Depending on the stimuli they encounter, B lymphocytes engage in signaling events that lead to immunity or tolerance. Both responses are mediated through antigen interactions with the B cell antigen receptor (BCR). Antigen valency is thought to be an important parameter in B cell signaling, but systematic studies are lacking. To explore this issue, we synthesized multivalent ligands of defined valencies using the ring-opening metathesis polymerization (ROMP). When mice are injected with multivalent antigens generated by ROMP, only those of high valencies elicit antibody production. These results indicate that ligands synthesized by ROMP can activate immune responses in vivo. All of the multivalent antigens tested activate signaling through the BCR. The ability of antigens to cluster the BCR, promote its localization to membrane microdomains, and augment intracellular Ca2+ concentration increases as a function of antigen valency. In contrast, no differences in BCR internalization were detected. Our results indicate that differences in the antigenicity of BCR ligands are related to their ability to elicit increases in intracellular Ca2+ concentration. Finally, we observed that unligated BCRs cluster with BCRs engaged by multivalent ligands, a result that suggests that signals mediated by the BCR are amplified through receptor arrays. Our data suggest a link between the mechanisms underlying signal initiation by receptors that must respond with high sensitivity.

bZip proteins contain a bipartite DNA-binding motif consisting of a "leucine zipper" dimerization domain and a highly charged "basic region" that directly contacts DNA. These transcription factors form dimeric complexes with each monomer recognizing half of a symmetric or nearly symmetric DNA site. We have found that the bZip protein GCN4 can also bind with high affinity to DNA sites containing only a single GCN4 consensus half-site. Because several recent lines of evidence have suggested a role for monomeric DNA binding by bZip proteins, we investigated the structure of the GCN4.half-site complex. Quantitative DNA binding and affinity cleaving studies support a model in which GCN4 binds as a dimer, with one monomer making specific contacts to the consensus half-site and the other monomer forming nonspecific contacts that are nonetheless important for binding affinity. We also examined the folding transition induced in the basic regions of this complex upon binding DNA. Circular dichroism (CD) studies demonstrate that the basic regions of both monomers are helical, suggesting that a protein folding transition may be required for both specific and nonspecific DNA binding by GCN4.

Basic region leucine zipper (bZip) proteins contain a bipartite DNA-binding motif consisting of a coiled-coil leucine zipper dimerization domain and a highly charged basic region that directly contacts DNA. The basic region is largely unfolded in the absence of DNA, but adopts a helical conformation upon DNA binding. Although a coil → helix transition is entropically unfavorable, this conformational change positions the DNA-binding residues appropriately for sequence-specific interactions with DNA. The N-terminal residues of the GCN4 DNA-binding domain, DPAAL, make no DNA contacts and are not part of the conserved basic region, but are nonetheless important for DNA binding. Asp and Pro are often found at the N-termini of ␣-helices, and such N-capping motifs can stabilize ␣-helical structure. In the present study, we investigate whether these two residues serve to stabilize a helical conformation in the GCN4 basic region, lowering the energetic cost for DNA binding. Our results suggest that the presence of these residues contributes significantly to helical structure and to the DNA-binding ability of the basic region in the absence of the leucine zipper. Similar helix-capping motifs are found in approximately half of all bZip domains, and the implications of these findings for in vivo protein function are discussed.

This article outlines the recent transformation of an intermediate undergraduate organic synthesis laboratory course at the University of Wisconsin–Madison. This course has had a unique design for over 30 years, with structured experiments performed in the teaching laboratory only for the first half of the course. In the second half of the course, students are assigned to projects in graduate research laboratories. The classroom component of the course, however, did not provide students with many of the skills essential for success in the research laboratory. Over the academic years 2003–2005, we systematically changed the classroom and laboratory components of this course so that it now provides experience using modern chemistry experimental techniques and chemical information resources, instruction in scientific writing and the use of chemical drawing software, and awareness of basic scientific ethics. Here, we outline our rationale behind each course component change, describe how the changes were implemented, and discuss how the effects on student learning were assessed. Overall, these changes have been greeted with enthusiasm by our students, faculty, and staff, and we believe this course provides a curricular model exportable to other chemistry departments.

Basic-region leucine zipper (bZip) proteins contain a bipartite DNA-binding motif consisting of a leucine zipper dimerization domain and a basic region that directly contacts DNA. In all naturally occurring bZip proteins, the basic region is positioned N-terminal to the leucine zipper. We have designed a series of model bZip peptides in which the basic region of the yeast transcriptional activator GCN4 is placed C-terminal to its leucine zipper. DNA-binding studies demonstrate that the optimal reverse GCN4 (rGCN4) peptide is able to bind specifically and with wild-type affinity to DNA despite this unnatural arrangement of the two subdomains. These results suggest that a thermodynamic basis for the observed N-terminal positioning of the basic region relative to the dimerization domain is unlikely.