7B3J

Dynamic complex between all-D-enantiomeric peptide D3 with wild-type amyloid precursor protein 672-726 fragment (amyloid beta 1-55)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

All - d - Enantiomeric Peptide D3 Designed for Alzheimer's Disease Treatment Dynamically Interacts with Membrane-Bound Amyloid-beta Precursors.

Bocharov, E.V.Gremer, L.Urban, A.S.Okhrimenko, I.S.Volynsky, P.E.Nadezhdin, K.D.Bocharova, O.V.Kornilov, D.A.Zagryadskaya, Y.A.Kamynina, A.V.Kuzmichev, P.K.Kutzsche, J.Bolakhrif, N.Muller-Schiffmann, A.Dencher, N.A.Arseniev, A.S.Efremov, R.G.Gordeliy, V.I.Willbold, D.

(2021) J Med Chem 64: 16464-16479

  • DOI: 10.1021/acs.jmedchem.1c00632
  • Primary Citation of Related Structures:  
    7B3J, 7B3K

  • PubMed Abstract: 
  • Alzheimer's disease (AD) is a severe neurodegenerative pathology with no effective treatment known. Toxic amyloid-β peptide (Aβ) oligomers play a crucial role in AD pathogenesis. All - d - Enantiomeric peptide D3 and its derivatives were developed to disassemble and destroy cytotoxic Aβ aggregates ...

    Alzheimer's disease (AD) is a severe neurodegenerative pathology with no effective treatment known. Toxic amyloid-β peptide (Aβ) oligomers play a crucial role in AD pathogenesis. All - d - Enantiomeric peptide D3 and its derivatives were developed to disassemble and destroy cytotoxic Aβ aggregates. One of the D3-like compounds is approaching phase II clinical trials; however, high-resolution details of its disease-preventing or pharmacological actions are not completely clear. We demonstrate that peptide D3 stabilizing Aβ monomer dynamically interacts with the extracellular juxtamembrane region of a membrane-bound fragment of an amyloid precursor protein containing the Aβ sequence. MD simulations based on NMR measurement results suggest that D3 targets the amyloidogenic region, not compromising its α-helicity and preventing intermolecular hydrogen bonding, thus creating prerequisites for inhibition of early steps of Aβ conversion into β-conformation and its toxic oligomerization. An enhanced understanding of the D3 action molecular mechanism facilitates development of effective AD treatment and prevention strategies.


    Organizational Affiliation

    Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform L-APP677 of Amyloid-beta precursor proteinA55Homo sapiensMutation(s): 0 
Gene Names: APPA4AD1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D3 all D-enantimeric peptideB12synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry 
  • OLDERADO: 7B3J Olderado

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation20-64-46027

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-17
    Changes: Data collection, Database references
  • Version 2.0: 2021-12-08
    Changes: Atomic model, Database references