molecular dynamics simulation

2021 ◽  
Author(s):  
Ashraf Fadhil Jomah ◽  
Sepideh Parvizpour ◽  
Jafar Razmara ◽  
Mohd Shahir Shamsir
Keyword(s):  
Prion Protein ◽  
Aqueous Media ◽  
Point Mutations ◽  
Cellular Prion Protein ◽  
Dynamics Simulation ◽  
Globular Domain ◽  
Salt Bridges ◽  
Wild Type ◽  
Structural Determinants ◽  
C Terminus

Abstract The point mutations in the gene coding of prion protein (PrP) originate human familial prion protein (HuPrP) diseases. Such diseases are caused by several amino acid mutations of HuPrP including V176G, I215V, and E196A located at the second, third native helix and in their loop, respectively. Determining the transition from cellular prion protein (PrPc) to pathogenic conformer (PrPSc) in the globular domain of HuPrP that results in pathogenic mutations is the key issue. The effects of mutation on monomeric PrP are detected in the absence of an unstructured N-terminal domain only. A MD simulation for each of these wild type mutants is performed to examine their structure in the aqueous media. The structural determinants are discerned to be different for wild-type HuPrP (125–228) variants compare to that of HuPrP mutations. These three mutations exhibiting diverse effects on the dynamical properties of PrP are attributed to the variations in the secondary structure, solvent accessible surface areas (SASAs), and salt bridges in the globular domain of HuPrP. High fluctuations that are evidenced around residues of the C-terminus of the helix 1 for V176G cause Gerstmann-Straussler-Scheinker (GSS) syndrome. Conversely, the occurrence of fluctuations around residues of helix 2, helix 3, and the loss of salt bridges in these regions for E196A and I215V mutants is responsible for Creutzfeldt-Jakob disease. Furthermore, small changes in the overall SASAs mutations strongly influence the intermolecular interactions during the aggregation process. The comparative results in this study demonstrate that the three mutants undergo different pathogenic transformations.

scholarly journals Analysis of the structural features of the C-terminus of GLUT1 that are required for transport catalytic activity

1995 ◽  
Vol 311 (2) ◽  
pp. 699-704 ◽  
Author(s):  
A Muraoka ◽  
M Hashiramoto ◽  
A E Clark ◽  
L C Edwards ◽  
H Sakura ◽  
...  
Keyword(s):  
Amino Acids ◽  
Glucose Transport ◽  
Cytochalasin B ◽  
Point Mutations ◽  
Chinese Hamster ◽  
Structural Features ◽  
Transport Activity ◽  
Wild Type ◽  
C Terminus ◽  
Wild Type Clone

C-terminally truncated and mutated forms of GLUT1 have been constructed to determine the minimum structure at the C-terminus required for glucose transport activity and ligand binding at the outer and inner binding sites. Four truncated mutants have been constructed (CTD24 to CTD27) in which 24 to 27 amino acids are deleted. In addition, point substitutions of R468-->L, F467-->L and G466-->E have been produced. Chinese hamster ovary clones which were transfected with these mutant GLUT1s were shown, by Western blotting and cell-surface carbohydrate labelling, to have expression levels which were comparable with the wild-type clone. Wild-type levels of 2-deoxy-D-glucose transport activity were retained only in the clone transfected with the construct in which 24 amino acids were deleted (CTD24). The CTD25, CTD26 and CTD27 clones showed markedly reduced transport activity. From a kinetic comparison of the CTD24 and CTD26 clones it was found that the reduced transport was mainly associated with a reduced Vmax. value for 2-deoxy-D-glucose uptake but with a slight lowering of the Km. These data establish that the 24 amino acids at the C-terminus of GLUT1 are not required for the transport catalysis. However, the point mutations of F467L and G466E (26 and 27 residues from the C-terminus) did not significantly perturb the kinetics of 2-deoxy-D-glucose transport. The substitution of R468L produced a slight, but significant, lowering of the Km. The ability of the truncated GLUt1s to bind the exofacial ligand, 2-N-4-(1-zai-2,2,2-trifluoroethyl)benzoyl-1,3-bis-(D-mannos- 4-yl-oxy) -2-propylamine (ATB-BMPA), and the endofacial ligand, cytochalasin B, were assessed by photolabelling procedures. The ability to bind ATB-BMPA was retained only in the CTD24 truncated mutant and was reduced to levels comparable with those of the non-transfected clone in the other mutant clones. Cytochalasin B labelling was unimpaired in all four mutated GLUT1s. These data establish that a minimum structure at the C-terminus of GLUT1, which is required for the conformational change to expose the exofacial site, includes amino acids at positions Phe-467 and Arg-468; however, these amino acids are not individually essential.

