Biology subjects

Dziedzic, N.

Publications and source records attributed to Dziedzic, N..

3 recordsLinked to original sources

bioRxiv2024

A domain-swapped CaMKII conformation facilitates linker-mediated allosteric regulation

Memory formation, fertilization, and cardiac function rely on precise Ca2+ signaling and subsequent Ca2+/calmodulin-dependent protein kinase II (CaMKII) activation. Ca2+ sensitivity of the four CaMKII paralogs in mammals has been linked to the length of the variable linker region that is a hot spot for alternative splicing. In this study, we determined that the position of charged residues within the linker modulates the Ca2+/CaM sensitivity. We present an X-ray crystal structure of the full-length CaMKII{delta} holoenzyme consisting of domain-swapped dimers within a dodecameric complex. In this structure, the kinase domain of one subunit is docked onto the hub domain of an adjacent subunit, providing an additional interface within the holoenzyme. Mutations at the hub equatorial and lateral interfaces led to alterations in the stoichiometry of CaMKII holoenzyme as well as Ca2+/CaM sensitivity. Using molecular dynamics (MD) to compare domain-swapped to non-domain-swapped CaMKIIs, we demonstrate that the domain-swapped conformation facilitates an interaction between the calmodulin binding region and the linker region. Based on MD simulations and small-angle X-ray scattering (SAXS) measurements, we propose a model where the position of charges on the linker region drives an interaction with the regulatory segment that modulates the degree of autoinhibition. Finally, we use live-cell imaging to show that the activation profiles we observe in vitro are recapitulated in cells. Our findings provide a new framework for understanding allosteric regulation of CaMKII by the linker region in Ca2+-sensitive cells.

biochemistry↗

bioRxiv2019

Heterogeneity in human hippocampal CaMKII transcripts reveals an allosteric role for the hub domain in activity regulation

Ca2+-calmodulin dependent protein kinase II (CaMKII) plays a central role in Ca2+ signaling throughout the body. Specifically in the hippocampus, CaMKII is required for learning and memory. CaMKII is encoded by four highly conserved genes in vertebrates: , {beta}, {gamma}, and {delta}. AllCaMKIIs are comprised of a kinase domain, regulatory segment, variable linker region, and hub domain responsible for oligomerization. The four genes differ primarily in linker length and composition due to extensive alternative splicing. Here, we unambiguously report the heterogeneity of CaMKII transcripts in 3 complex samples of human hippocampus using Illumina sequencing. Our results show that hippocampal cells contain a diverse collection of 70 CaMKII transcripts from all four CaMKII genes. We characterized the Ca2+/CaM sensitivity of hippocampal CaMKII variants spanning a broad range of linker lengths and compositions. We demonstrate that the effect of the variable linker on Ca2+/CaM sensitivity is conditional on kinase and hub domains. Moreover, we reveal a novel role for the hub domain as an allosteric regulator of kinase activity, which may provide a new pharmacological target for modulating CaMKII activity. Using small angle X-ray scattering and single-particle electron cryo-microscopy, we present evidence for extensive interaction between the kinase and the hub domain, even in the presence of a 30-residue linker. Taken together, we propose that Ca2+/CaM sensitivity in CaMKII is gene-dependent and includes significant contributions from the hub. Our sequencing approach combined with biochemistry provides new insights into understanding the complex pool of endogenous CaMKII. One Sentence SummaryCaMKII is a well-conserved protein that is essential for learning and memory. When CaMKII is mutated in a mouse, this mouse has difficulty learning and remembering how to get through a maze. The hippocampus is the part of the brain required for memory. Here, we used a specific experiment to determine every type of CaMKII that is in a human hippocampus. We found 70 different types and then asked how these differences affect CaMKII function. These data provide evidence that an assembly domain of CaMKII plays an unexpected role regulating its activity. This new finding helps us better understand endogenous CaMKII in the brain and provides a new mechanism for modulating CaMKII activity.

biochemistry↗

bioRxiv2018

Vesicular delivery of the antifungal antibiotics of Lysobacter enzymogenes C3

Lysobacter enzymogenes C3 is a predatory strain of gram-negative gliding bacteria that produces antifungal antibiotics by the polyketide synthetic pathway. Outer membrane vesicles (OMV) are formed as a stress response and can deliver virulence factors to host cells. The production of OMV by C3 and their role in antifungal activity are reported here. Vesicles in the range of 130-150 nm in diameter were discovered in the cell-free supernatants of C3 cultures. These OMV contain molecules characteristic of bacterial outer membranes, such as lipopolysaccharide and phospholipids. In addition, they contain chitinase activity and essentially all of the heat stable antifungal activity in cell supernatants. We show here that C3 OMV can directly inhibit growth of the yeast Saccharomyces cerevisiae as well as the filamentous fungus Fusarium subglutinans. The activity is dependent on physical contact between OMV and the cells. Furthermore, fluorescent lipid labeling of C3 OMV demonstrated transfer of the membrane-associated probe to yeast cells, suggesting the existence of a mechanism of delivery for membrane-associated molecules. Mass spectrometric analysis of C3 OMV extracts indicates the presence of molecules with molecular weights identical to some of the previously identified antifungal products of C3. These data together suggest that OMV act as an important remote mobile component of predation by Lysobacter.\n\nImportanceThe data presented here suggest a newly discovered function of outer membrane vesicles (OMV) that are produced from the outer membrane of the bacterial species Lysobacter enzymogenes C3. We show that these OMV can be released from the surface of the cells to deliver antibiotics to target fungal organisms as a mechanism of killing or growth inhibition. Understanding the role of OMV in antibiotic delivery can generally lead to improved strategies for dealing with antibiotic-resistant organisms. These results also add to the evidence that some bacterially produced antibiotics can be discovered and purified using methods designed for isolation of nanoscale vesicles. Information on these systems can lead to better identification of active molecules or design of delivery vehicles for these molecules.

microbiology↗