- Email: [email protected]
Biologically active analogs of CD4
lipophilicity potential. The residue database makes use of the Ponder-Richards side chain rotamer library, augmented by Zn:, Ca:, and Mg: templates for the simulation of metalloproteins. The force-field, minimizer, and solvation algorithms were adapted from the software Yeti. The program Yak is interactive, menu-driven, and includes a graphics shell, allowing for real-time 3D visualization and object transformation/analysis. Yak is available for VAX/VMS and selected UNIX/RISC workstations.
REFERENCES Snyder, J.P., Rao, S.N., Koehler, K.F., and Pellicciari, R. In: Trends in Receptor Research. (P. Angeli, U. Gulini, and W. Quaglia, Eds.), Elsevier, Amsterdam, 1992, pp. 367-403 Vedani, A., Zbinden, P., and Snyder, J.P. J. Receptor Research. 1993, in press Vedani, A. and Huhta, D.W. J. Am. Chem. Sot. 1990, 112, 4759-4767; and Vedani, A. and Huhta, D.W. J. Am. Chem. Sot. 1991, 113, 5860-5862
have been carried out. The simulations are based on a refined structure of BR as provided by R. Henderson. Additional internal water molecules, as well as part of the solvent, have been added to the model. In order to optimally support 3D perception, the animation was produced employing state-of-the-art, photorealistic ray-shading techniques, requiring a total of 2,500 CPUhours on a cluster of seven 20-MFlops workstations. Based on experience from several recent presentations, we conclude that such visualizations of data provided by molecular dynamics simulations can indeed serve as a powerful tool for efficient information transfer, if two prerequisites are fulfilled: Considerable effort has been made to develop a scenario that focuses on relevant details and avoids the confusion caused by thousands of jiggling atoms; and additional information is provided about the relation between reality and the particular computer model underlying the visualization.
BIOLOGICALLY CD4
ACTIVE
ANALOGS
OF
BR AT WORK: A COMPUTERANIMATION FOR THE 13-14-cis-MODEL OF THE PHOTOCHEMICAL CYCLE OF BACTERIORHODOPSIN
J.M. McDonnell, D. Wernicke-Jameson, Jameson Jefferson Cancer Institute, Thomas Jefferson Philadelphia, PA, USA
H. Grubmiiller, K. Dohring, P. Tavan, M. Nonella, and D. Oesterhelt lnstitut fur Medizinische Optik, Theoretische Biophysik, Universitat Miinchen. FRG
CD4, a protein expressed on the surface of helper T lymphocytes, is intimately involved in the signal transduction pathway leading to T cell activation. Helper T lymphocytes are a critical arm of the immune response, controlling both cellular and humoral responses to foreign pathogens. Loss of the CD4 + T cell subset leads to a severe immunodeficiency, as is seen in the later stages of AIDS. Given the central importance of this molecule, we sought to investigate the role of CD4 in T cell activation. A model structure of the mouse CD4 protein was constructed, based on the high resolution crystal structure of the human CD4 protein. A member of the immunoglobulin superfamily, CD4 shares the characteristic immunoglobulin-like fold. Based on the model protein structure, synthetic peptide analogs were synthesized, designed to mimic a region of CD4 analogous to the third complementarity-determining region (CDR3) of immunoglobulins. A combination of covalent closure and conformational restraints was used in an attempt to optimize potential overlap of peptide conformation with that of the parent protein. CDR3 analogs were able to specifically inhibit CDCdependent T cell responses in in vitro studies. NMR analysis of the analogs suggested the importance of the proper presentation of a surface of approximately 4-5 residues. Biological data suggested the immunomodulatory activity of the CDR3 analogs was due to an uncoupling of CD4 from the signal transduction machinery responsible for mediating T cell activation. A reverse-sequence D-amino acid (retro-inverso) CDR3 analog has demonstrated in vivo biological activity. This analog inhibits the clinical incidence of EAE, an experimentally induced, CD4-dependent autoimmune disorder, that is used as a mouse model of the human disease multiple sclero-
An understanding of biochemical processes, in particular protein function, in terms of chemical and physical notions typically requires familiarity with a large amount of experimental and theoretical detail related to the particular system under consideration. In the attempt to communicate that information, one is typically faced with a “communication bottleneck.” Computer animations can contribute to a solution of that communications problem. In order to demonstrate the possibility to efficiently communicate large amounts of biochemical information by means of computer animations, we present a 13-minute video employing advanced visualization techniques. The video provides, in condensed form, detailed insights into the functioning of the light-driven, transmembrane protonpump bacteriorhodopsin (BR), based on the so-called 1314-cis-model for the photochemical cycle. The video is broken into two parts. The first part introduces structural elements relevant to an understanding of the proton-pump process. These include the location of BR within a lipid bilayer membrane, the Schiff base, the aspartic acids ASP96 and ASP85 (which act as proton donator and acceptor, respectively), the proton channel with internal water molecules, and the sterical and electrostatic vicinity of the retinal. The second part is devoted to the dynamics of the photocycle, as described by the 13- 14-cis-model. For that purpose, molecular dynamics simulations covering all major known isomerization steps during the photochemical cycle
258
J. Mol. Graphics,
1993, Vol. 11, December
and
B.A.