scholarly journals A Promising Antiprion Trimethoxychalcone Binds to the Globular Domain of the Cellular Prion Protein and Changes Its Cellular Location

2017 ◽  
Vol 62 (2) ◽  
Author(s):  
N. C. Ferreira ◽  
L. M. Ascari ◽  
A. G. Hughson ◽  
G. R. Cavalheiro ◽  
C. F. Góes ◽  
...  
Keyword(s):  
Cell Surface ◽  
Real Time ◽  
Prion Protein ◽  
Molecular Mechanisms ◽  
Cellular Prion Protein ◽  
Transmissible Spongiform Encephalopathies ◽  
Globular Domain ◽  
Mrna Levels ◽  
Spongiform Encephalopathies

ABSTRACTThe search for antiprion compounds has been encouraged by the fact that transmissible spongiform encephalopathies (TSEs) share molecular mechanisms with more prevalent neurodegenerative pathologies, such as Parkinson's and Alzheimer's diseases. Cellular prion protein (PrPC) conversion into protease-resistant forms (protease-resistant PrP [PrPRes] or the scrapie form of PrP [PrPSc]) is a critical step in the development of TSEs and is thus one of the main targets in the screening for antiprion compounds. In this work, three trimethoxychalcones (compounds J1, J8, and J20) and one oxadiazole (compound Y17), previously identifiedin vitroto be potential antiprion compounds, were evaluated through different approaches in order to gain inferences about their mechanisms of action. None of them changed PrPCmRNA levels in N2a cells, as shown by reverse transcription-quantitative real-time PCR. Among them, J8 and Y17 were effective in real-time quaking-induced conversion reactions using rodent recombinant PrP (rPrP) from residues 23 to 231 (rPrP23–231) as the substrate and PrPScseeds from hamster and human brain. However, when rPrP from residues 90 to 231 (rPrP90–231), which lacks the N-terminal domain, was used as the substrate, only J8 remained effective, indicating that this region is important for Y17 activity, while J8 seems to interact with the PrPCglobular domain. J8 also reduced the fibrillation of mouse rPrP23–231seeded within vitro-produced fibrils. Furthermore, most of the compounds decreased the amount of PrPCon the N2a cell surface by trapping this protein in the endoplasmic reticulum. On the basis of these results, we hypothesize that J8, a nontoxic compound previously shown to be a promising antiprion agent, may act by different mechanisms, since its efficacy is attributable not only to PrP conversion inhibition but also to a reduction of the PrPCcontent on the cell surface.

scholarly journals NMR Structure and CD Titration with Metal Cations of Human Prionα2-Helix-Related Peptides

2007 ◽  
Vol 2007 ◽  
pp. 1-9 ◽  
Author(s):  
Luisa Ronga ◽  
Pasquale Palladino ◽  
Gabriella Saviano ◽  
Teodorico Tancredi ◽  
Ettore Benedetti ◽  
...  
Keyword(s):  
Prion Protein ◽  
Point Mutations ◽  
Metal Cations ◽  
Spectroscopic Studies ◽  
Cation Binding ◽  
Protein Domain ◽  
Wild Type ◽  
Peptide Complexes ◽  
Natural Target

The 173–195 segment corresponding to the helix 2 of the C-globular prion protein domain could be one of several “spots” of intrinsic conformational flexibility. In fact, it possesses chameleon conformational behaviour and gathers several disease-associated point mutations. We have performed spectroscopic studies on the wild-type fragment 173–195 and on its D178N mutant dissolved in trifluoroethanol to mimic the in vivo system, both in the presence and in the absence of metal cations. NMR data showed that the structure of the D178N mutant is characterized by two short helices separated by a kink, whereas the wild-type peptide is fully helical. Both peptides retained these structural organizations, as monitored by CD, in the presence of metal cations. NMR spectra were however not in favour of the formation of definite ion-peptide complexes. This agrees with previous evidence that other regions of the prion protein are likely the natural target of metal cation binding.

