title: Rational design of hyper-glycosylated interferon beta analogs: a computational strategy for glycoengineering.
abstract: Glycoengineering has been successfully used to improve the physicochemical and pharmaceutical properties of therapeutics. One aspect of glycoengineering is to introduce new N-linked glycosylation consensus sequences (Asn, X, Thr/Ser) into desirable positions in the peptide backbone by mutational insertion to generate proteins with increased sialic acid content. In the current work, human interferon beta (huIFN-β) was used as a model to identify the potential positions for the addition of new N-glycosylation sites. A computational strategy was employed to predict the structural distortions and functional alterations that might be caused by the change in amino acid sequence. Accordingly, three-dimensional (3D) structures of the designed huIFN-β analogs were generated by comparative modeling. Molecular dynamics (MD) simulation was carried out to assess the molecular stability and flexibility profile of the structures. Subsequently, for the purpose of glycoengineering huIFN-β, analogs with 3D structures more similar to the wild-type huIFN-β and exposed Asn residue in the new N-glycosylation site were identified. These modeling procedures indicated that the addition of the new N-glycosylation site in the loop regions had lower constraining effects on the tertiary structure of the protein. This computational strategy can be applied to avoid alterations in the 3D structure of proteins caused by changes in the amino acid sequences, when designing novel hyper-glycosylated therapeutics. This in turn reduces labor-intensive experimental analyses of each analog.
authors.affiliation: Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran. Electronic address: m.samoudi@nigeb.ac.ir.
authors.forename: Mojtaba
authors.initials: M
authors.lastname: Samoudi
authors.affiliation: Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran. Electronic address: taban_f@nigeb.ac.ir.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Tabandeh
authors.affiliation: Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran. Electronic address: minuchehr@nigeb.ac.ir.
authors.forename: Zarrin
authors.initials: Z
authors.lastname: Minuchehr
authors.affiliation: Department of Research and Development, Pasteur Institute of Iran, P.O. Box 1316942551, Tehran, Iran. Electronic address: cohan_r@yahoo.com.
authors.forename: Reza
authors.initials: R
authors.lastname: Ahangari Cohan
authors.affiliation: Department of Research and Development, Pasteur Institute of Iran, P.O. Box 1316942551, Tehran, Iran. Electronic address: d_nouriinanlou@yahoo.com.
authors.forename: Davoud
authors.initials: D
authors.lastname: Nouri Inanlou
authors.affiliation: Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran. Electronic address: saba@nigeb.ac.ir.
authors.forename: Mahvash
authors.initials: M
authors.lastname: Khodabandeh
authors.affiliation: Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran. Electronic address: mohammad_sa@nigeb.ac.ir.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Sabery Anvar
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006031:Glycosylation; D006801:Humans; D016899:Interferon-beta / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D015202:Protein Engineering; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012794:Sialic Acids / Q000737:chemistry*; D040681:Structural Homology, Protein; D013816:Thermodynamics
chemical_list: D012794:Sialic Acids; D016899:Interferon-beta
keywords: Comparative modeling; Glycoengineering; In silico design; Interferon beta; Molecular dynamics