University,
sis. These compounds represent a novel class of immunomodulatory agents with potential clinical applications, and demonstrate the power of structure-based design in rational drug development.
MOLECULAR DYNAMICS SIMULATIONS OF VIRAL PEPTIDES BOUND TO CLASS I MHC PROTEINS D. Rognan and G. Folkers Departement Pharmazie, ETH Zentrum, land
Zurich,
Switzer-
Major histocompatibility complex (MHC) encoded proteins form a family of highly polymorphic glycoproteins whose function is to bind antigenic peptides derived from intracellular processing of self or viral antigens and to present them to a T cell receptor (TCR) at the surface of infected cells. Self peptides bound to different class I MHC molecules have been recently eluted, identified, and sequenced. Most of these were nonapeptides, and revealed allele-specific motifs consisting of several anchor positions in addition to an hydrophobic C-terminus (VAL, ILE, LEU). In the present study, the human HLA-A2.1 MHC protein bound to naturally processed viral peptides (Influenza virus matrix protein 58-66, HIV 1-Reverse Transcriptase 276-284 nonapeptides) were simulated by molecular dynamics. Starting from the X-ray coordinates of HLA-A2.1 (182 residues for the antigen-binding domains), the viral nonapeptide were similarly docked, residue by residue, in the binding cleft according to the unresolved extra electron density map associated to that MHC molecule, and elution experiments on HLA-A2.1 restricted peptides. Each complex was then simulated for 100 ps in a shell of 1400 water molecules using the AMBER united-atoms and all-atoms force fields, on the CRAY-YMP at ETH-Zurich. Similar results were obtained for all simulations. The time-averaged simulated HLA-A2 conformation was found to be similar to the experimental one (rms deviation of 0.182 nm for backbone atoms), and most of the intramolecular H-bonds were reproduced. Both bound peptides exhibit an extended conformation. The antigen-HLA interactions proposed in this study are remarkably divided into conserved electrostatics interactions and specific hydrophobic contacts. Three peptide side chains (positions 2, 3, and 9) develop close van der Waals contacts with three polymorphic MHC pockets, whereas the backbone polar atoms are hydrogen-bonded to MHC conserved residues at the rim of the same pockets. This model is fully compatible with all available experimental data on HLA-A2 restricted peptides, as well as the posterior crystal structures of variant class I MHC proteins (HLA-Aw68, HLA-B27, H-2Kb) complexed by single peptides. Ninety percent of the conserved MHC-peptide interactions described in the crystal structures were reproduced in the MD study of the peptidebound HLA-A2 haplotype. To test the model’s consistency, antigenic sequences have been designed to optimally fit the MHC binding groove. When simulated under the previously described conditions, both peptides and the HLA-A2 protein exhibited decreased
atomic fluctuations when compared to natural MHC-peptide pairs. Restricting the conformational flexibility of MHCpeptide complexes will be experimentally studied by testing the binding of natural and designed peptides to recombinant HLA-A2 and their effect upon T cell recognition. Getting more and more into the atomic details of MHCpeptide complexes should facilitate the rational design of potential synthetic vaccines, useful in the individual treatment of viral infections, graft rejection, and autoimmune diseases.
