1% (v/v) TFA]. The elution was monitored
at 214 nm, and fractions were manually collected into 5 mL glass vials. MS analyses were conducted on an ion trap/time-of-flight mass spectrometer (IT-TOF/MS) (Shimadzu, Kyoto, Japan) equipped with an electrospray ionization source. The setting conditions for optimized operations were: positive mode, electrospray voltage 4.5 kV, CDL temperature 200 °C, block heater temperature 200 °C, nebulizer gas (N2) flow of 1.5 L/min, trap cooling gas (Ar) flow of 95 mL/min, ion trap pressure 1.7 × 10−2 Pa, TOF region pressure 1.5 × 10−4 Pa, ion accumulation time 50 ms. The auto-tuning was performed with a Na-TFA solution and showed the following parameters: for the positive mode, error 3.1 ppm and resolution 11,000; and for the negative mode, error 2.3 ppm and resolution
13,000. The search for templates for the AMP-I target 17-AAG cell line sequence was performed with Blastp (Altschul et al., 1997) and the alignment (Table 1) was formatted and input into the program. The structure of the homologous peptide (Mastoparan-X) was selected from the Protein Data Bank (PDB) (Berman et al., 2000), which was solved experimentally by RMN (PDB ID: 1A13) (Kusunoki et al., 1998). The AMP-I model was built with restrained-based modeling implemented in MODELLER9v8 (Sali and Blundell, 1993), with the standard protocol of the comparative protein structure modeling methodology, by satisfaction of spatial restraints (Sali and Overington, 1994; Marti-Renom et al., 2000). A total of 1000 models were created and the best models were selected according to MODELLER objective Cisplatin datasheet function (Shen and Sali, 2006) and stereochemical analysis with PROCHECK (Laskowsky et al., 1993). The primary sequence similarity between Fludarabine research buy the peptide with the template was 65% (identity 58%). The final models were selected with 100% residues in favored regions of the Ramachandran plot (Fig. 1), with the best values of the overall G-factor and the
lower values of energy minimization ( Table 2). For visualization of the model of AMP-I, the PyMOL program was used ( DeLano, 2002). The overall stereochemical quality of the final models for Agelaia MP-I was assessed by the PROCHECK program (Koradi et al., 1996). The root mean square deviation (rmsd) between Cα–Cα atom’s distance was superposed using the program LSQKAB from CCP4 (Konno et al., 2007). The cutoff for hydrogen bonds and salt bridges was 3.3 Å. The contact area for the complexes was calculated using AREAIMOL and RESAREA (Konno et al., 2007). The root mean square deviation (rmsd) differences from ideal geometries for bond lengths and bond angles were calculated with X-PLOR (Krishnakumari and Nagaraj, 1997). The G-factor value is essentially just log-odds score based on the observed distributions of the stereochemical parameters.