Modeling the anti‐CEA antibody combining site by homology and conformational search

A model for an antibody specific for the carcinoembryonic antigen (CEA) has been constructed using a method which combines the concept of canonical structure with conformational search. A conformational search technique is introduced which couples random generation of backbone loop conformations to a simulated annealing method for assigning side chain conformations. This technique was used both to verify conformations selected from the set of known canonical structures and to explore conformations available at the H3 loop in CEA ab initio. Canonical structures are not available for H3 due to its variability in length, sequence, and observed conformation in known antibody structures Analysis of the results of conformational search resulted in three equally probable conformations for H3 loop in CEA. Force field energies, solvation free energies, exposure of charged residues and burial of hydrophobic residues, and packing of hydrophobic residues at the base of the loop were used as selection criteria. The existence of three equally plausible structures may reflect the high degree of flexibility expected for an exposed loop of this length. The nature of the combining site and features which could be important to interaction with antigen are discussed. © 1992 Wiley‐Liss, Inc.

[1]  B Honig,et al.  Internal cavities and buried waters in globular proteins. , 1986, Biochemistry.

[2]  Y. Satow,et al.  Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. , 1985, Journal of molecular biology.

[3]  E. Kabat,et al.  Sequences of proteins of immunological interest , 1991 .

[4]  E. Padlan.  On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands , 1990, Proteins.

[5]  R. Huber,et al.  The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-A resolution. , 1975, Biochemistry.

[6]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations , 1986, Proteins.

[7]  J L Sussman,et al.  A 3D building blocks approach to analyzing and predicting structure of proteins , 1989, Proteins.

[8]  Jacopo Tomasi,et al.  Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation , 1989 .

[9]  R. Bruccoleri,et al.  Criteria that discriminate between native proteins and incorrectly folded models , 1988, Proteins.

[10]  M. Potter,et al.  A hypothetical space-filling model of the V-regions of the galactan-binding myeloma immunoglobulin J539. , 1981, Molecular immunology.

[11]  A. Lesk,et al.  Canonical structures for the hypervariable regions of immunoglobulins. , 1987, Journal of molecular biology.

[12]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[13]  G. Cohen,et al.  Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[15]  J. N. Varghese,et al.  Three-dimensional structure of a complex of antibody with influenza virus neuraminidase , 1987, Nature.

[16]  L M Amzel,et al.  The three dimensional structure of a combining region-ligand complex of immunoglobulin NEW at 3.5-A resolution. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[17]  N. Go,et al.  Ring Closure and Local Conformational Deformations of Chain Molecules , 1970 .

[18]  J Deisenhofer,et al.  Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 A and 1.0 A resolution. , 1980, Journal of molecular biology.

[19]  C Levinthal,et al.  Interactive computer graphics and representation of complex biological structures. , 1972, Annual review of biophysics and bioengineering.

[20]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[21]  B Honig,et al.  Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. , 1991, Science.

[22]  L M Amzel,et al.  Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 A resolution. , 1981, The Journal of biological chemistry.

[23]  R. Poljak,et al.  Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution , 1986, Science.

[24]  M. Lascombe,et al.  Three-dimensional structure of antibodies. , 1988, Annual review of immunology.

[25]  G. Petsko,et al.  Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten. , 1991, Biochemistry.

[26]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[27]  E. Padlan,et al.  Model-building studies of antigen-binding sites: the hapten-binding site of mopc-315. , 1977, Cold Spring Harbor symposia on quantitative biology.

[28]  T L Blundell,et al.  Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains. , 1987, Protein engineering.

[29]  K A Dill,et al.  The meaning of hydrophobicity. , 1990, Science.

[30]  M. Karplus,et al.  An analysis of incorrectly folded protein models. Implications for structure predictions. , 1984, Journal of molecular biology.

[31]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[32]  R J Feldmann,et al.  A refined model for the variable domains (Fv) of the J539 beta(1,6)-D-galactan-binding immunoglobulin. , 1984, Molecular immunology.

[33]  G. Air,et al.  Electron and X-ray diffraction studies of influenza neuraminidase complexed with monoclonal antibodies. , 1986, Journal of molecular biology.

[34]  Barry Honig,et al.  Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation , 1990 .

[35]  Harold A. Scheraga,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops , 1990 .

[36]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[37]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[38]  K. R. Ely,et al.  Binding of 2,4-dinitrophenyl compounds and other small molecules to a crystalline lambda-type Bence-Jones dimer. , 1974, Biochemistry.

[39]  A. Lesk,et al.  Conformations of immunoglobulin hypervariable regions , 1989, Nature.

[40]  C. Wagener,et al.  Monoclonal antibodies for carcinoembryonic antigen and related antigens as a model system: a systematic approach for the determination of epitope specificities of monoclonal antibodies. , 1983, Journal of immunology.

[41]  M. Karplus,et al.  Crystallographic refinement by simulated annealing: application to crambin , 1989 .

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

[43]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[44]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures , 1987, Biopolymers.

[45]  B C Finzel,et al.  Three-dimensional structure of an antibody-antigen complex. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[46]  A C Martin,et al.  Modeling antibody hypervariable loops: a combined algorithm. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[47]  W Furey,et al.  Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution. , 1983, Journal of molecular biology.

[48]  G. Cohen,et al.  The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[49]  B. Honig,et al.  On the calculation of electrostatic interactions in proteins. , 1985, Journal of molecular biology.

[50]  J. Moult,et al.  An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.

[51]  M. Karplus,et al.  Conformational sampling using high‐temperature molecular dynamics , 1990, Biopolymers.

[52]  L. J. Perry,et al.  Generation of antibody activity from immunoglobulin polypeptide chains produced in Escherichia coli. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Kurt Wüthrich,et al.  Secondary structure of the α-amylase polypeptide inhibitor Tendamistat from Streptomyces tendae determined in solution by 1H nuclear magnetic resonance , 1985 .

[54]  T. Bhat,et al.  The galactan‐binding immunoglobulin Fab J539: An x‐ray diffraction study at 2.6‐Å resolution , 1986, Proteins.

[55]  M. Pawlita,et al.  A monoclonal antibody that defines an idiotope with two subsites in galactan-binding myeloma proteins , 1981, The Journal of experimental medicine.

[56]  M. L. Mason,et al.  Three‐dimensional structure of a fluorescein–Fab complex crystallized in 2‐methyl‐2,4‐pentanediol , 1989, Proteins.