Conformational flexibility of the catalytic Asp dyad in HIV‐1 protease: An ab initio study on the free enzyme

The enzyme protease from the human immunodeficiency virus type 1 (HIV‐1 PR) is one of the main targets for therapeutic intervention in AIDS. Computer modeling is useful for probing the binding of novel ligands, yet empirical force field‐based methods have encountered problems in adequately describing interactions of the catalytic aspartyl pair. In this work we use ab initio dynamic methods to study the molecular interactions and the conformational flexibility of the Asp dyad in the free enzyme. Calculations are performed on model complexes that include, besides the Asp dyad, the conserved Thr26 and Gly27 residues and water molecules present in the active site channel. Our calculations provide proton location and binding mode of the active‐site water molecule, which turn out to be different from those of the eukariotic isoenzyme. Furthermore, the calculations reproduce well the structural features of the aspartyl dyad in the protein. Finally, they allow the identification of both dipole/charge interactions and a low‐barrier hydrogen bond as important stabilizing factors for the peculiar conformation of the active site. These findings are consistent with site‐directed mutagenesis experiments on the 27, 27` positions ( Bagossi et al. , Protein Eng 1996;9:997–1003). The electric field of the protein frame (included in some of the calculations) does not affect significantly the chemical bonding at the cleavage site. Proteins 2000;39:26–36. © 2000 Wiley‐Liss, Inc.

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

[2]  G. Folkers,et al.  Density functional studies on herpes simplex virus type 1 thymidine kinase–substrate interactions: The role of Tyr‐172 and Met‐128 in thymine fixation , 1998, Proteins.

[3]  Michele Parrinello,et al.  From silicon to RNA: The coming of age of ab initio molecular dynamics , 1997 .

[4]  Kari Laasonen,et al.  Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water , 1995 .

[5]  G. Folkers,et al.  Dimethyl Phosphate: Stereoelectronic versus Environmental Effects , 1999 .

[6]  P. Jadhav,et al.  Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV. , 1997, Journal of medicinal chemistry.

[7]  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.

[8]  K H Murthy,et al.  The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. , 1992, The Journal of biological chemistry.

[9]  Donald E. Williams,et al.  Representation of the molecular electrostatic potential by a net atomic charge model , 1981 .

[10]  A Wlodawer,et al.  Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.

[11]  P. Frey,et al.  A low-barrier hydrogen bond in the catalytic triad of serine proteases. , 1994, Science.

[12]  TWO-WEEK Loan COpy,et al.  University of California , 1886, The American journal of dental science.

[13]  Peter Pulay,et al.  Geometry optimization by direct inversion in the iterative subspace , 1984 .

[14]  M. Navia,et al.  Crystallization of the aspartylprotease from the human immunodeficiency virus, HIV-1. , 1989, The Journal of biological chemistry.

[15]  F. López-Ortiz,et al.  Theoretical Proposal of a Catalytic Mechanism for the HIV-1 Protease Involving an Enzyme-Bound Tetrahedral Intermediate , 1998 .

[16]  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.

[17]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[18]  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.

[19]  Kari Laasonen,et al.  Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water , 1995 .

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

[21]  J. Mavri.  Irreversible inhibition of the HIV‐1 protease: A theoretical study , 1998 .

[22]  Lee.  Interferences in photodissociation in the classical limit. , 1988, Physical review. A, General physics.

[23]  Lin Hong,et al.  Active‐site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant , 1998, Protein science : a publication of the Protein Society.

[24]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

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

[26]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[27]  Michele Parrinello,et al.  The Iron−Sulfur Bond in Cytochrome c , 1999 .

[28]  I. Boros,et al.  Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease. , 1994, Biochemistry.

[29]  H Liu,et al.  A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease. , 1996, Journal of molecular biology.

[30]  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.

[31]  K. Murthy,et al.  The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. , 1994 .

[32]  Amiram Goldblum,et al.  Determining proton positions in an enzyme-inhibitor complex is a first step for theoretical mechanistic studies of aspartic proteinases , 1993 .

[33]  C. Debouck,et al.  Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[35]  T. Darden,et al.  An ab Initio Quantum Mechanical Model for the Catalytic Mechanism of HIV-1 Protease , 1996 .

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

[37]  K D Stewart,et al.  A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease. , 1996, Journal of medicinal chemistry.

[38]  David L. Beveridge,et al.  Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation , 1993 .

[39]  E. Padlan,et al.  Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Joanna Trylska,et al.  Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease , 2008, Protein science : a publication of the Protein Society.

[41]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[42]  J. Springer,et al.  Structure and function of retroviral proteases. , 1991, Annual review of biophysics and biophysical chemistry.

[43]  A Tropsha,et al.  Relative binding free energies of peptide inhibitors of HIV-1 protease: the influence of the active site protonation state. , 1995, Journal of medicinal chemistry.

[44]  Charles J. Eyermann,et al.  NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor , 1994 .

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

[46]  Ian M. Brereton,et al.  Ionization states of the catalytic residues in HIV-1 protease , 1996, Nature Structural Biology.

[47]  S. Vasavanonda,et al.  ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[50]  Michele Parrinello,et al.  On the Quantum Nature of the Shared Proton in Hydrogen Bonds , 1997, Science.

[51]  T. Meek,et al.  Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. , 1991, Biochemistry.

[52]  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.

[53]  V. Bertolasi,et al.  Evidence for resonance-assisted hydrogen bonding. 2. Intercorrelation between crystal structure and spectroscopic parameters in eight intramolecularly hydrogen bonded 1,3-diaryl-1,3-propanedione enols , 1991 .

[54]  I. Weber,et al.  Molecular dynamics simulations of HIV-1 protease with peptide substrate. , 1994, Protein engineering.

[55]  N. Marzari,et al.  Maximally localized generalized Wannier functions for composite energy bands , 1997, cond-mat/9707145.

[56]  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.

[57]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[58]  Barnett,et al.  Born-Oppenheimer molecular-dynamics simulations of finite systems: Structure and dynamics of (H2O)2. , 1993, Physical review. B, Condensed matter.

[59]  W. Cleland,et al.  Low-barrier hydrogen bonds and enzymic catalysis. , 1994, Science.

[60]  D. Turk,et al.  Theoretical investigations of structure and enzymatic mechanisms of aspartyl proteinases: Part I. Ab-initio calculations on an active site model: hydrogen diformiate with H2O and H3O+ , 1987 .

[61]  A. Beveridge,et al.  A quantum mechanical study of the active site of aspartic proteinases. , 1993, Biochemistry.

[62]  Maximally-localized Wannier functions for disordered systems: application to amorphous silicon , 1998, cond-mat/9804019.

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

[64]  V. Turk,et al.  Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

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

[66]  Michele Parrinello,et al.  Glucose in Aqueous Solution by First Principles Molecular Dynamics , 1998 .

[67]  M. Chiarelli,et al.  General Chemistry , 2019, Basic Chemical Concepts and Tables.

[68]  B. Brooks,et al.  HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation , 1995 .

[69]  Tomi K. Sawyer,et al.  A synthetic HIV-1 protease inhibitor with antiviral activity arrests HIV-like particle maturation. , 1990, Disease markers.

[70]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

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