PDBsum entry: 1znt

Antimicrobial protein

PDB-id: 1znt

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

31 a.a.

Ligands

NAG-NAG-NAG

Tools

Clefts Calculation

PDB id:

1znt

Name:

Antimicrobial protein

Title:

18 nmr structures of acamp2-like peptide with non natural fluoroaromatic residue (acamp2f18pff/y20pff) complex with n,n,n-triacetylchitotriose

Structure:

Amaranthus caudatus antimicrobial peptide 2. Chain: a. Synonym: acmp2. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in amaranthus caudatus (inca-wheat). Sequence prepared by standard solid phase peptide synthesis protocols using fmoc chemistry. Phe18 and tyr20 have been mutated to the non proteinogenic aminoacid 4-fluorophenyalanine.

UniProt:

P27275 (AMP_AMACA)

Seq:

86 a.a.

Struc:

31 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Resolution:

not givenÅ

NMR structure:

18 models

Authors:

M.I.Chavez,C.Andreu,P.Vidal,N.Aboitiz,F.Freire,P.Groves, J.L.Asensio,G.Asensio,M.Muraki,F.J.Canada,J.Jimenez-Barbero

Key ref:

M.I.Chávez et al. (2005). On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues.. Chemistry, 11, 7060-7074. [PubMed id: 16220560] [DOI: 10.1002/chem.200500367]

Date:

12-May-05

Release date:

06-Dec-05

Related entries:

1mmc
nmr structure of acamp2 (amaranthus caudatus antimicrobial
peptide 2) in the free state

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1002/chem.200500367

Chemistry 11:7060-7074 (2005)

PubMed id: 16220560

On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues.

M.I.Chávez, C.Andreu, P.Vidal, N.Aboitiz, F.Freire, P.Groves, J.L.Asensio, G.Asensio, M.Muraki, F.J.Cañada, J.Jiménez-Barbero.

ABSTRACT

The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar complexes have been obtained. The thermodynamic analysis of the interactions that occur upon complex formation have also been carried out. Regarding binding affinity, the obtained data have permitted the deduction that the larger the aromatic group, the higher the association constant and the binding enthalpy. In all cases, entropy opposes binding. In contrast, deactivation of the aromatic rings by attaching fluorine atoms decreases the binding affinity, with a concomitant decrease in enthalpy. The role of the chemical nature of the aromatic ring for establishing sugar contacts has been thus evaluated.