scholarly journals Mapping the Prion Protein Using Recombinant Antibodies

1998 ◽  
Vol 72 (11) ◽  
pp. 9413-9418 ◽  
Author(s):  
R. Anthony Williamson ◽  
David Peretz ◽  
Clemencia Pinilla ◽  
Hadyn Ball ◽  
Raiza B. Bastidas ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Cell Surface ◽  
Prion Protein ◽  
Disease Process ◽  
Cellular Prion Protein ◽  
Epitope Region ◽  
Molecular Events ◽  
C Terminus ◽  
Phage Display Libraries ◽  
Recombinant Molecule

ABSTRACT The fundamental event in prion disease is thought to be the posttranslational conversion of the cellular prion protein (PrPC) into a pathogenic isoform (PrPSc). The occurrence of PrPC on the cell surface and PrPSc in amyloid plaques in situ or in aggregates following purification complicates the study of the molecular events that underlie the disease process. Monoclonal antibodies are highly sensitive probes of protein conformation which can be used under these conditions. Here, we report the rescue of a diverse panel of 19 PrP-specific recombinant monoclonal antibodies from phage display libraries prepared from PrP deficient (Prnp0/0) mice immunized with infectious prions either in the form of rods or PrP 27-30 dispersed into liposomes. The antibodies recognize a number of distinct linear and discontinuous epitopes that are presented to a varying degree on different PrP preparations. The epitope reactivity of the recombinant PrP(90-231) molecule was almost indistinguishable from that of PrPC on the cell surface, validating the importance of detailed structural studies on the recombinant molecule. Only one epitope region at the C terminus of PrP was well presented on both PrPC and PrPSc, while epitopes associated with most of the antibodies in the panel were present on PrPCbut absent from PrPSc.

Investigation on salt bridge interactions of mammalian prion proteins by molecular dynamics simulation / Memeli prion proteinlerinin moleküler dinamik simulasyon ile tuz köprüleri etkileşimlerinin araştırılması

2016 ◽  
Vol 41 (3) ◽  
Author(s):  
Xiliang Chen ◽  
Xin Chen ◽  
Yafang Liu
Keyword(s):  
Molecular Dynamics ◽  
Prion Protein ◽  
Electrostatic Interactions ◽  
Prion Proteins ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Tertiary Structures ◽  
Local Structures ◽  
The Stability

AbstractObjective: Salt bridge interaction is one of the most important electrostatic interactions to stabilize the secondary and tertiary structures of protein. To obtain more insight into the molecular basis of prion proteins, the salt bridge networks in two animal prion proteins are studied in this work.Methods: Molecular dynamics (MD) and Flow MD (FMD) simulations are employed to investigate the salt bridges interactions of rabbit prion protein (rPrPc), Syrian hamster prion protein (syPrPc) and the variants of the two prion proteins.Results: The dynamic behaviors of salt bridges are characterized, and the relation between salt bridge interactions and local structures are also discussed. The type of salt bridges in the two prion proteins is divided into the helixloop, intra-helix and inter-helix salt bridges. It is found that the helix-loop salt bridges is more important for the stability of prion proteins than the other two kinds of slat bridge.Conclusion: The Asp201-Arg155 (rS1), Asp177-Arg163 (rS3) and Asp178-Arg164 (syS1) are the important salt bridges to stabilize the structures of rPrPc and syPrPc, respectively. The structural stability is partly depended on the number of helix-loop salt bridge.

scholarly journals New and distinct chronic wasting disease strains associated with cervid polymorphism at codon 116 of the Prnp gene

