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Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).

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The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 A resolution by molecular replacement methods. The starting model was the refined 2.7 A structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA. In the 4-4-20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol-arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2-3 orders of magnitude in the 4-4-20 molecule relative to other members of an idiotypic family of monoclonal antifluorescyl antibodies. The phenyl carboxyl group of fluorescein appears to be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2-methyl-2,4-pentanediol (MPD), trapped in the interface of the variable domains just below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.

X-ray analysis at 3.2-A resolution revealed that the Mcg IgGl (A chain) immunoglobulin is a compact T-shaped molecule. Because of the hinge deletion, the Fc fragment lobe is pulled tightly upward into the junction of the Fab arms. Along the molecular twofold axis, the Fab arms are joined by an interchain disulfide bond between the two light chains. The antigen combining sites consist of large irregular cavities at the tips of the Fab regions. Potential complement (Clq) binding sites on Fc are sterically shielded by the Fab arms, but putative attachment sites are accessible for docking with the FcRI receptor on human monocytes and with protein A of Staphylococcus aureus.Progress in the elucidation of three-dimensional structures of intact antibodies has been slow for two principal reasons. (i) Supplies of crystalline proteins have been limited, and (ii) the Fc units have been disordered in crystals of immunoglobulins containing hinge regions. Like Mcg (1-4), the Dob IgGl protein has a hinge deletion (5) and an Fc region that appears to be ordered in the crystal lattice (6). In the Kol IgGl, the Fc is disordered, but the structures of the Fab arms and the hinge region are well defined (7,8). Similarly, a comparison of the Zie IgG2 molecule and its F(ab)2 fragment indicated that the Fc does not contribute significantly to the diffraction pattern of the intact IgG2 protein (9).The absence of a hinge region is associated with a substantial loss of segmental flexibility in an antibody molecule (10-13). Such a protein is more compact in solution, since sedimentation coefficients increase as hinge regions become shorter (13,14 crystal was used to collect 3.2-A data at 13°C with a Siemens area detector and a rotating anode operated at 40 kV and 80 mA. These data were 94.5% complete for intensities I > cr(I), where oa is the standard deviation based on counting statistics (see Table 1).With diffractometer data from 8-to 3.5-A (5132 reflections, 46% complete), the MIR model was previously refined in stages to an R factor of 28% with the program PROLSQ (26). The amino acid sequence of the light chain was provided by Fett and Deutsch (27). D. C. Shaw (personal communication) determined the sequences ofresidues 1-69 and 109-117 ofthe VH domain. The remaining residues in VH and in the three CH domains were assigned sequences by comparisons with similar heavy chains (28).Data from the diffractometer were replaced with the area detector set, and the refinement was continued by the procedure outlined in Table 2. X-PLOR (29) was used for rigidbody refinement, first with the Fab and Fc regions treated as intact units and then with six individual domains. The R factor for the 10-to 4-A set (99% complete) was 46.9%. Small rotations and translations from their starting positions were noted for all domains, but especially for CL. X-PLOR was next used for positional refinement (600 cycles) and simulated annealing ("slow-cooling" protocol) with 10-to 3.5-A data. To reduce the effects of model bias, the three complementarity-det...

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The role of electrostatics in the adsorption process of proteins to preformed negatively-charged (phosphatidylcholine/phosphatidylglycerol) and neutral (phosphatidylcholine) liposomes was studied. The interaction was monitored at low ionic strength for a set of model proteins as a function of pH. The adsorption behavior of trypsin inhibitor (pI = 4.6), myoglobin (pI = 7.4), ribonuclease (pI = 9.6), and lysozyme (pI = 10.7) with preformed liposomes was investigated, along with changes in the electrophoretic mobility of liposomes through the adsorption of charged proteins. Mean protein charge was determined by acid/base titration. Significant adsorption of the proteins to negatively-charged liposomes was only found at pH values where the number of positive charge moieties exceeds the number of negative charge moieties on the protein by at least three charge units. Negligible adsorption to liposomes composed of zwitterionic lipids was observed in the pH range tested (4-9). The absolute value of the electrophoretic mobilities of negatively-charged, empty liposomes decreased after adsorption of positively-charged proteins. With increasing protein to phospholipid ratio, the drop in the electrophoretic mobility leveled off and reached a plateau; protein adsorption profiles showed a similar shape. Analysis of the data demonstrated that neutralization of the liposome charge due to the adsorption of the positively-charged proteins is the controlling factor in their adsorption. The plateau level reached depended on the type of protein and the pH of the incubation medium. This pH dependency could be ascribed to the mean positive charge of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

The surface forces apparatus was used to identify the molecular forces that control the interactions of monoclonal 4-4-20 antifluorescyl IgG Fab' fragments with fluorescein-presenting supported planar bilayers. At long range, the electrostatic force between oriented Fab' and fluorescein monolayers was controlled by the composition of the protein exterior surrounding the antigen-combining site rather than by the overall protein charge. The measured positive electrostatic potential of the Fab' monolayer at pH > pI(Fab') was consistent with the structure of the exposed Fab' surface in which a ring of positive charge at the mouth of the antigen-combining site dominates the local electrostatic surface properties. Substantial differences in the electrostatic forces measured with denatured Fab' further demonstrated that the measured electrostatic surface properties and the consequent long-range interaction forces are controlled by the protein surface composition. At short range, the strength of the Fab'-mediated adhesion was modulated not only by the length of the fluorescein tether but also by membrane hydration. Steric hydration barriers at the membrane surface reduced the adhesion strength in proportion to their range of influence. These results provide direct evidence that long-range protein interactions with immobilized ligands are controlled by both the protein and the membrane surface compositions, while short-range, specific binding is modulated by both the protein structure and the membrane interfacial properties.