title: Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling.
abstract: Defensins are part of the innate immune system in plants with activity against a broad range of pathogens, including bacteria, fungi and viruses. Several defensins from conifers, including Scots pine defensin 1 (Pinus sylvestris defensin 1, (PsDef1)) have shown a strong antifungal activity, however structural and physico-chemical properties of the family, needed for establishing the structure-dynamics-function relationships, remain poorly characterized. We use several spectroscopic and computational methods to characterize the structure, dynamics, and oligomeric state of PsDef1. The three-dimensional structure was modeled by comparative modeling using several programs (Geno3D, SWISS-MODEL, I-TASSER, Phyre(2), and FUGUE) and verified by circular dichroism (CD) and infrared (FTIR) spectroscopy. Furthermore, FTIR data indicates that the structure of PsDef1 is highly resistant to high temperatures. NMR diffusion experiments show that defensin exists in solution in the equilibrium between monomers and dimers. Four types of dimers were constructed using the HADDOCK program and compared to the known dimer structures of other plant defensins. Gaussian network model was used to characterize the internal dynamics of PsDef1 in monomer and dimer states. PsDef1 is a typical representative of P. sylvestris defensins and hence the results of this study are applicable to other members of the family.
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia. Electronic address: ermakova@kibb.knc.ru.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Ermakova
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Dzhigangir A
authors.initials: DA
authors.lastname: Faizullin
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Bulat Z
authors.initials: BZ
authors.lastname: Idiyatullin
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Bulat I
authors.initials: BI
authors.lastname: Khairutdinov
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Liya N
authors.initials: LN
authors.lastname: Mukhamedova
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Nadezhda B
authors.initials: NB
authors.lastname: Tarasova
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Yana Y
authors.initials: YY
authors.lastname: Toporkova
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Osipova
authors.affiliation: Ukrainian National Forestry University, Lviv, Ukraine.
authors.forename: Valentina
authors.initials: V
authors.lastname: Kovaleva
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Yuri V
authors.initials: YV
authors.lastname: Gogolev
authors.affiliation: Kazan Institute of Biochemistry and Biophysics RAS, Kazan, Russia.
authors.forename: Yuriy F
authors.initials: YF
authors.lastname: Zuev
authors.affiliation: Department of Physics and Optical Science and Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, NC, USA. Electronic address: Irina.Nesmelova@uncc.edu.
authors.forename: Irina V
authors.initials: IV
authors.lastname: Nesmelova
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D023082:Defensins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D041605:Pinus sylvestris / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry*; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D055503:Protein Multimerization; D055550:Protein Stability; D017433:Protein Structure, Secondary; D066244:Proton Magnetic Resonance Spectroscopy; D011994:Recombinant Proteins; D016415:Sequence Alignment; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D023082:Defensins; D010940:Plant Proteins; D011994:Recombinant Proteins
keywords: Circular dichroism; Computational modeling; Defensin; Dimer; FTIR; Structure