TEXTURE MAPPING IN MOLECULAR GRAPHICS Michael Teschner,* Jtirgen Brickmann,? and Christian Henn** *Chemical and Pharmaceutical Technical Center, Silicon Graphics, Basel, Switzerland tJtirgen Brickmann, TH Darmstadt, Germany **Christian Henn, Maurice E. Miiller-Institute for HighResolution Electron Microscopy, University of Basel, Switzerland Texture mapping is well known to the computer graphics community as a technique for projecting an image onto a surface of a three-dimensional object, as if it were a decal or a cellophane shrink-wrap. While adding to the realism and the visual quality of rendered images, the technique has largely been neglected by interactive, molecular graphics developers, since adequate rendering performance has been lacking for a long time. Modem graphics workstations have recently emerged with hardware support for texture mapping, leading to new levels of performance and changing the way one may treat molecular graphics. To demonstrate the potential of texture mapping in realtime molecular graphics, we have explored various scenarios, focusing on four issues of particular interest: (1) increased shading quality of arbitrarily curved surfaces without degradation of rendering performance, (2) enhanced rendering performance of standard molecular representations, (3) improved accuracy of color-coded properties mapped onto geometric surfaces, and (4) high-performance volume rendering used to represent isosurfaces as well as contiguous volume segments:
(1)
(2)
Gouraud-shaded surfaces are known to produce artifacts with strongly curved, but nevertheless sparsely tessellated surfaces. Such surfaces are not only unpleasant to look at, but can even lead to misinterpretations of object’s shape. Texture-mapping techniques such as environment (or reflection) mapping can well overcome these problems: the image of a perfectly rendered sphere is directly applied to control the interpretation of surface normal vectors. Consequently, higher quality Phong-shading can be emulated without performance penalty. A traditional problem with the visualization of large ball-and-stick models in molecular models has been the use of tessellated primitives such as triangulated spheres or cylinders; an improvement in rendering per-
J. Mol. Graphics,
1993, Vol. 11, December
259
REFERENCES Snyder, J.P., Rao, S.N., Koehler, K.F., and Pellicciari, R. In: Trends in Receptor Research. (P. Angeli, U. Gulini, and W. Quaglia, Eds.), Elsevier, Amsterdam, 1992, pp. 367-403 Vedani, A., Zbinden, P., and Snyder, J.P. J. Receptor Research. 1993, in press Vedani, A. and Huhta, D.W. J. Am. Chem. Sot. 1990, 112, 4759-4767; and Vedani, A. and Huhta, D.W. J. Am. Chem. Sot. 1991, 113, 5860-5862
have been carried out. The simulations are based on a refined structure of BR as provided by R. Henderson. Additional internal water molecules, as well as part of the solvent, have been added to the model. In order to optimally support 3D perception, the animation was produced employing state-of-the-art, photorealistic ray-shading techniques, requiring a total of 2,500 CPUhours on a cluster of seven 20-MFlops workstations. Based on experience from several recent presentations, we conclude that such visualizations of data provided by molecular dynamics simulations can indeed serve as a powerful tool for efficient information transfer, if two prerequisites are fulfilled: Considerable effort has been made to develop a scenario that focuses on relevant details and avoids the confusion caused by thousands of jiggling atoms; and additional information is provided about the relation between reality and the particular computer model underlying the visualization.
