7B3J

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

• PDB DOI:  https://doi.org/10.2210/pdb7B3J/pdb
• BMRB: 34577

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2020-12-01 Released: 2021-01-13 
• Deposition Author(s): Bocharov, E.V., Volynsky, P.E., Okhrimenko, I.S., Urban, A.S.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

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

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

• PubMed: 34739758 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content

• Total Structure Weight: 7.6 kDa 
• Atom Count: 534 
• Modelled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform L-APP677 of Amyloid-beta precursor protein	A	55	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D3 all D-enantimeric peptide	B	12	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Bocharov, E.V., Volynsky, P.E., Okhrimenko, I.S., Urban, A.S.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	20-64-46027

Revision History  

• 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