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  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2005
    In:  BMC Structural Biology Vol. 5, No. 1 ( 2005-12)
    In: BMC Structural Biology, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2005-12)
    Abstract: The polypeptides involved in amyloidogenesis may be globular proteins with a defined 3D-structure or natively unfolded proteins. The first class includes polypeptides such as β2-microglobulin, lysozyme, transthyretin or the prion protein, whereas β-amyloid peptide, amylin or α-synuclein all belong to the second class. Recent studies suggest that specific regions in the proteins act as "hot spots" driving aggregation. This should be especially relevant for natively unfolded proteins or unfolded states of globular proteins as they lack significant secondary and tertiary structure and specific intra-chain interactions that can mask these aggregation-prone regions. Prediction of such sequence stretches is important since they are potential therapeutic targets. Results In this study we exploited the experimental data obtained in an in vivo system using β-amyloid peptide as a model to derive the individual aggregation propensities of natural amino acids. These data are used to generate aggregation profiles for different disease-related polypeptides. The approach detects the presence of "hot spots" which have been already validated experimentally in the literature and provides insights into the effect of disease-linked mutations in these polypeptides. Conclusion The proposed method might become a useful tool for the future development of sequence-targeted anti-aggregation pharmaceuticals.
    Type of Medium: Online Resource
    ISSN: 1472-6807
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2005
    detail.hit.zdb_id: 2050440-8
    SSG: 12
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  • 2
    In: Enzyme Research, Hindawi Limited, Vol. 2011 ( 2011-07-25), p. 1-8
    Abstract: A high-resolution carboxypeptidase-Zn 2+ -citrate complex was studied by X-ray diffraction and enzyme kinetics for the first time. The citrate molecule acts as a competitive inhibitor of this benchmark zinc-dependent peptidase, chelating the catalytic zinc ion in the active site of the enzyme and inducing a conformational change such that carboxypeptidase adopts the conformation expected to occur by substrate binding. Citrate adopts an extended conformation with half of the molecule facing the zinc ion, while the other half is docked in the S1′ hydrophobic specificity pocket of the enzyme, in contrast with the binding mode expected for a substrate like phenylalanine or a peptidomimetic inhibitor like benzylsuccinic acid. Combined structural and enzymatic analysis describes the characteristics of the binding of this ligand that, acting against physiologically relevant zinc-dependent proteases, may serve as a general model in the design of new drug-protecting molecules for the oral delivery of drugs of peptide origin.
    Type of Medium: Online Resource
    ISSN: 2090-0414
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2011
    detail.hit.zdb_id: 2573712-0
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  • 3
    Online Resource
    Online Resource
    Frontiers Media SA ; 2022
    In:  Frontiers in Molecular Biosciences Vol. 9 ( 2022-5-18)
    In: Frontiers in Molecular Biosciences, Frontiers Media SA, Vol. 9 ( 2022-5-18)
    Abstract: Proteome-wide analyses suggest that most globular proteins contain at least one amyloidogenic region, whereas these aggregation-prone segments are thought to be underrepresented in intrinsically disordered proteins (IDPs). In recent work, we reported that intrinsically disordered regions (IDRs) indeed sustain a significant amyloid load in the form of cryptic amyloidogenic regions (CARs). CARs are widespread in IDRs, but they are necessarily exposed to solvent, and thus they should be more polar and have a milder aggregation potential than conventional amyloid regions protected inside globular proteins. CARs are connected with IDPs function and, in particular, with the establishment of protein-protein interactions through their IDRs. However, their presence also appears associated with pathologies like cancer or Alzheimer’s disease. Given the relevance of CARs for both IDPs function and malfunction, we developed CARs-DB, a database containing precomputed predictions for all CARs present in the IDPs deposited in the DisProt database. This web tool allows for the fast and comprehensive exploration of previously unnoticed amyloidogenic regions embedded within IDRs sequences and might turn helpful in identifying disordered interacting regions. It contains & gt;8,900 unique CARs identified in a total of 1711 IDRs. CARs-DB is freely available for users and can be accessed at http://carsdb.ppmclab.com . To validate CARs-DB, we demonstrate that two previously undescribed CARs selected from the database display full amyloidogenic potential. Overall, CARs-DB allows easy access to a previously unexplored amyloid sequence space.
    Type of Medium: Online Resource
    ISSN: 2296-889X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2814330-9
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  • 4
    Online Resource
    Online Resource
    Wiley ; 2021
    In:  FEBS Open Bio Vol. 11, No. 9 ( 2021-09), p. 2400-2417
    In: FEBS Open Bio, Wiley, Vol. 11, No. 9 ( 2021-09), p. 2400-2417
    Abstract: Prions are self‐perpetuating proteins able to switch between a soluble state and an aggregated‐and‐transmissible conformation. These proteinaceous entities have been widely studied in yeast, where they are involved in hereditable phenotypic adaptations. The notion that such proteins could play functional roles and be positively selected by evolution has triggered the development of computational tools to identify prion‐like proteins in different kingdoms of life. These algorithms have succeeded in screening multiple proteomes, allowing the identification of prion‐like proteins in a diversity of unrelated organisms, evidencing that the prion phenomenon is well conserved among species. Interestingly enough, prion‐like proteins are not only connected with the formation of functional membraneless protein–nucleic acid coacervates, but are also linked to human diseases. This review addresses state‐of‐the‐art computational approaches to identify prion‐like proteins, describes proteome‐wide analysis efforts, discusses these unique proteins' functional role, and illustrates recently validated examples in different domains of life.
