Structures of porcine β-trypsin–detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol

Abstract

Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent and its subsequent action on proteins. Here, three crystal structures of serine protease trypsin are reported in the presence of varying concentrations of polydocanol in order to elucidate its mode of binding and interactions with proteins. Polydocanol binds to the protein with its hydrophilic head rather than the hydrophobic tail as is the case with other detergents such as SDS and MEGA-8. This hydrophilic binding mode results in the binding sites of polydocanol being distributed on the surface of the enzyme. There are at least 11 binding sites for polydocanol in trypsin. Polydocanol forms part of the large-scale water networks which connect distant regions of the enzyme, thereby stabilizing it. The hydrophilic binding of polydocanol also results in cross-linked pairs of trypsin molecules.

FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin and Trypsin under Neutral Salts

“…According to the previous spectral studies of globular and fibrillar proteins [33], the Amide I area and peaks obtained from its second derivative deconvolution correspond to the following secondary structures (Table 2). Albumin peaks at 1650 and 1657 cm -1 refer to 60.3% of the total area of the second derivative ( Figure 1b), and peak 1655 cm -1 of trypsin refer to 11.2%, which agrees with the data obtained from the DSSP, STRIDE, and the secondary structure assigned by authors of the X-ray structures PDB codes 1AO6 (HSA) and 1FMG porcine beta trypsin) [34][35][36][37][38][39] (Table 3). HSA proteins do not have a Albumin peaks at 1650 and 1657 cm −1 refer to 60.3% of the total area of the second derivative ( Figure 1b), and peak 1655 cm −1 of trypsin refer to 11.2%, which agrees with the data obtained from the DSSP, STRIDE, and the secondary structure assigned by authors of the X-ray structures PDB codes 1AO6 (HSA) and 1FMG porcine beta trypsin) [34][35][36][37][38][39] (Table 3).…”

“…Albumin peaks at 1650 and 1657 cm -1 refer to 60.3% of the total area of the second derivative ( Figure 1b), and peak 1655 cm -1 of trypsin refer to 11.2%, which agrees with the data obtained from the DSSP, STRIDE, and the secondary structure assigned by authors of the X-ray structures PDB codes 1AO6 (HSA) and 1FMG porcine beta trypsin) [34][35][36][37][38][39] (Table 3). HSA proteins do not have a Albumin peaks at 1650 and 1657 cm −1 refer to 60.3% of the total area of the second derivative ( Figure 1b), and peak 1655 cm −1 of trypsin refer to 11.2%, which agrees with the data obtained from the DSSP, STRIDE, and the secondary structure assigned by authors of the X-ray structures PDB codes 1AO6 (HSA) and 1FMG porcine beta trypsin) [34][35][36][37][38][39] (Table 3). HSA proteins do not have a maximum at the second derivative deconvolution curves that correspond to a random coil conformation defined by the range of 1640-1649 cm −1 [33], which is also consistent with the previous FTIR studies [33,[40][41][42].…”

Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents

“…The GROMOS 96 force fields were implemented in the GROMACS. The starting conformation for the simulations of the enzyme was obtained from the Protein Data Bank (PDB ID, 1FNI ). The protein was solvated with either simple point charge (SPC) water, a mixture of sorbitol, or a mixture of glycerol and SPC water and placed in a cube large enough to contain the protein and 1.1 nm of solvent on all sides.…”

Structural and mechanistic insights into a novel non-competitive Kunitz trypsin inhibitor from Adenanthera pavonina L. seeds with double activity toward serine- and cysteine-proteinases

“…HEX v.5.1 [34] program was used to examine possible modes of interaction of ApTKI with papain (9pap), a sulphydryl protease from the latex of the papaya fruit, and trypsin (1fn6) a hydrolase from the porcine pancreas [35,36]. Briefly, this procedure performed global rotational and translational space scan by using Fourier transformations, which rank the output according to surface complementarity and electrostatic characteristics.…”

“…The complex between ApTKI and trypsin structure PDB: 1fn6 [36] was used for the study of the enzyme-inhibitor interaction (Fig. 5A).…”