Bence Jones KWR protein structures determined by X-ray crystallography

Abstract

A Bence Jones protein isolated in the early 1960s from a patient (initials KWR) suffering from plasma-cell dyscrasia was crystallized and its structure was analyzed in four different unit cells by X-ray diffraction. The final models of the molecule in all crystal forms were virtually the same, although the elbow angles relating the constant and variable domains of the Bence Jones dimers varied over a range of 10 . The tetragonal form had an R factor of 22.6% and an R free of 28.3% at 2.2 Å resolution. Phosphate or sulfate ions (depending on the crystallization conditions) were found in the antigen-combining sites in all crystals, as well as an unidentified ligand tightly bound in the hydrophobic 'deep pocket' beneath the antigen-binding site. The ligand was treated as a phenol molecule. Two trigonal crystal forms were among those solved. One was grown at pH 4.0 and the other was only obtained after sitting for more than eight months at room temperature. The latter crystal was composed of molecules that were degraded in their constant domains. Both low pH and proteolytic degradation of constant domains are known to promote the polymerization of some Bence Jones proteins into amyloid fibrils. Indeed, in both trigonal crystal forms the molecules are organized with pseudo-hexagonal symmetry about the unique crystallographic axes in a manner suggestive of such fibrils. The arrangement of Bence Jones dimers is also consistent with other observations regarding Bence Jones amyloid-fibril structure and current models. PDB References: Bence Jones KWR protein, P3 1 21, 2omb, r2ombsf; P3 2 21, 2old, r2oldsf; P4 3 2 1 2, 2omn, r2omnsf.

Formation of Amyloid Fibers by Monomeric Light Chain Variable Domains

“…In full-length LCs, V L s are connected to C L s through a joining (J) segment, which provides the domains with the flexibility to acquire conformations independent of each other. Such an architecture of the protein does not impose a particular orientation on V L s relative to connected C L s, as affirmed by the existence of several crystal structures (42,52,53). Therefore, a dimer of V L s maintains the ability to disassociate into amyloid-prone V L monomers, while still covalently attached to C L s. This flexibility explains why amyloid fibers of immunoglobulin can consist of fulllength LCs, just their V L s, or both.…”

A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring λ6 Light-Chain Fibrillogenesis

“…In this regard, it is noted that fibrillogenesis closely resembles the crystallization process due to similarities in the nucleation-dependent kinetics of fibril formation in vitro and the requirement of a critical protein concentration, below which polymerization cannot occur. 28 A salient feature of our results is the presence of a monomer in the C222 1 structure, which suggests a lower affinity in the V L -V L interactions for the P7S mutant. Moreover, the conformational change at the sheet switch in P7S promoted the establishment of three additional hydrogen bonds between Ser7 of the N-terminus and Ser21 of β-strand B, thereby increasing the intramolecular interactions with this strand and decreasing the interaction with the Cterminal region (Fig.…”

Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain

“…Although our experiments were performed using only V L s rather than full-length LCs, the ligand-binding site between V L s is maintained in full-length LCs. While full-length LCs are disulfide linked at their C L C-termini, crystal structures indicate that the conformation of V L s is independent of connected constant domains ( Ely et al, 1989 ; Terzyan et al, 2003 ; Makino et al, 2007 ). In full-length LCs, the joining (J) segment between V L s and C L s provides the flexibility for V L s to maintain the same hydrophobic cavity as that seen in the V L homo-dimer alone.…”