Sharon G. Wolf

Structure of the alpha beta tubulin dimer by electron crystallography.

The αβ tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is non-exchangeable when it is bound in the α subunit, or N site, and exchangeable when bound in the β subunit, or E site. The α- and β-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of post-translational modifications. Limited sequence homology has been found with the proteins FtsZ and Misato, which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the αβ tubulin dimer fitted to a 3.7-Å density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of α- and β-tubulin are basically identical: each monomer is formed by a core of two β-sheets surrounded by α-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.

DNA protection by stress-induced biocrystallization

The crystalline state is considered to be incompatible with life. However, in living systems exposed to severe environmental assaults, the sequestration of vital macromolecules in intracellular crystalline assemblies may provide an efficient means for protection. Here we report a generic defence strategy found in Escherichia coli, involving co-crystallization of its DNA with the stress-induced protein Dps,. We show that when purified Dps and DNA interact, extremely stable crystals form almost instantaneously, within which DNA is sequestered and effectively protected against varied assaults. Crystalline structures with similar lattice spacings are formed in E. coli in which Dps is slightly over expressed, as well as in starved wild-type bacteria. Hence, DNA–Dps co-crystallization is proposed to represent a binding mode that provides wide-range protection of DNA by sequestration. The rapid induction and large-scale production of Dps in response to stress, as well as the presence of Dps homologues in many distantly related bacteria, indicate that DNA protection by biocrystallization may be crucial and widespread in prokaryotes.

Supramolecular gel based on a perylene diimide dye: multiple stimuli responsiveness, robustness, and photofunction.

Design of an extensive supramolecular three-dimensional network that is both robust and adaptive represents a significant challenge. The molecular system PP2b based on a perylene diimide chromophore (PDI) decorated with polyethylene glycol groups self-assembles in aqueous media into extended supramolecular fibers that form a robust three-dimensional network resulting in gelation. The self-assembled systems were characterized by cryo-TEM, cryo-SEM, and rheological measurements. The gel possesses exceptional robustness and multiple stimuli-responsiveness. Reversible charging of PP2b allows for switching between the gel state and fluid solution that is accompanied by switching on and off the materials birefringence. Temperature triggered deswelling of the gel leads to the (reversible) expulsion of a large fraction of the aqueous solvent. The dual sensibility toward chemical reduction and temperature with a distinct and interrelated response to each of these stimuli is pertinent to applications in the area of adaptive functional materials. The gel also shows strong absorption of visible light and good exciton mobility (elucidated using femtosecond transient absorption), representing an advantageous light harvesting system.

Regulated phase transitions of bacterial chromatin: a non‐enzymatic pathway for generic DNA protection

The enhanced stress resistance exhibited by starved bacteria represents a central facet of virulence, since nutrient depletion is regularly encountered by pathogens in their natural in vivo and ex vivo environments. Here we explore the notion that the regular stress responses, which are mediated by enzymatically catalyzed chemical transactions and promote endurance during the logarithmic growth phase, can no longer be effectively induced during starvation. We show that survival of bacteria in nutrient‐depleted habitats is promoted by a novel strategy: finely tuned and fully reversible intracellular phase transitions. These non‐enzymatic transactions, detected and studied in bacteria as well as in defined in vitro systems, result in DNA sequestration and generic protection within tightly packed and highly ordered assemblies. Since this physical mode of defense is uniquely independent of enzymatic activity or de novo protein synthesis, and consequently does not require energy consumption, it promotes virulence by enabling long‐term bacterial endurance and enhancing antibiotic resistance in adverse habitats.

Pathway-dependent self-assembly of perylene diimide/peptide conjugates in aqueous medium.

Most molecular self-assembly strategies involve equilibrium systems, leading to a single thermodynamic product as a result of weak, reversible non-covalent interactions. Yet, strong non-covalent interactions may result in non-equilibrium self-assembly, in which structural diversity is achieved by forming several kinetic products based on a single covalent building block. We demonstrate that well-defined amphiphilic molecular systems based on perylene diimide/peptide conjugates exhibit kinetically controlled self-assembly in aqueous medium, enabling pathway-dependent assembly sequences, in which different organic nanostructures are evolved in a stepwise manner. The self-assembly process was characterized using UV/Vis circular dichroism (CD) spectroscopy, and cryogenic transmission electron microscopy (cryo-TEM). Our findings show that pathway-controlled self-assembly may significantly broaden the methodology of non-covalent synthesis.

Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL

In a newly isolated temperature-sensitive lethal Escherichia coli mutant affecting the chaperonin GroEL, we observed wholesale aggregation of newly translated proteins. After temperature shift, transcription, translation, and growth slowed over two to three generations, accompanied by filamentation and accretion (in ≈2% of cells) of paracrystalline arrays containing mutant chaperonin complex. A biochemically isolated inclusion body fraction contained the collective of abundant proteins of the bacterial cytoplasm as determined by SDS/PAGE and proteolysis/MS analyses. Pulse–chase experiments revealed that newly made proteins, but not preexistent ones, were recruited to this insoluble fraction. Although aggregation of “stringent” GroEL/GroES-dependent substrates may secondarily produce an “avalanche” of aggregation, the observations raise the possibility, supported by in vitro refolding experiments, that the widespread aggregation reflects that GroEL function supports the proper folding of a majority of newly translated polypeptides, not just the limited number indicated by interaction studies and in vitro experiments.

Nucleoid restructuring in stationary‐state bacteria

The textbook view of the bacterial cytoplasm as an unstructured environment has been overturned recently by studies that highlighted the extent to which non‐random organization and coherent motion of intracellular components are central for bacterial life‐sustaining activities. Because such a dynamic order critically depends on continuous consumption of energy, it cannot be perpetuated in starved, and hence energy‐depleted, stationary‐state bacteria. Here, we show that, at the onset of the stationary state, bacterial chromatin undergoes a massive reorganization into ordered toroidal structures through a process that is dictated by the intrinsic properties of DNA and by the ubiquitous starvation‐induced DNA‐binding protein Dps. As starvation proceeds, the toroidal morphology acts as a structural template that promotes the formation of DNA–Dps crystalline assemblies through epitaxial growth. Within the resulting condensed assemblies, DNA is effectively protected by means of structural sequestration. We thus conclude that the transition from bacterial active growth to stationary phase entails a co‐ordinated process, in which the energy‐dependent dynamic order of the chromatin is sequentially substituted with an equilibrium crystalline order.

Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis.

The eukaryotic cytoplasmic chaperonin containing TCP-1 (CCT) is a hetero-oligomeric complex that assists the folding of actins, tubulins and other proteins in an ATP-dependent manner. To understand the allosteric transitions that occur during the functional cycle of CCT, we imaged the chaperonin complex in the presence of different ATP concentrations. Labeling by monoclonal antibodies that bind specifically to the CCTα and CCTδ subunits enabled alignment of all the CCT subunits of a given type in different particles. The analysis shows that the apo state of CCT has considerable apparent conformational heterogeneity that decreases with increasing ATP concentration. In contrast with the concerted allosteric switch of GroEL, ATP-induced conformational changes in CCT are found to spread around the ring in a sequential fashion that may facilitate domain-by-domain substrate folding. The approach described here can be used to unravel the allosteric mechanisms of other ring-shaped molecular machines.

Control over Self-Assembly through Reversible Charging of the Aromatic Building Blocks in Photofunctional Supramolecular Fibers

Self-assembling systems, whose structure and function can be reversibly controlled in situ are of primary importance for creating multifunctional supramolecular arrays and mimicking the complexity of natural systems. Herein we report on photofunctional fibers self-assembled from perylene diimide cromophores, in which interactions between aromatic monomers can be attenuated through their reduction to anionic species that causes fiber fission. Oxidation with air restores the fibers. The sequence represents reversible supramolecular depolymerization-polymerization in situ and is accompanied by a reversible switching of photofunction.

SP1 protein-based nanostructures and arrays.

Controlled formation of complex nanostructures is one of the main goals of nanoscience and nanotechnology. Stable Protein 1 (SP1) is a boiling-stable ring protein complex, 11 nm in diameter, which self-assembles from 12 identical monomers. SP1 can be utilized to form large ordered arrays; it can be easily modified by genetic engineering to produce various mutants; it is also capable of binding gold nanoparticles (GNPs) and thus forming protein-GNP chains made of alternating SP1s and GNPs. We report the formation and the protocols leading to the formation of those nanostructures and their characterization by transmission electron microscopy, atomic force microscopy, and electrostatic force microscopy. Further control over the GNP interdistances within the protein-GNP chains may lead to the formation of nanowires and structures that may be useful for nanoelectronics.