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Russian Journal of Bioorganic Chemistry, Vol. 25, No. 6, 1999, ð . 366
Mechanism of Action of Aspartic Proteases: III. 1 Conformational Characteristics of JG-365, an Inhibitor of the HIV-1 Protease
M. E. Popov 2 , I. V. Kashparov, L. D. Rumsh, and E. M. Popov †
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow , 117871 Russia
Abstract: A set of conformations was shown to be characteristic of the free-state spatial structure of substrate-like inhibitor JG-365 for aspartic protease from HIV-1. Among them, the lowest-energy conformations have a folded form of the peptide backbone. The inhibitor has a noncleavable hydroxyethylamine group with an addi-tional chiral center in its structure. Our calculations showed that only the S-isomer of the inhibitor displays conformational characteristics that practically coincide with those of the native substrate for HIV-1 protease. One of the calculated conformations with a completely extended main chain and a relative energy of 9.5 kcal/mol very closely mimics the experimentally observed structure of the inhibitor in the enzyme–inhibitor complex. The realization of this structure is unlikely for a free inhibitor, because it has only a small number of interresidual noncovalent interactions in the extended conformation; these are presumably compensated for by intermo-lecular interactions at the active site of the enzyme.
Key words: aspartic proteases, conformational analysis, inhibitor
Russian Journal of Bioorganic Chemistry, Vol. 25, No. 6, 1999, ð . 371
Mechanism of Action of Aspartic Proteases: IV. 1 Conformational Characteristics of a Substrate and an Inhibitor of Rhizopuspepsin
I. V. Kashparov, 2 M. E. Popov , and E. M. Popov †
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow , 117871 Russia
Abstract: On the basis of theoretical conformational analysis of separate peptide fragments, the conformational characteristics of two substrates and a substrate-like inhibitor of aspartic protease rhizopuspepsin were studied. It was shown that the spatial structure of these molecules is described by several families of conforma-tions, the transition between which does not require the overcoming of high energy barriers. It was assumed that the stabilization of -structural conformations experimentally observed in inhibitor complexes is due to the greater predisposition of extended structures to the formation of effective intermolecular contacts with amino acid residues of the active site of the enzyme.
Key words: aspartic proteases, conformational analysis, rhizopuspepsin
Russian Journal of Bioorganic Chemistry, Vol. 25, No. 8, 1999, ð . 532
Mechanism of Action of Aspartic Proteases: 1 V. Conformational Characteristics of Fragments of Substrate-binding Sites in Rhizopuspepsin and HIV-1 Protease
I. V. Kashparov 2 , M. E. Popov, L. D. Rumsh, and E. M. Popov †
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 Russia
Abstract: The conformational states of side chains of catalytic Asp residues in active sites of HIV-1 protease and rhizopuspepsin in the potential field of free enzymes were studied by using theoretical conformational analysis. Structural factors that stabilize the conformation of these residues in free enzymes were revealed. Methods of molecular mechanics were used to estimate the stabilization energy of the Met46–Phe53 labile fragments of HIV-1 protease in the potential field of their nearest surrounding amino acid residues for the conformations characteristic of the free protein and similar to that of the protein in enzyme–inhibitor complexes. In solution, the conformational state of the fragments of the free enzyme was concluded to be similar to that observed in the enzyme complex with the ligand and different from that determined by X-ray diffraction analysis. This difference was ascribed to the effect of crystal packing.
Key words: aspartic proteases, active site, conformational analysis, HIV-1