Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling

• Published in: International journal of biological macromolecules 2016-03, Vol.84, p.142-152
• Main Authors: Ermakova, Elena A., Faizullin, Dzhigangir A., Idiyatullin, Bulat Z., Khairutdinov, Bulat I., Mukhamedova, Liya N., Tarasova, Nadezhda B., Toporkova, Yana Y., Osipova, Elena V., Kovaleva, Valentina, Gogolev, Yuri V., Zuev, Yuriy F., Nesmelova, Irina V.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Circular Dichroism; Computational modeling; Defensin; Defensins - chemistry; Dimer; FTIR; Models, Molecular; Molecular Sequence Data; Pinus sylvestris - chemistry; Plant Proteins - chemistry; Position-Specific Scoring Matrices; Protein Conformation; Protein Multimerization; Protein Stability; Protein Structure, Secondary; Proton Magnetic Resonance Spectroscopy; Recombinant Proteins; Sequence Alignment; Spectroscopy, Fourier Transform Infrared; Structure
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2015.12.011

•Three-dimensional structure of PsDef1 was modeled using 5 computational programs.•Structural model was verified experimentally by CD and FTIR spectroscopy.•PsDef1 exists in the temperature-dependent equilibrium between monomers and dimers.•Structural models for PsDef1 dimer were constructed.•The structure of PsDef1 is highly temperature resistant. 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, Phyre2, 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.