BIOLOGICALLY CD4
ACTIVE
ANALOGS
OF
BR AT WORK: A COMPUTERANIMATION FOR THE 13-14-cis-MODEL OF THE PHOTOCHEMICAL CYCLE OF BACTERIORHODOPSIN
J.M. McDonnell, D. Wernicke-Jameson, Jameson Jefferson Cancer Institute, Thomas Jefferson Philadelphia, PA, USA
H. Grubmiiller, K. Dohring, P. Tavan, M. Nonella, and D. Oesterhelt lnstitut fur Medizinische Optik, Theoretische Biophysik, Universitat Miinchen. FRG
CD4, a protein expressed on the surface of helper T lymphocytes, is intimately involved in the signal transduction pathway leading to T cell activation. Helper T lymphocytes are a critical arm of the immune response, controlling both cellular and humoral responses to foreign pathogens. Loss of the CD4 + T cell subset leads to a severe immunodeficiency, as is seen in the later stages of AIDS. Given the central importance of this molecule, we sought to investigate the role of CD4 in T cell activation. A model structure of the mouse CD4 protein was constructed, based on the high resolution crystal structure of the human CD4 protein. A member of the immunoglobulin superfamily, CD4 shares the characteristic immunoglobulin-like fold. Based on the model protein structure, synthetic peptide analogs were synthesized, designed to mimic a region of CD4 analogous to the third complementarity-determining region (CDR3) of immunoglobulins. A combination of covalent closure and conformational restraints was used in an attempt to optimize potential overlap of peptide conformation with that of the parent protein. CDR3 analogs were able to specifically inhibit CDCdependent T cell responses in in vitro studies. NMR analysis of the analogs suggested the importance of the proper presentation of a surface of approximately 4-5 residues. Biological data suggested the immunomodulatory activity of the CDR3 analogs was due to an uncoupling of CD4 from the signal transduction machinery responsible for mediating T cell activation. A reverse-sequence D-amino acid (retro-inverso) CDR3 analog has demonstrated in vivo biological activity. This analog inhibits the clinical incidence of EAE, an experimentally induced, CD4-dependent autoimmune disorder, that is used as a mouse model of the human disease multiple sclero-
An understanding of biochemical processes, in particular protein function, in terms of chemical and physical notions typically requires familiarity with a large amount of experimental and theoretical detail related to the particular system under consideration. In the attempt to communicate that information, one is typically faced with a “communication bottleneck.” Computer animations can contribute to a solution of that communications problem. In order to demonstrate the possibility to efficiently communicate large amounts of biochemical information by means of computer animations, we present a 13-minute video employing advanced visualization techniques. The video provides, in condensed form, detailed insights into the functioning of the light-driven, transmembrane protonpump bacteriorhodopsin (BR), based on the so-called 1314-cis-model for the photochemical cycle. The video is broken into two parts. The first part introduces structural elements relevant to an understanding of the proton-pump process. These include the location of BR within a lipid bilayer membrane, the Schiff base, the aspartic acids ASP96 and ASP85 (which act as proton donator and acceptor, respectively), the proton channel with internal water molecules, and the sterical and electrostatic vicinity of the retinal. The second part is devoted to the dynamics of the photocycle, as described by the 13- 14-cis-model. For that purpose, molecular dynamics simulations covering all major known isomerization steps during the photochemical cycle
258
J. Mol. Graphics,
1993, Vol. 11, December
and
B.A.
University,
sis. These compounds represent a novel class of immunomodulatory agents with potential clinical applications, and demonstrate the power of structure-based design in rational drug development.