2021 ◽  
Vol 17 (7) ◽  
pp. e1009795
Author(s):  
Samia Hannaoui ◽  
Elizabeth Triscott ◽  
Camilo Duque Velásquez ◽  
Sheng Chun Chang ◽  
Maria Immaculata Arifin ◽  
...  
Keyword(s):  
Prion Protein ◽  
Chronic Wasting Disease ◽  
Prnp Gene ◽  
Biochemical Properties ◽  
Cellular Prion Protein ◽  
Proteinase K ◽  
Wild Type ◽  
Wasting Disease ◽  
Prion Strains ◽  
The Impact

Chronic wasting disease (CWD) is a prion disease affecting cervids. Polymorphisms in the prion protein gene can result in extended survival of CWD-infected animals. However, the impact of polymorphisms on cellular prion protein (PrPC) and prion properties is less understood. Previously, we characterized the effects of a polymorphism at codon 116 (A>G) of the white-tailed deer (WTD) prion protein and determined that it destabilizes PrPC structure. Comparing CWD isolates from WTD expressing homozygous wild-type (116AA) or heterozygous (116AG) PrP, we found that 116AG-prions were conformationally less stable, more sensitive to proteases, with lower seeding activity in cell-free conversion and reduced infectivity. Here, we aimed to understand CWD strain emergence and adaptation. We show that the WTD-116AG isolate contains two different prion strains, distinguished by their host range, biochemical properties, and pathogenesis from WTD-116AA prions (Wisc-1). Serial passages of WTD-116AG prions in tg(CerPrP)1536+/+ mice overexpressing wild-type deer-PrPC revealed two populations of mice with short and long incubation periods, respectively, and remarkably prolonged clinical phase upon inoculation with WTD-116AG prions. Inoculation of serially diluted brain homogenates confirmed the presence of two strains in the 116AG isolate with distinct pathology in the brain. Interestingly, deglycosylation revealed proteinase K-resistant fragments with different electrophoretic mobility in both tg(CerPrP)1536+/+ mice and Syrian golden hamsters infected with WTD-116AG. Infection of tg60 mice expressing deer S96-PrP with 116AG, but not Wisc-1 prions induced clinical disease. On the contrary, bank voles resisted 116AG prions, but not Wisc-1 infection. Our data indicate that two strains co-existed in the WTD-116AG isolate, expanding the variety of CWD prion strains. We argue that the 116AG isolate does not contain Wisc-1 prions, indicating that the presence of 116G-PrPC diverted 116A-PrPC from adopting a Wisc-1 structure. This can have important implications for their possible distinct capacities to cross species barriers into both cervids and non-cervids.

scholarly journals Liquid-liquid phase separation and aggregation of the prion protein globular domain modulated by a high-affinity DNA aptamer

2019 ◽  
Author(s):  
Carolina O. Matos ◽  
Yulli M. Passos ◽  
Mariana J. do Amaral ◽  
Bruno Macedo ◽  
Matheus Tempone ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Prion Protein ◽  
Liquid Phase Separation ◽  
Cellular Prion Protein ◽  
Globular Domain ◽  
Structural Conversion ◽  
High Affinity ◽  
Liquid Liquid Phase Separation

ABSTRACTStructural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events for the onset of Transmissible Spongiform Encephalopathies (TSEs). Experimental evidences support the role of nucleic acids (NAs) in assisting the protein conversion process. Here, we used the SELEX methodology to identify two 25-mer DNA aptamers against the globular domain of recombinant murine PrP (rPrP90-231), namely A1 and A2. High-affinity binding of A1 and A2 to rPrP was verified by ITC. Aptamers structure was characterized by theoretical predictions, CD, NMR and SAXS, revealing that A1 adopts a hairpin conformation. Aptamer binding caused dynamic aggregation of rPrP90-231, resulting from the ability of rPrP90-231to undergo liquid-liquid phase separation (LLPS). While free rPrP90-231phase separated into large droplets, aptamer binding increased the amount but reduced the size of the condensates. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced transition to an ordered state, suggestive of amyloid formation on the surface of the droplets. Our results describe for the first time PrP:NA interaction leading to LLPS and modulation of this effect depending on NA structure and binding stoichiometry, shedding light on the role of NAs in PrP misfolding and TSEs.

scholarly journals Calbindin-D28kin the Brain Influences the Expression of Cellular Prion Protein

