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The association of two or more macromolecules results in the formation of a complex characterized by a larger Stokes radius than that of its components. Therefore, analytical procedures such as ultracentrifugation and size-exclusion gel chromatography that resolve molecules on the basis of size have been used to characterize the association. In this paper we describe an iterative computer simulation of small-zone size-exclusion gel filtration. The simulation describes univalent and bivalent interactions of proteins of equal and nonequal molecular weight and appears to have both qualitative and quantitative application to the evaluation of protein-protein interaction as revealed by alteration of chromatographic elution profiles. To test the validity of the simulation, the model was applied to an antibody-antigen interaction by determining the association constant (Ka) for the interaction between the binding fragment derived from a human immunoglobulin A rheumatoid factor and the antigenic fragment obtained from a human myeloma immunoglobulin G. The self-consistency of the estimated Ka values obtained with a valence value of 2 in contrast to the lack of self-consistency if an antigenic valence of 1 was assumed was taken to support the ability of the algorithm to reasonably emulate the chromatographic processes of interacting proteins. In conjunction with the computer simulation, a sensitive microcomputer-interfaced chromatography system was assembled, which is capable of analyzing 300 ng of protein in less than 1 h. This combination of rapid reagent-conservative chromatography and simulation analysis may contribute to the usefulness of small-zone gel filtration in studies of protein-protein interaction.

A complete human λ Bence Jones protein dimer (Cle) has been isolated and crystallized. Protein Cle was characterized immunochemically and chemically as having a variable region amino acid sequence associated with light chains of the λ chain subgroup, λIII, and a constant region sequence characteristic of “non-Mcg” type λ chains. Bence Jones protein Cle contains two covalently bound intact monomers, each having a molecular weight of ~23,000. Crystals of Bence Jones protein Cle, obtained from ammonium sulfate solutions, diffract to 2.6 A resolution and have the orthorhombic space group P212121 with cell dimensions a = 113.0 A , b = 72.3 A , and c = 48.9 A . The asymmetric unit consists of a dimer with a molecular weight of ~ 46,000.

Available crystallographic data for homologous immunoglobulin constant domains were correlated with measured association constants for these domains. High correlation was found between the association constant and both the buried surface area (number of interdomain contacts) and the number of salt bridges formed in the interaction, whereas no correlation with the number of hydrogen bonds between domains was evident. The total free energy of binding, as determined from the association constant, was related to the number of contacts, hydrogen bonds and salt bridges found in the domain: domain interface by the crystallographic studies. These calculations yielded reasonable average energy terms for each interaction category.

Immunoglobulin light chain (LC) normally is a soluble, secreted protein, but some LC assemble into ordered fibrils whose deposition in tissues results in amyloidosis and organ failure. Here we reconstitute fibril formation in vitro and show that preformed fibrils can nucleate polymerization of soluble LC. This prion-like behavior has important physiological implications, since somatic mutations generate multiple related LC sequences. Furthermore, we demonstrate that fibril formation in vitro and aggregation of whole LC within cells are inhibited by BiP and by a synthetic peptide that is identical to a major LC binding site for BiP. We propose that LC form fibrils via an interprotein loop swap and that the underlying conformational change should be amenable to drug therapy.

We have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-A resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding "pocket". The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion (Chang et al., 1985). The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry.

Size-exclusion HPLC provides direct observation of antibody-antigen interactions in free solution without chemical modification of either component. HPLC data collection systems are now a routine resource in both academic and industrial research laboratories. Monoclonal antibodies are, in principle, homogeneous reagents whose interactions with epitope are suitable for unambiguous quantitative characterization. HPLC-based methods, therefore, have the potential to contribute significantly to efficient quantitative characterization of monoclonal antibodies in studies directed to the fundamental physiological roles of these molecules as well as to the optimized selection and quality control of these reagents in biotechnical applications such as represented by the immunodiagnostic industry. In many cases, HPLC-based methods may represent the simplest and most rapid approach for evaluation of relative epitope specificities and affinity/kinetic characteristics of interaction.

Previous work in this laboratory [e.g., Peraino, C., Bunville, L. G.,Tahmisian, T. N. (1969) J. Biol. Chem. 244, 2241--2249, and Morris, J. E., Peraino, C.,Strayer, D. (1974) Proc. Soc. Exp. Biol. Med. 147, 707--709] has shown that the molecular weight of ornithine aminotransferase (OAT) is concentration dependent. In the present study this property of OAT was further characterized by using sedimentation equilibrium centrifugation to determine the molecular weight of OAT in a range of enzyme concentrations. It was shown that OAT aggregates in a two-stage process as its concentration increases. The first stage involves the association of enzymatically active monomers into trimers, with association of the trimers into higher order aggregates occurring in the second stage. Decreasing the pH or raising the ionic strength enhances aggregation while raising the pH inhibits aggregation; however, the two-stage nature of the aggregation process was not affected by changes in pH and ionic strength. Kinetic analyses of purified enzyme showed that aggregation results in an increase in the kM for both substrates with the Vmax remaining constant, indicating that aggregation of monomers sterically hinders substrate binding. Increased Km values were also obtained for OAT sequestered in mitochondria from rats fed a high-protein diet to increase mitochondrial OAT levels. The higher Km values suggest that the elevation of OAT in vivo is accompanied by aggregation of the enzyme within the mitochondrion. We propose that the aggregation-dependent increase of Km in vivo has adaptive value in that it spares ornithine for use in the urea cycle.

