Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

[1]  D. Phillips,et al.  Crystallographic studies of the dynamic properties of lysozyme , 1979, Nature.

[2]  Marianne Manchester,et al.  Complete mutagenesis of the HIV-1 protease , 1989, Nature.

[3]  C. Dobson,et al.  Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol. , 1996, Journal of molecular biology.

[4]  T. P. Flores,et al.  Comparison of conformational characteristics in structurally similar protein pairs , 1993, Protein science : a publication of the Protein Society.

[5]  L. Everitt,et al.  Selection of multiple human immunodeficiency virus type 1 variants that encode viral proteases with decreased sensitivity to an inhibitor of the viral protease. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J F Davies,et al.  Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. , 1997, Journal of medicinal chemistry.

[7]  R. Wiegel,et al.  Nile delta erosion. , 1996, Science.

[8]  M Karplus,et al.  Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations". , 1996, Journal of molecular biology.

[9]  L. Kuo,et al.  Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme. , 1998, Acta crystallographica. Section D, Biological crystallography.

[10]  C. Dobson,et al.  Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme. , 1995, Biochemistry.

[11]  Database of HIV proteinase structures. , 1997, Trends in biochemical sciences.

[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]  R E Cachau,et al.  Inhibition and catalytic mechanism of HIV-1 aspartic protease. , 1996, Journal of molecular biology.

[14]  Analysis of the structure of HIV‐1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region , 1997, Proteins.

[15]  K D Watenpaugh,et al.  Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors. , 1995, Journal of medicinal chemistry.

[16]  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.

[17]  Mark A. Spackman,et al.  Potential derived charges using a geodesic point selection scheme , 1996, J. Comput. Chem..

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

[19]  M. Summers,et al.  Structural biology of HIV. , 1999, Journal of molecular biology.

[20]  M Karplus,et al.  The contribution of vibrational entropy to molecular association. The dimerization of insulin. , 1994, Journal of molecular biology.

[21]  J. Erickson,et al.  Calculation of Relative Binding Free Energies of Peptidic Inhibitors to HIV-1 Protease and Its I84V Mutant , 1998 .

[22]  C. Schiffer,et al.  How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. , 2000, Journal of molecular biology.

[23]  M. Karplus,et al.  Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. , 1993, Journal of medicinal chemistry.

[24]  Dusanka Janezic,et al.  Harmonic analysis of large systems. I. Methodology , 1995, J. Comput. Chem..

[25]  S. Swaminathan,et al.  Molecular dynamics of HIV‐1 protease , 1992, Proteins.

[26]  E D Blair,et al.  Human Immunodeficiency Virus , 1996, The Journal of Biological Chemistry.

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

[28]  Brendan A. Larder,et al.  Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: a survey of over 6000 samples , 2000, AIDS.

[29]  S Foundling,et al.  Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases. , 1996, Biochemistry.

[30]  M. Karplus,et al.  Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. , 1987, Science.

[31]  Hans Frauenfelder,et al.  Temperature-dependent X-ray diffraction as a probe of protein structural dynamics , 1979, Nature.

[32]  D. Beveridge,et al.  Mechanism for the destabilization of the dimer interface in a mutant HIV-1 protease: A molecular dynamics study , 1993 .

[33]  R. DesJarlais,et al.  A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor. , 1995, Journal of medicinal chemistry.

[34]  J. Åqvist,et al.  Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities. , 1997, Journal of medicinal chemistry.

[35]  I. Luque,et al.  Structural stability of binding sites: Consequences for binding affinity and allosteric effects , 2000, Proteins.

[36]  J. Collins,et al.  Dynamic Flexibility of Protein−Inhibitor Complexes: A Study of the HIV-1 Protease/KNI-272 Complex , 1998 .

[37]  Dagmar Ringe,et al.  [19]Study of protein dynamics by X-ray diffraction , 1986 .

[38]  R. DesJarlais,et al.  Inhibition of human immunodeficiency virus-1 protease by a C2-symmetric phosphinate. Synthesis and crystallographic analysis. , 1993, Biochemistry.

[39]  Yun-Xing Wang,et al.  Flexibility and Function in HIV Protease: Dynamics of the HIV-1 Protease Bound to the Asymmetric Inhibitor Kynostatin 272 (KNI-272) , 1998 .

[40]  Alexander Wlodawer,et al.  Database of three-dimensional structures of HIV proteinases , 1997, Nature Structural Biology.

[41]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[42]  T. Yamazaki,et al.  Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272. , 1996, Biochemistry.

[43]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[44]  L Hong,et al.  Crystal structure of an in vivo HIV‐1 protease mutant in complex with saquinavir: Insights into the mechanisms of drug resistance , 2000, Protein science : a publication of the Protein Society.

[45]  R. Myers,et al.  In vitro selection and characterization of human immunodeficiency virus type 1 (HIV-1) isolates with reduced sensitivity to hydroxyethylamino sulfonamide inhibitors of HIV-1 aspartyl protease , 1995, Journal of virology.

[46]  J M Thornton,et al.  LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. , 1995, Protein engineering.

[47]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[48]  T. Bhat,et al.  Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine. , 1995, Structure.

[49]  Structure of HIV-1 protease with KNI-272: a transition state mimetic inhibitor containing allophenylnorstatine. , 1995, Advances in experimental medicine and biology.

[50]  A. Mark,et al.  Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. , 1995, Journal of molecular biology.

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

[52]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

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

[54]  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.

[55]  M. Murcko,et al.  Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .

[56]  R. DesJarlais,et al.  Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere. , 1994, Journal of medicinal chemistry.

[57]  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.

[58]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[59]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[60]  B. G. Rao,et al.  In vitro selection and characterization of VX-478 resistant HIV-1 variants. , 1998, Advances in Experimental Medicine and Biology.

[61]  H Frauenfelder,et al.  Dynamics of ligand binding to myoglobin. , 1975, Biochemistry.

[62]  J. Louis,et al.  Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. , 1998, Biochemistry.

[63]  M Karplus,et al.  Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. , 1997, Journal of molecular biology.

[64]  M. Karplus,et al.  Internal mobility of ferrocytochrome c , 1980, Nature.

[65]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[66]  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.

[67]  M G Grütter,et al.  Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor. , 1995, Structure.

[68]  P Murray-Rust,et al.  X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease. , 1994, Biochemistry.