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Yeong-Min Yoo ◽  
Eui-Bae Jeung
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Expression ◽  
Prion Protein ◽  
Calcium Transport ◽  
Transport Proteins ◽  
Cellular Prion Protein ◽  
Marker Protein ◽  
Wild Type ◽  
Calbindin D9k ◽  
The Brain

The phenotypes ofcalbindin-D9k- (CaBP-9k-) knockout (KO),calbindin-D28k- (CaBP-28k-) KO, andCaBP-9k/28k-KO mice are similar to those of wild-type (WT) mice due to the compensatory action of other calcium transport proteins. In this study, we investigated the expression of cellular prion protein (PrPC) in the brains ofCaBP-9k-,CaBP-28k-, andCaBP-9k/28k-KO mice. PrPCexpression was significantly upregulated in the brain of all three strains. Levels of phospho-Akt (Ser473) and phospho-Bad (Ser136) were significantly elevated, but those of phospho-ERK and phospho-Bad (Ser155 and 112) were significantly reduced in the brains ofCaBP-9k-,CaBP-28k-, andCaBP-9k/28k-KO mice. The expressions of the Bcl-2, p53, Bax, Cu/Zn-SOD, and Mn-SOD proteins were decreased in the brains of all KO mice. Expression of the endoplasmic reticulum marker protein BiP/GRP78 was decreased, and that of the CHOP protein was increased in the brains of those KO mice. To identify the roles ofCaBP-28k, we transfected PC12 cells with siRNA forCaBP-28kand found increased expression of the PrPCprotein compared to the levels in control cells. These results suggest thatCaBP-28kexpression may regulate PrPCprotein expression and these mice may be vulnerable to the influence of prion disease.

scholarly journals Molecular determinants of the physicochemical properties of a critical prion protein region comprising residues 106–126

1999 ◽  
Vol 342 (1) ◽  
pp. 207-214 ◽  
Author(s):  
Mario SALMONA ◽  
Paolo MALESANI ◽  
Luca DE GIOIA ◽  
Stefano GORLA ◽  
Maurizio BRUSCHI ◽  
...  
Keyword(s):  
Prion Protein ◽  
Conformational Changes ◽  
Amyloid Fibrils ◽  
Physicochemical Characteristics ◽  
Cellular Prion Protein ◽  
Random Coil ◽  
Neuronal Cultures ◽  
Primary Neuronal Cultures ◽  
C Terminus ◽  
Molecular Determinants

Prion diseases are marked by the cerebral accumulation of conformationally modified forms of the cellular prion protein (PrPC), known as PrPres. The region comprising the residues 106-126 of human PrP seems to have a key role in this conformational conversion, because a synthetic peptide homologous with this sequence (PrP106-126) adopts different secondary structures in different environments. To investigate the molecular determinants of the physicochemical characteristics of PrP106-126, we synthesized a series of analogues including PrP106-126 HD, PrP106-126 A and PrP106-126 K, with L-His → D-His, His → Ala and His → Lys substitutions respectively at position 111, PrP106-126 NH2 with amidation of the C-terminus, PrP106-126 V with an Ala → Val substition at position 117, and PrP106-126 VNH2 with an Ala → Val substitution at position 117 and amidation of the C-terminus. The analysis of the secondary structure and aggregation properties of PrP106-126 and its analogues showed the following. (1) His111 is central to the conformational changes of PrP peptides. (2) Amidation of the C-terminal Gly126 yields a predominantly random coil structure, abolishes the molecular polymorphism and decreases the propensity of PrP106-126 to generate amyloid fibrils. (3) PrP106-126 V, carrying an Ala → Val substitution at position 117, does not demonstrate a fibrillogenic ability superior to that of PrP106-126. However, the presence of Val at position 117 increases the aggregation properties of the amidated peptide. (4) Amyloid fibrils are not required for neurotoxicity because the effects of PrP106-126 NH2 on primary neuronal cultures were similar to those of the wild-type sequence. Conversely, astroglial proliferation is related to the presence of amyloid fibrils, suggesting that astrogliosis in prion encephalopathies without amyloid deposits is a mediated effect rather than a direct effect of disease-specific PrP isoforms.

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