Affiliation:
1. ATILIM ÜNİVERSİTESİ, MÜHENDİSLİK FAKÜLTESİ
2. ALTINBAS UNIVERSITY, SCHOOL OF MEDICINE
3. ATILIM ÜNİVERSİTESİ, TIP FAKÜLTESİ
Abstract
Aim: Fourier Transform Infrared (FTIR) spectroscopy can provide relative proportion of secondary structure elements in a protein. However, extracting this information from the Amide I band area of an FTIR spectrum is difficult. In addition to experimental methods, several protein secondary structure prediction algorithms serving on the Web can be used as supplementary tools requiring only protein amino acid sequences as inputs. WeIn addition, web-server based docking tools can provide structure information when proteins are mixed and potentially interacting. Accordingly, we aimed to utilize web-server based structure predictors in fibroblast growth factor (FGF) protein structure determination through the FTIR data.
Materials and methods: Seven such predictors arewere selected and tested on basic FGF (bFGF) protein, to predict FGF secondary structure. Results arewere compared to available structure-files deposited in the Protein Data Bank (PDB). Then, FTIR spectra of bFGF and the acidic form of the protein with 50 folds more bovine serum albumin as carrier protein (1FGFA/50BSA) arewere collected. Optimized Amide I curve-fit parameters of bFGF with low (
Publisher
Turkish Computational and Theoretical Chemistry
Reference42 articles.
1. Y. Adıgüzel, P.I. Haris, F. Severcan, Screening of proteins in cells and tissues by vibrational spectroscopy, in: Severcan F, Haris PI (Eds.), Vibrational Spectroscopy in Diagnosis and Screening, IOS Press, Amsterdam, 2012, 53–108.
2. M. Baldassarre, C. Li, N. Eremina, E. Goormaghtigh, A. Barth, Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra, Molecules 20 (2015) 12599–12622.
3. N.L. Benbow, S. Karpiniec, M. Krasowska, D.A. Beattie, Incorporation of FGF-2 into Pharmaceutical Grade Fucoidan/Chitosan Polyelectrolyte Multilayers, Mar Drugs 18 (2020) 531.
4. D.M. Byler, H. Susi, Examination of the secondary structure of proteins by deconvolved FTIR spectra, Biopolymers 25 (1986) 469–487.
5. F. Coulier, P. Pontarotti, R. Roubin, H. Hartung, M. Goldfarb, D. Birnbaum, Of worms and men: an evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families, J Mol Evol 44 (1997) 43–56.