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Dive into the research topics where Zachary T. Graber is active.

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Featured researches published by Zachary T. Graber.


Chemistry and Physics of Lipids | 2012

Phosphatidylinositol-4,5-bisphosphate ionization and domain formation in the presence of lipids with hydrogen bond donor capabilities.

Zachary T. Graber; Zhiping Jiang; Arne Gericke; Edgar E. Kooijman

Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P(2)) is an important lipidic signaling molecule that is involved in a broad range of cellular processes. Its interaction with proteins and its lateral distribution are governed by the ionization state of the phosphomonoester groups and its ability to form intra- and intermolecular hydrogen bonds. In this study we have investigated the ionization state of PI(4,5)P(2) in ternary lipid vesicle systems that contain in addition to PI(4,5)P(2) and phosphatidylcholine (PC) either phosphatidylethanolamine (PE), phosphatidylserine (PS) or phosphatidylinositol (PI). In the presence of PE we find an increased ionization of PI(4,5)P(2), which can be attributed to increased deprotonation due to hydrogen bond formation between PE and the PI(4,5)P(2) phosphomonoester groups. However, the effect of PE on PI(4,5)P(2) ionization is significantly smaller than it had been found previously for phosphatidic acid in the presence of PE (Kooijman et al., 2005). The reduced impact of PE on PI(4,5)P(2) ionization can be attributed to competing intramolecular hydrogen bond formation between the phosphomonoester groups and neighboring hydroxyl groups. It is noteworthy that the presence of PE affects more strongly the ionization of the 5-phosphate group than that of the 4-phosphate, suggesting that the interaction of PE with the 5-phosphate is stronger. In PI(4,5)P(2)/PS/PC lipid vesicles, the presence of PS was expected to yield an increased protonation of the PI(4,5)P(2) phosphomonoester groups due to a decreased interfacial pH as a result of the increased negative interfacial charge. However, the effect of PS on PI(4,5)P(2) ionization is only minor, potentially suggesting that PS and PI(4,5)P(2) are demixed. The PI(4,5)P(2)/PI/PC vesicle system was characterized by a surprising mixing behavior that has potentially far reaching consequences: fluorescence microscopy measurements of giant unilammellar vesicles composed of PI(4,5)P(2)/PI/PC at physiological concentrations show that PI and PI(4,5)P(2) form macroscopic, fluid phase domains in contact with a fluid PC rich phase (fluid/fluid demixing). Despite the fact that PI and PI(4,5)P(2) co-localize, the effect of PI on PI(4,5)P(2) ionization behavior is only noticeable above pH 7. Apparently two opposing effects lead to the observed behavior: Due to the presence of the anionic PI, the interfacial pH drops, which is expected to lead to an enhanced protonation of the PI(4,5)P(2) phosphomonoester groups. In turn, hydrogen bond formation between PI and PI(4,5)P(2) would lead to the opposite, i.e. increased deprotonation of the phosphomonoester group. Apparently these two effects compensate each other for pH values smaller than about 7, while for higher pH values the increased interfacial pH in the presence of PI has a stronger impact than PI/PI(4,5)P(2) hydrogen bond formation. The cooperative formation of PI/PI(4,5)P(2) mixed domains has potentially important ramifications for the spatial organization of phosphoinositide mediated signaling events.


Chemistry and Physics of Lipids | 2014

Phosphatidylinositol-4,5-bisphosphate ionization in the presence of cholesterol, calcium or magnesium ions.

Zachary T. Graber; Arne Gericke; Edgar E. Kooijman

Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) is an important signaling lipid and plays a crucial role in a wide variety of cellular processes by interacting with protein targets and localizing proteins at the plasma membrane. These interactions are strongly influenced by the lateral distribution of PI(4,5)P2 as well as its ionization state. The characterization of the PI(4,5)P2 ionization state provides important information about how PI(4,5)P2 interacts with other membrane resident or associated chemical species. In this study we have used solid-state MAS (31)P NMR to investigate the interactions of PI(4,5)P2 with potential cluster promoting agents, divalent cations and cholesterol. Both Ca(2+) and cholesterol were found previously to promote formation of local PI(4,5)P2 clusters in vitro. The NMR approach allows us to probe independently the ionization state of PI(4,5)P2 two phosphomonoester groups. We investigated mixed phosphatidylcholine (PC)/PI(4,5)P2 multilamellar vesicles in the presence of micro and millimolar concentrations of Ca(2+) and Mg(2+). We found that both cations lead to an increased downfield chemical shift of the PI(4,5)P2 phosphomonoester peaks, indicating an increased ionization in the presence of the divalent cations. Ca(2+) has a much larger effect on PI(4,5)P2 as compared to Mg(2+) at similar concentrations. Physiological concentrations of Ca(2+) are significantly lower than those found for Mg(2+) and the comparison of the PI(4,5)P2 ionization in the presence of Ca(2+) and Mg(2+) at physiological concentrations resulted in similar charges of the phosphomonoester groups for both cations. PI(4,5)P2 was also examined with vesicles containing cholesterol since cholesterol has been shown to promote PI(4,5)P2 clustering. In the presence of 40 mol% cholesterol, the PI(4,5)P2 phosphomonoester (31)P NMR peaks shifted slightly downfield, indicating a small increase in charge. Previously published data suggest that PI(4,5)P2 is capable of forming an intra- and intermolecular hydrogen bond network, which leads to a reduction of the charge at the phosphomonoester groups through dissipation of the charge across the bilayer/water interface. We hypothesize that cholesterol participates in this intermolecular hydrogen bond network, resulting in a stabilization of PI(4,5)P2 enriched domains due an increased spacing between the PI(4,5)P2 headgroup. We also examined the cumulative effects of cholesterol combined with the divalent cations, phosphatidylethanolamine (PE), and phosphatidylinositol (PI), separately. The combination of cholesterol and divalent cations results in an additive effect on PI(4,5)P2 ionization, while the effect of cholesterol on PI(4,5)P2 ionization is reduced in the presence of PE or PI.


