1.9 Å x‐ray study shows closed flap conformation in crystals of tethered HIV‐1 PR

Three‐dimensional structure of an asymmetrically mutated (C95M) tethered human immunodeficiency virus type 1 protease enzyme (HIV‐1 PR) has been determined in an unliganded form using X‐ray diffraction data to 1.9 Å resolution. The structure, refined using X‐PLOR to an R factor of 19.5%, is unexpectedly similar to the ligand‐bound native enzyme, rather than to the ligand‐free native enzyme. In particular, the two flaps in the tethered dimer are in a closed configuration. The environments around M95 and C1095 are identical, showing no structural effect of this asymmetric mutation at position 95. Oxidation of Cys1095 has been observed for the first time. There is one well‐defined water molecule that hydrogen bonds to both carboxyl groups of the essential aspartic acids in the active site. Proteins 2001;43:57–64. © 2001 Wiley‐Liss, Inc.

[1]  R M Stroud,et al.  Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. , 1998, Biochemistry.

[2]  R. Gilcher Human retroviruses and AIDS. , 1988, The Journal of the Oklahoma State Medical Association.

[3]  S. Foundling,et al.  Stability and activity of human immunodeficiency virus protease: comparison of the natural dimer with a homologous, single-chain tethered dimer. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[4]  C. Debouck,et al.  The 80's loop (residues 78 to 85) is important for the differential activity of retroviral proteases. , 1997, Journal of molecular biology.

[5]  Erik De Clercq,et al.  Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. , 1995 .

[6]  C. Debouck,et al.  Expression systems for retroviral proteases. , 1994, Methods in enzymology.

[7]  Narmada Thanki,et al.  Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling , 1992, Protein science : a publication of the Protein Society.

[8]  A Wlodawer,et al.  Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. , 1998, Annual review of biophysics and biomolecular structure.

[9]  R. Levine,et al.  Copper inhibits the protease from human immunodeficiency virus 1 by both cysteine-dependent and cysteine-independent mechanisms. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[10]  John P. Overington,et al.  X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes , 1989, Nature.

[11]  M. Jaskólski,et al.  Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. , 1989, Science.

[12]  Dale J. Kempf,et al.  Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based Diol Inhibitors of HIV-1 Protease , 1994 .

[13]  J. Mieyal,et al.  Thioltransferase (Glutaredoxin) Is Detected Within HIV-1 and Can Regulate the Activity of Glutathionylated HIV-1 Protease in Vitro * , 1997, The Journal of Biological Chemistry.

[14]  A. Yasui,et al.  Role of cysteine residues in the activity of rat glutathione transferase P (7-7): elucidation by oligonucleotide site-directed mutagenesis. , 1991, Biochemical and biophysical research communications.

[15]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[16]  M. Doyle,et al.  Human immunodeficiency virus protease ligand specificity conferred by residues outside of the active site cavity. , 1996, Biochemistry.

[17]  C. Debouck,et al.  The HIV-1 protease as a therapeutic target for AIDS. , 1992, AIDS research and human retroviruses.

[18]  T. Darden,et al.  Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. , 1993, Biochemistry.

[19]  S. Oroszlan,et al.  Retroviral proteinases. , 1990, Current topics in microbiology and immunology.

[20]  E. De Clercq,et al.  Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. , 1995, Journal of medicinal chemistry.

[21]  D. Davies,et al.  Structure and Function of the Aspartic Proteinases , 1990, Advances in Experimental Medicine and Biology.

[22]  A. Skalka Retroviral proteases: First glimpses at the anatomy of a processing machine , 1989, Cell.

[23]  K Y Hui,et al.  Toward a universal inhibitor of retroviral proteases: Comparative analysis of the interactions of LP‐130 complexed with proteases from HIV‐1, FIV, and EIAV , 1998, Protein science : a publication of the Protein Society.

[24]  H. B. Schock,et al.  Three-dimensional Structure of a Mutant HIV-1 Protease Displaying Cross-resistance to All Protease Inhibitors in Clinical Trials (*) , 1995, The Journal of Biological Chemistry.

[25]  A. Wlodawer,et al.  Structure-based inhibitors of HIV-1 protease. , 1993, Annual review of biochemistry.

[26]  R. Dixon,et al.  Characterization of an active single polypeptide form of the human immunodeficiency virus type 1 protease. , 1990, The Journal of biological chemistry.

[27]  C. Vlahos,et al.  Substitutions at the P2' site of gag p17-p24 affect cleavage efficiency by HIV-1 protease. , 1990, Biochemical and biophysical research communications.

[28]  Joanne I. Yeh,et al.  Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation. , 1999, Biochemistry.

[29]  Jack R. Collins,et al.  Flap opening in HIV-1 protease simulated by ‘activated’ molecular dynamics , 1995, Nature Structural Biology.

[30]  B. Dunn,et al.  Interactions of substrates and inhibitors with a family of tethered HIV-1 and HIV-2 homo- and heterodimeric proteinases. , 1994, The Journal of biological chemistry.

[31]  A. Wilderspin,et al.  Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase. , 1994, Journal of molecular biology.

[32]  Tom Blundell,et al.  A second front against AIDS , 1989, Nature.

[33]  S. Rick,et al.  Reaction path and free energy calculations of the transition between alternate conformations of HIV‐1 protease , 1998, Proteins.

[34]  P. Wingfield,et al.  Regulation of HIV-1 protease activity through cysteine modification. , 1996, Biochemistry.

[35]  L J Davis,et al.  Active human immunodeficiency virus protease is required for viral infectivity. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Retroviral proteinases. A second front against AIDS. , 1989, Nature.

[37]  D. Norbeck,et al.  Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease. , 1990, Science.

[38]  C. Hutchison,et al.  Identification of temperature-sensitive mutants of the human immunodeficiency virus type 1 protease through saturation mutagenesis. Amino acid side chain requirements for temperature sensitivity. , 1994, The Journal of biological chemistry.

[39]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[40]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[41]  H. Duckworth,et al.  The role of cysteine 206 in allosteric inhibition of Escherichia coli citrate synthase. Studies by chemical modification, site-directed mutagenesis, and 19F NMR. , 1991, The Journal of biological chemistry.

[42]  I. Luque,et al.  Structure-based thermodynamic analysis of HIV-1 protease inhibitors. , 1997, Biochemistry.

[43]  J. C. Martin,et al.  Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[44]  L. Kuo,et al.  Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. , 1996, The Journal of biological chemistry.

[45]  E. Freire,et al.  The structural stability of the HIV-1 protease. , 1998, Journal of molecular biology.

[46]  M. Navia,et al.  Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1 , 1989, Nature.