Fibers of the differently selected phages/peptides interact due to different compositions of amino acid sequences on the exposed peptides, which was confirmed by transmission electron microscopy. Numerical and experimental studies showed that the P3 consistently peptide is the best CRP binder. demonstrates a new trend in science where calculations can replace or support laborious experimental techniques. Finally, the best CRP binderthe P3 peptidewas used for CRP recognition on silicate-modified indium tin oxide-coated glass electrodes. The obtained electrodes exhibit a wide range of operation (1.0C100 g mLC1) with a detection limit (LOD = 3/= 120 C) for 90 min. The silanization process was to create succinic anhydride groups that react with amines, thereby binding peptides via peptide bonds {1 h incubation of peptide [5.0 g mLC1 in phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, and GSK-650394 10 mM phosphate buffer, pH7.4)] or antibodies (2.5 g mLC1 in PBS). This approach has been applied to immobilize various biological components already.49 The last step of the modification was blocking the remaining sites with 1% bovine serum albumin (BSA) in PBS by immersing the electrodes for 20 min at room temperature. The electrode surface was limited using Scotch tape (electrode area 0.2 cm2). The obtained electrode was incubated with 20 L of studied protein [CRP, fibrinogen (Fib), troponin T (TnT), or interleukin 6 (IL-6)] dissolved in PBS for 30 min at room temperature to study molecular interactions between the immobilized peptide and studied proteins. Electrodes were rinsed with PBS (a few seconds) after each step. The amino acid sequences of the peptides are as follows; P2 (GGSDPEGMQGNY), P3 (VHWDFRQWWQPS), and P9 (SWFSDWDLELHA). The electrochemical studies were performed in GSK-650394 a three-electrode setup comprising a modified ITO working electrode, platinum wire counter electrode, and Ag|AgCl|KClsat as a reference electrode. A AutolabIII (Metrohm Autolab) potentiostat powered by GPES 4.9 software was used for recording electrochemical data. Detection of CRP is based on the blocking of the electrode as the CRP binds to the immobilized recognition element [peptide or antibody (mAb)]. Measurements were performed with 1 mM ferrocenodimethanol (Fc(CH2OH)2) in PBS as a redox molecule using differential GSK-650394 pulse voltammetry (DPV) (DPV parameters: scan rate 20 mV/s, step 4 mV, pulse amplitude 50 mV, pulse width 50 ms, and pulse GSK-650394 interval 100 ms). The total results are average values from three repetitions of the measurement at three separate electrodes, with RSD represented by error bars. Identification and Characterization of CRP-Binding Phages/Peptides Details on identification of CRP-binding phages/peptides and characterization of interactions between CRP and new CRP-binding peptide materials using experimental methods are provided in the Supporting Information. Molecular Docking The molecular structure of the CRP pentamer was taken from the Protein Data Bank id: 3PVO.50 The crystal structure of CRP was determined with a resolution of 3.0 ?, and all right parts of the structure were visible in the crystal. The calcium ions, coordinated mostly by aspartic and glutamic acids in each subunit of the CRP, were removed. The peptideCprotein docking was performed in the ICM-Pro v.3.8 program (ICM-Pro; Version 3.8; Molsoft, L.L.C.: San Diego, Rabbit Polyclonal to EDG4 CA, USA, 2020). As there is no experimental knowledge about peptide interactions with CRP complex, binding pocket searching was used.51 The pockets proposed by the scheduled program were ranked by volume as the interacting peptides are quite long. Four of the best-ranked pockets were used for docking. The ICM docking procedure is based on the stochastic global optimization algorithm.52 The binding energy function was calculated from five grid potentials describing interactions of the flexible ligand with the receptor and the internal conformational energy of the ligand. The involved energy terms are van der Waals interactions for hydrogen atoms, van der Waals interactions for heavy atoms, electrostatic interactions, hydrophobic contacts, and the lone-pair-based potential, describing directional preferences in hydrogen bonds. The energy terms are based on the GSK-650394 all-atom vacuum force field ECEPP/3 with appended terms to account for the solvation free energy and entropic contribution. The biased probability Monte Carlo (BPMC) procedure was used for the conformational space sampling of fully flexible ligands and side chains of the protein. The ICM program relies on global optimization of the entire flexible ligand in the receptor field and combines large-scale random moves of several types with gradient local minimization and a search history mechanism. Discussion and Results Similar to our previous study,36 the phage-display technique was used to identify CRP binders. The affinity of the selected clones toward CRP was evaluated using two methods: plaque test (Figure S1A) and ELISA (Figure S1B). The P3 clone resulted in the highest binding efficiency to CRP (2.17 10C4) based on the plaque test (O/I),.