PDBsum entry: 1zuv

Antimicrobial protein

PDB id: 1zuv

Contents

Protein chain

30 a.a.

PDB id:

1zuv

Name:

Antimicrobial protein

Title:

24 nmr structures of acamp2-like peptide with phenylalanine 18 mutated to tryptophan

Structure:

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

Source:

Synthetic: yes. Other_details: the residue phe18 was changed to tryptophan. The sequence by standard solid phase synthesis using fmoc chemistry according to standard protocols.

NMR struc:

24 models

Authors:

M.I.Chavez,C.Andreu,P.Vidal,F.Freire,N.Aboitiz,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:

01-Jun-05 Release date: 06-Dec-05

Protein chain

P27275  (AMP_AMACA) -  Antimicrobial peptide 2

Seq: 86 a.a.

Struc: 30 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: cell wall macromolecule catabolic process (2 terms)
• Biochemical function: chitin binding (2 terms)

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.