Fred J. Stevens

Modification of an Elisa-based procedure for affinity determination: correction necessary for use with bivalent antibody

A recently described procedure for the evaluation of the affinity of monoclonal antibodies [Friguet et al., J. Immun. Meth. 77, 305-319 (1985)] uses an ELISA system to determine the quantity of free antibody present in a mixture of antigen and antibody. However, an intact IgG may bind antigen by either of two binding sites, and an IgG can bind to a solid-phase antigen whether one or two of its binding sites are free. Therefore, this procedure does not directly provide the concn of liganded binding sites, the quantity necessary for calculation of the thermodynamic association constant. A binomial probability distribution relates the fraction of liganded binding sites to the concn of unliganded, singly liganded, and doubly liganded IgG assuming that the binding of each Fab to antigen is independent. Simulated experiments were used to compare the apparent binding characteristics of bivalent IgG and monovalent Fab and to calculate apparent association constants in each case. It was found that the affinity of binding sites on intact IgG was underestimated by a factor of at least 2 and that the error was inversely related to the fraction of liganded binding sites. Binding site affinity of an antibody may be underestimated by several orders of magnitude. On the basis of binomial analysis, it is possible to convert apparent concns of bound IgG to actual concns of liganded binding site resulting in the calculation of valid association constants for intact IgG without alteration of the experimental protocol.

Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions.

MOTIVATION Data that characterize primary and tertiary structures of proteins are now accumulating at a rapid and accelerating rate and require automated computational tools to extract critical information relating amino acid changes with the spectrum of functionally attributes exhibited by a protein. We propose that immunoglobulin-type beta-domains, which are found in approximate 400 functionally distinct forms in humans alone, provide the immense genetic variation within limited conformational changes that might facilitate the development of new computational tools. As an initial step, we describe here an approach based on Support Vector Machine (SVM) technology to identify amino acid variations that contribute to the functional attribute of pathological self-assembly by some human antibody light chains produced during plasma cell diseases. RESULTS We demonstrate that SVMs with selective kernel scaling are an effective tool in discriminating between benign and pathologic human immunoglobulin light chains. Initial results compare favorably against manual classification performed by experts and indicate the capability of SVMs to capture the underlying structure of the data. The data set consists of 70 proteins of human antibody kappa1 light chains, each represented by aligned sequences of 120 amino acids. We perform feature selection based on a first-order adaptive scaling algorithm, which confirms the importance of changes in certain amino acid positions and identifies other positions that are key in the characterization of protein function.

Four structural risk factors identify most fibril-forming kappa light chains.

Antibody light chains (LCs) comprise the most structurally diverse family of proteins involved in amyloidosis. Many antibody LCs incorporate structural features that impair their stability and solubility, leading to their assembly into fibrils and to their subsequent pathological deposition when produced in excess during multiple myeloma and primary amyloidosis. The particular amino acid variations in antibody LCs that account for fibril formation and amyloidogenesis have not been identified. This study focuses on amyloidogenesis within the Kl family of human LCs. Reanalysis of the current database of primary structures of proteins from more than 100 patients who produced Kl LCS, 37 of which were amyloidogenic, reveals apparent structural features that may contribute to amyloidosis. These features include loss of conserved residues or the gain of particular residues through mutation at sites involving a repertoire of approximately 20% of the amino acid positions in the light chain variable domain (VL). Moreover, 80% of all K1 amyloidogenic VLs are identifiable by the presence of at least one of three single-site substitutions or the acquisition of an N-linked glycosylation site through mutations. These findings suggest that it is feasible to predict fibril propensity by analysis of primary structure.

Orchestration of secretory protein folding by ER chaperones.

The endoplasmic reticulum is a major compartment of protein biogenesis in the cell, dedicated to production of secretory, membrane and organelle proteins. The secretome has distinct structural and post-translational characteristics, since folding in the ER occurs in an environment that is distinct in terms of its ionic composition, dynamics and requirements for quality control. The folding machinery in the ER therefore includes chaperones and folding enzymes that introduce, monitor and react to disulfide bonds, glycans, and fluctuations of luminal calcium. We describe the major chaperone networks in the lumen and discuss how they have distinct modes of operation that enable cells to accomplish highly efficient production of the secretome. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.

Inhibition of Amyloid Fiber Assembly by Both BiP and Its Target Peptide

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.

Tertiary structure of human lambda 6 light chains.

AL amyloidosis is a disease process characterized by the pathologic deposition of monoclonal light chains in tissue. To date, only limited information has been obtained on the molecular features that render such light chains amyloidogenic. Although protein products of the major human V kappa and V lambda gene families have been identified in AL deposits, one particular subgroup--lambda 6--has been found to be preferentially associated with this disease. Notably, the variable region of lambda 6 proteins (V lambda 6) has distinctive primary structural features including the presence in the third framework region (FR3) of two additional amino acid residues that distinguish members of this subgroup from other types of light chains. However, the structural consequences of these alterations have not been elucidated. To determine if lambda 6 proteins possess unique tertiary structural features, as compared to light chains of other V lambda subgroups, we have obtained x-ray diffraction data on crystals prepared from two recombinant V lambda 6 molecules. These components, isolated from a bacterial expression system, were generated from lambda 6-related cDNAs cloned from bone marrow-derived plasma cells from a patient (Wil) who had documented AL amyloidosis and another (Jto) with multiple myeloma and tubular cast nephropathy, but no evident fibrillar deposits. The x-ray crystallographic analyses revealed that the two-residue insertion located between positions 68 and 69 (not between 66 and 67 as previously surmised) extended an existing loop region that effectively increased the surface area adjacent to the first complementarity determining region (CDR1). Further, an unusual interaction between the Arg 25 and Phe 2 residues commonly found in lambda 6 molecules was noted. However, the structures of V lambda 6 Wil and Jto also differed from each other, as evidenced by the presence in the latter of certain ionic and hydrophobic interactions that we posit increased protein stability and thus prevented amyloid formation.