MOLECULAR DYNAMICS SIMULATIONS OF VIRAL PEPTIDES BOUND TO CLASS I MHC PROTEINS D. Rognan and G. Folkers Departement Pharmazie, ETH Zentrum, land
Zurich,
Switzer-
Major histocompatibility complex (MHC) encoded proteins form a family of highly polymorphic glycoproteins whose function is to bind antigenic peptides derived from intracellular processing of self or viral antigens and to present them to a T cell receptor (TCR) at the surface of infected cells. Self peptides bound to different class I MHC molecules have been recently eluted, identified, and sequenced. Most of these were nonapeptides, and revealed allele-specific motifs consisting of several anchor positions in addition to an hydrophobic C-terminus (VAL, ILE, LEU). In the present study, the human HLA-A2.1 MHC protein bound to naturally processed viral peptides (Influenza virus matrix protein 58-66, HIV 1-Reverse Transcriptase 276-284 nonapeptides) were simulated by molecular dynamics. Starting from the X-ray coordinates of HLA-A2.1 (182 residues for the antigen-binding domains), the viral nonapeptide were similarly docked, residue by residue, in the binding cleft according to the unresolved extra electron density map associated to that MHC molecule, and elution experiments on HLA-A2.1 restricted peptides. Each complex was then simulated for 100 ps in a shell of 1400 water molecules using the AMBER united-atoms and all-atoms force fields, on the CRAY-YMP at ETH-Zurich. Similar results were obtained for all simulations. The time-averaged simulated HLA-A2 conformation was found to be similar to the experimental one (rms deviation of 0.182 nm for backbone atoms), and most of the intramolecular H-bonds were reproduced. Both bound peptides exhibit an extended conformation. The antigen-HLA interactions proposed in this study are remarkably divided into conserved electrostatics interactions and specific hydrophobic contacts. Three peptide side chains (positions 2, 3, and 9) develop close van der Waals contacts with three polymorphic MHC pockets, whereas the backbone polar atoms are hydrogen-bonded to MHC conserved residues at the rim of the same pockets. This model is fully compatible with all available experimental data on HLA-A2 restricted peptides, as well as the posterior crystal structures of variant class I MHC proteins (HLA-Aw68, HLA-B27, H-2Kb) complexed by single peptides. Ninety percent of the conserved MHC-peptide interactions described in the crystal structures were reproduced in the MD study of the peptidebound HLA-A2 haplotype. To test the model’s consistency, antigenic sequences have been designed to optimally fit the MHC binding groove. When simulated under the previously described conditions, both peptides and the HLA-A2 protein exhibited decreased
atomic fluctuations when compared to natural MHC-peptide pairs. Restricting the conformational flexibility of MHCpeptide complexes will be experimentally studied by testing the binding of natural and designed peptides to recombinant HLA-A2 and their effect upon T cell recognition. Getting more and more into the atomic details of MHCpeptide complexes should facilitate the rational design of potential synthetic vaccines, useful in the individual treatment of viral infections, graft rejection, and autoimmune diseases.
TEXTURE MAPPING IN MOLECULAR GRAPHICS Michael Teschner,* Jtirgen Brickmann,? and Christian Henn** *Chemical and Pharmaceutical Technical Center, Silicon Graphics, Basel, Switzerland tJtirgen Brickmann, TH Darmstadt, Germany **Christian Henn, Maurice E. Miiller-Institute for HighResolution Electron Microscopy, University of Basel, Switzerland Texture mapping is well known to the computer graphics community as a technique for projecting an image onto a surface of a three-dimensional object, as if it were a decal or a cellophane shrink-wrap. While adding to the realism and the visual quality of rendered images, the technique has largely been neglected by interactive, molecular graphics developers, since adequate rendering performance has been lacking for a long time. Modem graphics workstations have recently emerged with hardware support for texture mapping, leading to new levels of performance and changing the way one may treat molecular graphics. To demonstrate the potential of texture mapping in realtime molecular graphics, we have explored various scenarios, focusing on four issues of particular interest: (1) increased shading quality of arbitrarily curved surfaces without degradation of rendering performance, (2) enhanced rendering performance of standard molecular representations, (3) improved accuracy of color-coded properties mapped onto geometric surfaces, and (4) high-performance volume rendering used to represent isosurfaces as well as contiguous volume segments:
(1)
(2)
Gouraud-shaded surfaces are known to produce artifacts with strongly curved, but nevertheless sparsely tessellated surfaces. Such surfaces are not only unpleasant to look at, but can even lead to misinterpretations of object’s shape. Texture-mapping techniques such as environment (or reflection) mapping can well overcome these problems: the image of a perfectly rendered sphere is directly applied to control the interpretation of surface normal vectors. Consequently, higher quality Phong-shading can be emulated without performance penalty. A traditional problem with the visualization of large ball-and-stick models in molecular models has been the use of tessellated primitives such as triangulated spheres or cylinders; an improvement in rendering per-
J. Mol. Graphics,
1993, Vol. 11, December
259