Structural analysis of peptides that interact with Newcastle disease virus Suet Lin Chia a , Wen Siang Tan a,c , Khozirah Shaari b,c , Noorsaadah Abdul Rahman d , Khatijah Yusoff a,c , Seetharama D. Satyanarayanajois e, * a Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Malaysia b Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Malaysia c Institute of Bioscience, Universiti Putra Malaysia, Malaysia d Department of Chemistry, Faculty of Science, Universiti Malaya, Malaysia e Department of Pharmacy, Faculty of Science, 18 Science Drive 4, National University of Singapore, Singapore 117543, Singapore 1. Introduction Newcastle disease is an avian disease that causes substantial loss to the poultry industry [1]. The severity of the disease is based upon the pathotype of the virus, Newcastle disease virus (NDV). Basically, there are three viral pathotypes which cause mild respiratory disease (lentogenic strains), moderate-mor- tality respiratory and nervous diseases (mesogenic strains), or severe intestinal lesions or neurological disease by velogenic strains that cause death to the infected birds. NDV strain AF2240 is a viscerotropic velogenic strain that was isolated during an outbreak in Malaysia in the 1960s [15]. NDV initiates infection by fusion of the viral envelope with the cellular membrane [16]. The protruding glycoproteins on the viral envelope, the hemagglutinin-neuraminidase (HN) and fusion (F) proteins, are involved in the attachment and fusion activities. The HN protein consists of a sialic acid binding site which facilitates the adsorption of the virion to sialic acid containing cell receptors. In addition, the neur- aminidase degrades the sialic acid molecule from the cell peptides 27 (2006) 1217–1225 article info Article history: Received 2 September 2005 Received in revised form 11 November 2005 Accepted 11 November 2005 Published on line 27 December 2005 Keywords: Alanine-substitution b-Turn Circular dichroism Filamentous M13 bacteriophage Molecular modeling Mutagenesis Newcastle disease virus abstract A peptide with the sequence CTLTTKLYC has previously been identified to inhibit the propagation of Newcastle disease virus (NDV) in embryonated chicken eggs and tissue culture. NDV has been classified into two main groups: the velogenic group, and mesogenic with lentogenic strains as the other group based on its dissociation constants. In this study the peptide, CTLTTKLYC, displayed on the pIII protein of a filamentous M13 phage was synthesized and mutated in order to identify the amino acid residues involved in the interactions with NDV. Mutations of C1 and K6 to A1 and A6 did not affect the binding significantly, but substitution of Y8 with A8 dramatically reduced the interaction. This suggests that Y8 plays an important role in the peptide–virus interaction. The three- dimensional structure of the peptide was determined using circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular modeling. The peptide exhibited two possible conformers. One that consists of consecutive b-turns around T2–L3–T4–T5 and K6–L7–Y8– C9. The other conformer exhibited a b-hairpin bend type of structure with a bend around L3– T4–T5–K6. # 2005 Elsevier Inc. All rights reserved. * Corresponding author. Tel.: +65 6 874 2653; fax: +65 6 779 1554. E-mail address: phasdsj@nus.edu.sg (S.D. Satyanarayanajois). available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/peptides 0196-9781/$ – see front matter # 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.peptides.2005.11.018