    Type of Medium: Online Resource
    ISSN: 2211-5463 , 2211-5463
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2651702-4
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  • 5
    Online Resource
    Online Resource
    Medknow ; 2023
    In:  Neural Regeneration Research Vol. 18, No. 5 ( 2023), p. 1027-
    In: Neural Regeneration Research, Medknow, Vol. 18, No. 5 ( 2023), p. 1027-
    Type of Medium: Online Resource
    ISSN: 1673-5374
    Language: English
    Publisher: Medknow
    Publication Date: 2023
    detail.hit.zdb_id: 2388460-5
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  • 6
    Online Resource
    Online Resource
    Elsevier BV ; 2022
    In:  Trends in Biochemical Sciences Vol. 47, No. 8 ( 2022-08), p. 641-644
    In: Trends in Biochemical Sciences, Elsevier BV, Vol. 47, No. 8 ( 2022-08), p. 641-644
    Type of Medium: Online Resource
    ISSN: 0968-0004
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 194216-5
    detail.hit.zdb_id: 1498901-3
    SSG: 12
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  • 7
    In: European Journal of Medicinal Chemistry, Elsevier BV, ( 2023-10), p. 115837-
    Type of Medium: Online Resource
    ISSN: 0223-5234
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2005170-0
    SSG: 15,3
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  • 8
    In: Biopolymers, Wiley, Vol. 93, No. 2 ( 2010-02), p. 178-185
    Abstract: A new triclinic crystal structure form of porcine pancreatic procarboxypeptidase B (PCPB) was obtained at higher resolution than the previously known tetragonal crystal structure. This new crystal polymorph has allowed for a corrected, accurate assignment of residues along the polypeptide chain based on the currently available gene sequence information and crystallographic data. The present structure shows unbound PCPB in a distinct molecular packing as compared to the previous benzamidine complexed form. Its catalytically important Tyr248 residue is oriented and hydrogen‐bonded to solvent water molecules, and locates the furthest away from the catalytic zinc ion as compared to previous structures. A relatively long stretch of residues flanking Tyr248 and guarding the access to the catalytic zinc ion was found to be sequentially unique to the M14 family of peptidases. Predictions from a normal mode analysis indicated that this stretch of residues belongs to a rigid subdomain in the protein structure. The specific presence of a tyrosyl residue at the most exposed position in this region would allow for a delicate balance between extreme hydrophobicity and hydrophilicity, and affect substrate binding and the kinetic efficiency of the enzyme. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 178–185, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
    Type of Medium: Online Resource
    ISSN: 0006-3525 , 1097-0282
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 2159538-0
    detail.hit.zdb_id: 1480801-8
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2005
    In:  Proceedings of the National Academy of Sciences Vol. 102, No. 11 ( 2005-03-15), p. 3978-3983
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 102, No. 11 ( 2005-03-15), p. 3978-3983
    Abstract: The only endogenous protein inhibitor known for metallocarboxypeptidases (MCPs) is latexin, a 25-kDa protein discovered in the rat brain. Latexin, alias endogenous carboxypeptidase inhibitor, inhibits human CPA4 (hCPA4), whose expression is induced in prostate cancer cells after treatment with histone deacetylase inhibitors. hCPA4 is a member of the A/B subfamily of MCPs and displays the characteristic α/β-hydrolase fold. Human latexin consists of two topologically equivalent subdomains, reminiscent of cystatins, consisting of an α-helix enveloped by a curved β-sheet. These subdomains are packed against each other through the helices and linked by a connecting segment encompassing a third α-helix. The enzyme is bound at the interface of these subdomains. The complex occludes a large contact surface but makes rather few contacts, despite a nanomolar inhibition constant. This low specificity explains the flexibility of latexin in inhibiting all vertebrate A/B MCPs tested, even across species barriers. In contrast, modeling studies reveal why the N/E subfamily of MCPs and invertebrate A/B MCPs are not inhibited. Major differences in the loop segments shaping the border of the funnel-like access to the protease active site impede complex formation with latexin. Several sequences ascribable to diverse tissues and organs have been identified in vertebrate genomes as being highly similar to latexin. They are proposed to constitute the latexin family of potential inhibitors. Because they are ubiquitous, latexins could represent for vertebrate A/B MCPs the counterparts of tissue inhibitors of metalloproteases for matrix metalloproteinases.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2005
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    MDPI AG ; 2018
    In:  International Journal of Molecular Sciences Vol. 19, No. 5 ( 2018-05-06), p. 1384-
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 19, No. 5 ( 2018-05-06), p. 1384-
    Type of Medium: Online Resource
    ISSN: 1422-0067
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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