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F A Saul

Publications and source records attributed to F A Saul.

11 recordsLinked to original sources
PubMed1993

Structural patterns at residue positions 9, 18, 67 and 82 in the VH framework regions of human and murine immunoglobulins.

VH framework regions of human and mouse immunoglobulins display three characteristic patterns in the conformation of the main polypeptide chain and side-chains at residue positions 9, 18, 67 and 82. These structural patterns are associated with the amino acid sequence at positions 9 and 67. Human and murine VH sequences show a strong correlation between the occurrence of Gly at position 9 and Phe at position 67 in VH subgroup III, and the frequent occurrence of Pro, Ala or Ser at position 9 and a non-aromatic residue at position 67 in other VH subgroups. Variations in VH framework segments have been shown to be of importance in procedures to humanize monoclonal murine antibodies and may be involved in the conformation of epitopes recognized by anti-VH antibodies. The structural patterns described here can be expected to influence the results of rotation and translation search functions in the crystallographic structure determination of Fab and Fv fragments by the molecular replacement method.

Amino Acid Sequence↗
PubMed1992

Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution.

The three-dimensional structure of the human immunoglobulin fragment Fab New (IgG1, lambda) has been refined to a crystallographic R-factor of 16.9% to 2 A resolution. Rms deviations of the final model from ideal geometry are 0.014 A for bond distances and 3.03 degrees for bond angles. Refinement was based on a new X-ray data set including 28,301 reflections with F > 2.5 sigma(F) from 6.0 to 2.0 A resolution. The starting model for the refinement procedure reported here is from the Brookhaven Protein Data Bank entry 3FAB (rev. 1981). Differences between the initial and final models include modified polypeptide-chain folding in the third complementarity-determining region (CDR3) and the third framework region (FR3) of VH and in some exposed loops of CL and CH1. Amino acid sequence changes were determined at a number of positions by inspection of difference electron density maps. The incorporation of amino acid sequence changes results in an improved VH framework model for the "humanization" of monoclonal antibodies.

Amino Acid Sequence↗
PubMed1990

Three-dimensional structure and antigen binding specificity of antibodies.

A number of specific Fab and Fv fragments and their complexes with antigens (avian lysozymes), haptens, and anti-idiotopic Fabs have been studied by immunochemical and crystallographic techniques. Antigen and antibody interact through closely complementary contacting surfaces, without major conformational changes. An idiotopic determinant of a monoclonal antibody is shown to include parts of most of its complementarity determining regions. The specificity of antigen recognition resides in the close complementarity of the antigenic determinant with the antibody combining site.

Animals↗
PubMed1989

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

Using X-ray coordinates of antigen-antibody complexes McPC 603, D1.3, and HyHEL-5, we made semiquantitative estimates of Gibbs free energy changes (delta G) accompanying noncovalent complex formation of the McPC 603 Fv fragment with phosphocholine and the D1.3 or HyHEL-5 Fv fragments with hen egg white lysozyme. Our empirical delta G function, which implicitly incorporates solvent effects, has the following components: hydrophobic force, solvent-modified electrostatics, changes in side-chain conformational entropy, translational/overall rotational entropy changes, and the dilutional (cratic) entropy term. The calculated delta G ranges matched the experimentally determined delta G of McPC 603 and D1.3 complexes and overestimated it (i.e., gave a more negative value) in the case of HyHEL-5. Relative delta G contributions of selected antibody residues, calculated for HyHEL-5 complexes, agreed with those determined independently in site-directed mutagenesis experiments. Analysis of delta G attribution in all three complexes indicated that only a small number of amino acids probably contribute actively to binding energetics. These form a subset of the total antigen-antibody contact surface. In the antibodies, the bottom part of the antigen binding cavity dominated the energetics of binding whereas in lysozyme, the energetically most important residues defined small (2.5-3 nm2) "energetic" epitopes. Thus, a concept of protein antigenicity emerges that involves the active, attractive contributions mediated by the energetic antigenic epitopes and the passive surface complementarity contributed by the surrounding contact area. The D1.3 energetic epitope of lysozyme involved Gly 22, Gly 117, and Gln 121; the HyHEL-5 epitope consisted of Arg 45 and Arg 68. These are also the essential antigenic residues determined experimentally. The above positions belong to the most protruding parts of the lysozyme surface, and their backbones are not exceptionally flexible. Least-squares analysis of six different antibody binding regions indicated that the geometry of the VH-VL interface beta-barrel is well conserved, giving no indication of significant changes in domain-domain contacts upon complex formation.

Amino Acids↗
PubMed1984

Crystallization of the fab fragments of monoclonal anti-p-azophenylarsonate antibodies and their complexes with haptens.

We report on the preparation, crystallization, and preliminary x-ray crystallographic study of Fab fragments from monoclonal anti-p-azophenylarsonate antibodies. Several crystalline forms were obtained with the Fab fragment from the R19.9 monoclonal antibody as well as with the complex between the hapten p-aminobenzenearsonic acid and Fab R19.9. The crystals of this hapten-Fab complex are similar to but not always isomorphous with the native Fab crystals. All the native and complex crystals were obtained using polyethylene glycol 6000 as crystallizing agent. Some of these crystalline forms diffract to a 2-A resolution or beyond and are suitable for high resolution x-ray diffraction analysis. A possible interpretation of hapten binding to crystalline Fab fragments from R19.9 and from the R9.3 monoclonal anti-p-azophenylarsonate antibody, implying conformational changes, is discussed.

Animals↗
PubMedDate not supplied

X-ray diffraction studies of an anti-azophenylarsonate antibody and of an antigen-antibody complex.

X-ray crystallographic studies of the Fab fragments of two murine monoclonal antibodies of predefined specificity are under way. Diffracted X-ray intensities of the crystalline native Fab fragment of an anti-azophenylarsonate antibody and of three heavy atom derivatives have been measured to a resolution of 3.5 A. A preliminary 6-A resolution electron density map has been obtained. The 6-A resolution structure of an antigen-antibody (hen lysozyme-Fab) complex has been determined. There are close contacts between the antigen and the antibody over a large contact area, about 20 X 25 A. At least two segments of the polypeptide chain of lysozyme, of about 10 amino acids each (positions 19-27 and 116-129), are involved in the contacts, as well as all six complementarity-determining regions of the antibody. No gross conformational changes are observed in the antigen at this resolution, although there are some smaller local changes in areas in contact with the antibody and elsewhere. The effects of amino acid substitutions on antigen recognition by the monoclonal anti-hen lysozyme antibody were investigated using different, closely related lysozymes. These effects can be readily explained in terms of the three-dimensional model presented here. A 3.5-A resolution electron density map has been calculated and is currently under study.

Animals↗