[Mechanism of action of aspartyl proteinases. VI. Nonvalent enzyme-inhibitory and enzyme-substrate complexes of the aspartyl proteinase rhizopus pepsin].
The structure of a complex of rhizopuspepsin, a fungal aspartyl protease, with Pro1-Phe2-His3-Phe4-psi[CH2-NH]-Phe5-Val6, its substrate-like inhibitor, was calculated by theoretical conformational analysis. The search for energetically favorable conformational variants of the ligand structure was based on the fragmental approach using the dynamic library of peptide fragments, which were successively extended in the potential field of the protein. The root-mean-square deviation of atom positions in the calculated and experimental inhibitor conformations was 0.56 A. A similar approach was used to model a noncovalent complex of rhizopuspepsin with Pro1-Phe2-His3-Lys4-Phe5-Val6, its specific substrate. As a result, two isoenergetic structures of the complex with different arrangements of the cleavable peptide group and a nucleophilic water molecule were calculated. The possibility of the achieving each of these conformations during the catalytic act is considered. It is shown that there are no structural prerequisites for the distortion of the cleavable bond in the active site of the enzyme. On the basis of the resulting structural data, the assumption was made that Asp35 may be protonated at a late stage of formation of the tetrahedral intermediate rather than at the basic state of the complex.
Kashparov
I V
IV
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. ilko@enzyme.siobc.ras.ru
Popov
M E
ME
Rumsh
L D
LD
Popov
E M
EM
D000595:Amino Acid Sequence; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry / Q000378:metabolism*; D006868:Hydrolysis; D008958:Models, Molecular; D011480:Protease Inhibitors / Q000378:metabolism*; D011487:Protein Conformation; D013379:Substrate Specificity
D011480:Protease Inhibitors; D016282:Aspartic Acid Endopeptidases; C035794:rhizopuspepsin