Biological Assembly 1  

 3D View: Structure

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1.65 kDa 
• Atom Count: 119 
• Residue Count: 17 
• Unique protein chains: 1

2M1F

NMR Structure of Antiamoebin I (peptaibol antibiotic) bound to DMPC/DHPC bicelles

• DOI: 10.2210/pdb2M1F/pdb
• BMRB: 18861

• Classification: ANTIBIOTIC
• Organism(s): Emericellopsis minima
• Mutation(s): No 


• Deposited: 2012-11-27 Released: 2012-12-12 
• Deposition Author(s): Shenkarev, Z.O., Paramonov, A.S., Gizatullina, A.K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Peptaibol antiamoebin I: spatial structure, backbone dynamics, interaction with bicelles and lipid-protein nanodiscs, and pore formation in context of barrel-stave model.

Shenkarev, Z.O., Paramonov, A.S., Lyukmanova, E.N., Gizatullina, A.K., Zhuravleva, A.V., Tagaev, A.A., Yakimenko, Z.A., Telezhinskaya, I.N., Kirpichnikov, M.P., Ovchinnikova, T.V., Arseniev, A.S.

(2013) Chem Biodivers 10: 838-863

• PubMed: 23681729 
• DOI: 10.1002/cbdv.201200421
• Primary Citation of Related Structures:  
  2M1F


• PubMed Abstract: 
  

Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. In comparison with other 16-amino acid-residue peptaibols, e.g., zervamicin IIB (Zrv-IIB), Aam-I possesses relatively weak biological and channel-forming activities. In MeOH solution, Aam-I demonstrates fast cooperative transitions between right-handed and left-handed helical conformation of the N-terminal (1-8) region. We studied Aam-I spatial structure and backbone dynamics in the membrane-mimicking environment (DMPC/DHPC bicelles)(1) ) by heteronuclear (1) H,(13) C,(15) N-NMR spectroscopy. Interaction with the bicelles stabilizes the Aam-I right-handed helical conformation retaining significant intramolecular mobility on the ms-μs time scale. Extensive ms-μs dynamics were also detected in the DPC and DHPC micelles and DOPG nanodiscs. In contrast, Zrv-IIB in the DPC micelles demonstrates appreciably lesser mobility on the μs-ms time scale. Titration with Mn(2+) and 16-doxylstearate paramagnetic probes revealed Aam-I binding to the bicelle surface with the N-terminus slightly immersed into hydrocarbon region. Fluctuations of the Aam-I helix between surface-bound and transmembrane (TM) state were observed in the nanodisc membranes formed from the short-chain (diC12 : 0) DLPC/DLPG lipids. All the obtained experimental data are in agreement with the barrel-stave model of TM pore formation, similarly to the mechanism proposed for Zrv-IIB and other peptaibols. The observed extensive intramolecular dynamics explains the relatively low activity of Aam-I.

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Organizational Affiliation: 

Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiamoebin I	A	17	Emericellopsis minima	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PHL	A	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000161	A	Antiamoebin 1	Peptaibol /  Antibiotic		--

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2M1F Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-27 
• Released Date: 2012-12-12 
Deposition Author(s): Shenkarev, Z.O., Paramonov, A.S., Gizatullina, A.K.

Revision History 

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references