Bence Jones proteins: a powerful tool for the fundamental study of protein chemistry and pathophysiology.

Bence Jones proteins are typically found in patients with monoclonal plasma cell or related B-cell immunoproliferative disorders. Because of their monoclonal origin and resulting chemical homogeneity much of the fundamental information on immunoglobulin structure came initially from their analysis. Amino acid analyses of these components revealed an N-terminal variable (V) and C-terminal constant (C) domain as well as the existence within the V domain of hypervariable segments that account for the specificity and diversity of antibodies. Over the past three decades, the primary structures of hundreds of light chains (complete and partial), from human and other sources, have been determined, aligned, and archived. Bence Jones proteins and V{sub L} dimers were the crystallizable homogeneous proteins which provided much of the early three-dimensional conformational data that helped explain the structural basis of antibody function. Remarkably, a single Bence Jones protein in two solvent systems (low and high ionic strength) exhibited significant differences in the interactions of the two monomeric subunits comprising the dimer, resulting in substantial variation in the structure of the antigen combining site under the two solution conditions. This observation led to a prediction that heterogeneity of domain interactions may contribute to antibody-antigen interactions. Experimental support for this hypothesis has come from comparisons of the detailed structures of antibody-antigen complexes. The interactions at the interface of the V{sub L} dimer are a function of primary structure and solution conditions. Study of these interactions has led to new information on the relationship between protein structure and function and, as discussed below, can account for specific pathophysiological properties associated with Bence Jones proteins.

Pathogenic light chains and the B-cell repertoire

Dysfunctional immunoglobulins (Igs) that are prone to aggregation are unavoidably generated by the diverse repertoire of B cells. Here, Fred Stevens and Yair Argon analyse the patterns of mutations that lead to pathological Igs, account for non-random mutations in human Ig sequences and suggest the exertion of selective forces, which contribute to determining and limiting the Ig repertoire.

Hypothetical structure of human serum amyloid A protein

The proteins known as serum amyloid A (SAA) play major, but relatively uncharacterized, roles in the acute phase response and are important components of the innate immune system of humans and probably all vertebrates. N-terminal fragments of the inducible isoforms, SAA1 and SAA2, are the major constituents of fibrils formed during secondary or reactive amyloidosis. Little is known about the structure of SAA beyond secondary structure analyses and circular dichroism spectroscopic data indicating significant alpha helix conformation. Analysis of the primary structure of human SAA indicates probable homology to the N-terminal domain of hemocyanins of arthropods and suggests that approximately 80% of the molecule may consist of a helical bundle with the remaining portion of the C-terminus potentially disordered. This model of SAA suggests that proposed binding sites for laminin, fibronectin, and calcium are segregated to one face of the molecule and that the heparin/heparan binding site is found in the putatively disordered region of the protein. It is possible that removal of the N-terminal 76 amino acid fragment by proteolytic cleavage found generates an unstable entity that undergoes a helix to beta strand transition analogous to the fibril process of A-beta and prion peptides.

Somatic Mutations of the L12a Gene in V-κ1 Light Chain Deposition Disease : Potential Effects on Aberrant Protein Conformation and Deposition

Light chain deposition disease (LCDD) and light chain amyloidosis (AL) are disorders of monoclonal immunoglobulin deposition in which normally soluble serum precursors form insoluble deposits in tissues. A common feature in both is the clonal proliferation of B-cells that produce pathogenic light chains. However, the deposits in LCDD differ from those in AL in that they are ultrastructurally granular rather than fibrillar and do not bind Congo red or colocalize with amyloid P component or apolipoprotein E. The reason(s) for their differences are unknown but are likely multifactorial and related to their protein conformation and their interaction with other molecules and tissue factors in the microenvironment. Knowledge of the primary structure of the light chains in LCDD is very limited. In the present study two new kappa(1) light chains from patients with LCDD are described and compared to seven other reported kappa-LCDD proteins. The N-terminal amino acid sequences of light chain GLA extracted from the renal biopsy and light chain CHO from myocardial tissue were each identical to the respective light chains isolated from the urines and to the V-region amino acid sequences translated from the cloned cDNAs obtained from bone marrow cells. The germline V-region sequences, determined from the genomic DNA in both and in MCM, a previously reported kappa(1) LCDD light chain, were identical and related to the L12a germline gene. The expressed light chains in all three exhibit amino acid substitutions that arise from somatic mutation and result in increased hydrophobicity with the potential for protein destabilization and disordered conformation.