Evidence that tumorigenesis is a multistage process first emerged from experiments showing that wounding of skin previously treated with coal tar resulted in tumor formation at the wound site (1). Subsequent experiments in which physical trauma was replaced by the application of chemical irritants not intrinsically tumorigenic yielded similar results (2,3). These observations were codified by Rous, who coined the terms “initiation” and “promotion” to denote respectively (a) the production of potentially tumorigenic cells by limited carcinogen treatment and (b) the completion of the neoplastic transformation resulting from subsequent treatment with any of a wide variety of noncarcinogenic irritants and proliferative stimuli (3).

We have characterized and crystallized a human lambda I light-chain dimer, Bence-Jones protein Loc, which has variable (V) region antigenic determinants characteristic for the lambda I subgroup and constant (C) region determinants of the C lambda I gene Mcg. The crystal structure was determined to 3-A resolution; the R factor is 0.27. The angle formed by the twofold axes of the V and C domains, the "elbow bend", is 97 degrees, the smallest found so far for an antibody fragment. The antigen-binding site formed by the two V domains of the Loc light chain differs significantly from those of other immunoglobulin molecules (light-chain dimers and Fab fragments) for which X-ray crystallographic data are available. Whereas, in other antibody fragments, the V domains are related by a local twofold axis, a local twofold screw axis with a translational component of 3.5 A relates the V domains in protein Loc. In contrast to the classic antigen binding "pocket" formed by V domain interactions in the previously characterized antibody structures, the V region associations in protein Loc result in a central protrusion in the binding site, with grooves on two sides of the protrusion. The structure of protein Loc indicates that immunoglobulins are physically capable of forming a more diverse spectrum of antigen-binding sites than has been heretofore apparent. Moreover, the unusual protruding nature of the binding site may be analogous to structures required for some anti-idiotypic antibodies. Further, the complementarity-determining residues form parts of two independent grooves.(ABSTRACT TRUNCATED AT 250 WORDS)

Relationships between phenotypic and growth characteristics of carcinogen-induced altered hepatocyte foci were investigated. Male and female rats were given a single i.p. injection of carcinogen (diethylnitrosamine or benzo[a]pyrene) within 1 day after birth and were exposed to dietary promoter (phenobarbital) beginning at weaning. Groups of these rats were then killed at intervals, and their livers were examined for foci exhibiting various phenotypic markers through the use of serial frozen sectioning techniques, histochemical staining and computer-assisted image analysis. These procedures permitted the identification and sizing of foci with different specific phenotypes (identities of focus markers) within each phenotypic complexity level (number of markers per focus). The data suggest that foci growth rates differ with respect to specific focus phenotypes within complexity levels. This observation complements previous demonstrations of a direct relationship between foci growth rates and levels of phenotypic complexity and indicates that the observed diversity of focus phenotypes reflects true biological diversity within the focus population. Given the prior evidence for (i) the stability of focus phenotypes; (ii) the rapid emergence of phenotypically dissimilar foci following a single carcinogen treatment; and (iii) the production of foci by single initiation events, we suggest that each proliferatively and phenotypically distinct member of the focus population reflects the occurrence of a lesion at a unique genetic locus during initiation.

Background Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeline for Protein Annotation) that has these capabilities. Results PIPA annotates protein functions by combining the results of multiple programs and databases, such as InterPro and the Conserved Domains Database, into common Gene Ontology (GO) terms. The major algorithms implemented in PIPA are: (1) a profile database generation algorithm, which generates customized profile databases to predict particular protein functions, (2) an automated ontology mapping generation algorithm, which maps various classification schemes into GO, and (3) a consensus algorithm to reconcile annotations from the integrated programs and databases. PIPA's profile generation algorithm is employed to construct the enzyme profile database CatFam, which predicts catalytic functions described by Enzyme Commission (EC) numbers. Validation tests show that CatFam yields average recall and precision larger than 95.0%. CatFam is integrated with PIPA. We use an association rule mining algorithm to automatically generate mappings between terms of two ontologies from annotated sample proteins. Incorporating the ontologies' hierarchical topology into the algorithm increases the number of generated mappings. In particular, it generates 40.0% additional mappings from the Clusters of Orthologous Groups (COG) to EC numbers and a six-fold increase in mappings from COG to GO terms. The mappings to EC numbers show a very high precision (99.8%) and recall (96.6%), while the mappings to GO terms show moderate precision (80.0%) and low recall (33.0%). Our consensus algorithm for GO annotation is based on the computation and propagation of likelihood scores associated with GO terms. The test results suggest that, for a given recall, the application of the consensus algorithm yields higher precision than when consensus is not used. Conclusion The algorithms implemented in PIPA provide automated genome-wide protein function annotation based on reconciled predictions from multiple resources.