Characterizing structural features of cuticle-degrading proteases from fungi by molecular modeling

BMC Structural Biology

Table 2 Geometrical properties of the proteinase K (1IC6) and the three cuticle-degrading enzymes (PR1, VCP1 and Ver112).

Protease	RMSD^a (Å)	SASA^b (Å²)	Rg^c (Å)	NHB^d	NNC^e	NSB^f	ENE^g	DIH^h	SSEⁱ
									α helix	β sheet	Turn
1IC6	0	109.2	1.67	223	134896	14	-9288.2	0	69	66	43
PR1	0.75	113.4	1.67	189	129252	12	-8560.3	0	67	66	42
VCP1	0.75	111.0	1.67	189	128896	12	-8560.0	0	70	64	47
Ver112	0.58	106.6	1.66	195	132572	13	-8732.7	1	70	66	43

^a Backbone RMSD with respect to 1IC6.
^b Total solvent accessible surface area.
^c Radius of gyration.
^d Number of hydrogen bonds. A hydrogen bond is considered to exist when the donor-hydrogen-acceptor angle is larger than 120° and the donor-acceptor distance is smaller than 3.5 Å.
^e Number of native contacts. A native contact is considered to exist if the distance between two atoms is less than 6 Å.
^f Number of salt bridges. A salt bridge is considered to exist if the distance between two oppositely charged residues is within 6 Å.
^g Potential energy after energy minimization in the GROMOS96 force field.
^h Number of residues in the disallowed regions in the Ramachandran plot.
ⁱ Number of residues in the corresponding secondary structure elements.

ISSN: 1472-6807