6KBO

Three-dimensional LPS bound structure of VG16KRKP-KYE28.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic-aromatic interactions in antibacterial synergism.

Ilyas, H.Kim, J.Lee, D.Malmsten, M.Bhunia, A.

(2019) J Biol Chem 294: 14615-14633

  • DOI: 10.1074/jbc.RA119.009955
  • Primary Citation of Related Structures:  
    6KBO, 6KBV

  • PubMed Abstract: 
  • The recent development of plants that overexpress antimicrobial peptides (AMPs) provides opportunities for controlling plant diseases. Because plants employ a broad-spectrum antimicrobial defense, including those based on AMPs, transgenic modification for AMP overexpression represents a potential way to utilize a defense system already present in plants ...

    The recent development of plants that overexpress antimicrobial peptides (AMPs) provides opportunities for controlling plant diseases. Because plants employ a broad-spectrum antimicrobial defense, including those based on AMPs, transgenic modification for AMP overexpression represents a potential way to utilize a defense system already present in plants. Herein, using an array of techniques and approaches, we report on VG16KRKP and KYE28, two antimicrobial peptides, which in combination exhibit synergistic antimicrobial effects against plant pathogens and are resistant against plant proteases. Investigating the structural origin of these synergistic antimicrobial effects with NMR spectroscopy of the complex formed between these two peptides and their mutated analogs, we demonstrate the formation of an unusual peptide complex, characterized by the formation of a bulky hydrophobic hub, stabilized by aromatic zippers. Using three-dimensional structure analyses of the complex in bacterial outer and inner membrane components and when bound to lipopolysaccharide (LPS) or bacterial membrane mimics, we found that this structure is key for elevating antimicrobial potency of the peptide combination. We conclude that the synergistic antimicrobial effects of VG16KRKP and KYE28 arise from the formation of a well-defined amphiphilic dimer in the presence of LPS and also in the cytoplasmic bacterial membrane environment. Together, these findings highlight a new application of solution NMR spectroscopy to solve complex structures to study peptide-peptide interactions, and they underscore the importance of structural insights for elucidating the antimicrobial effects of AMP mixtures.


    Organizational Affiliation

    Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India bhunia@jcbose.ac.in anirbanbhunia@gmail.com.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VG16KRKPA16Dengue virusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heparin cofactor 2B28Homo sapiensMutation(s): 0 
Gene Names: SERPIND1HCF2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05546 (Homo sapiens)
Explore P05546 
Go to UniProtKB:  P05546
PHAROS:  P05546
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 6KBO Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2019-06-26 
  • Released Date: 2019-08-14 
  • Deposition Author(s): Ilyas, H., Bhunia, A.

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references