Biochimica et Biophysica Acta | 2017

Magic angle spinning 31 P NMR spectroscopy reveals two essentially identical ionization states for the cardiolipin phosphates in phospholipid liposomes

Edgar E. Kooijman; L.A. Swim; Zachary T. Graber; Yulia Y. Tyurina; Hülya Bayır; Valerian E. Kagan

Specific membrane lipid composition is crucial for optimized structural and functional organization of biological membranes. Cardiolipin is a unique phospholipid and important component of the inner mitochondrial membrane. It is involved in energy metabolism, inner mitochondrial membrane transport, regulation of multiple metabolic reactions and apoptotic cell death. The physico-chemical properties of cardiolipin have been studied extensively but despite all these efforts there is still lingering controversy regarding the ionization of the two phosphate groups of cardiolipin. Results obtained in the 1990s and early 2000s suggested that cardiolipin has two disparate pKa values where one of the protons was proposed to be stabilized by an intramolecular hydrogen bond. This has led to extensive speculations on the roles of these two putative ionization states of cardiolipin in mitochondria. More recently the notion of two pKa values has been challenged and rejected by several groups. These studies relied on external measurements of proton adsorption or electrophoretic mobility of membranes but did not take into account the low pH phase behavior and chemical stability of cardiolipin. Here we used 31P NMR to show that in the physiologically relevant membrane phospholipid environment, cardiolipin carries two negative charges at physiological pH. We additionally demonstrate the pH dependent phase behavior and chemical stability of cardiolipin containing membranes.


RSC Advances | 2015

Competitive cation binding to phosphatidylinositol-4,5-bisphosphate domains revealed by X-ray fluorescence

Zachary T. Graber; Wenji Wang; Gautam Singh; Ivan Kuzmenko; David Vaknin; Edgar E. Kooijman

Phosphatidylinositol-4,5-bisphosphate (PIP2) is an important signaling phospholipid in the inner leaflet of the cell membrane. Due to the high negative charge of its headgroup, PIP2 strongly interacts with cellular cations. We have used synchrotron diffraction and fluorescence techniques to determine preferential cation binding to two-dimensional PIP2 templates. The natural, highly unsaturated PIP2 is manipulated as a Langmuir monolayer on a physiological buffer containing 100 mM KCl and varying amounts of Ca2+ and Mg2+. X-ray fluorescence shows an 800% surface enhancement in K+ concentration (bound to PIP2) compared to bulk concentration. Adding physiological levels of Ca2+( 1–100 μM) results in gradual replacement of K+ by Ca2+ ions, leading to a significant change in the organization of the PIP2 model membrane, while higher concentrations (100–1000 μM) lead to three orders of magnitude increase in surface [Ca2+]. Similar experiments with Mg2+ ions also show strong ion binding to PIP2 at physiological levels (1 mM) with a lesser structural effect. For mixed solutions of Mg2+ and Ca2+ we find that Ca2+ occupies the majority of binding sites. Remarkably we find that, with both 1 mM Mg2+ and 1 mM Ca2+ in the subphase there is still a 400% surface enrichment of K+ ions at the headgroup region.


Methods of Molecular Biology | 2013

Ionization behavior of polyphosphoinositides determined via the preparation of pH titration curves using solid-state 31P NMR.

Zachary T. Graber; Edgar E. Kooijman

Detailed knowledge of the degree of ionization of lipid titratable groups is important for the evaluation of protein-lipid and lipid-lipid interactions. The degree of ionization is commonly evaluated by acid-base titration, but for lipids localized in a multicomponent membrane interface this is not a suitable technique. For phosphomonoester-containing lipids such as the polyphosphoinositides, phosphatidic acid, and ceramide-1-phosphate, this is more conveniently accomplished by (31)P NMR. Here, we describe a solid-state (31)P NMR procedure to construct pH titration curves to determine the degree of ionization of phosphomonoester groups in polyphosphoinositides. This procedure can also be used, with suitable sample preparation conditions, for other important signaling lipids. Access to a solid-state, i.e., magic angle spinning, capable NMR spectrometer is assumed. The procedures described here are valid for a Bruker instrument, but can be adapted for other spectrometers as needed.


bioRxiv | 2018

Cell membranes resist flow

Zheng Shi; Zachary T. Graber; Tobias Baumgart; Howard A. Stone; Adam E. Cohen

The fluid-mosaic model posits a liquid-like plasma membrane, which can flow in response to tension gradients. It is widely assumed that membrane flow transmits local changes in membrane tension across the cell in milliseconds. This conjectured signaling mechanism has been invoked to explain how cells coordinate changes in shape, motility, and vesicle fusion, but the underlying propagation has never been observed. Here we show that propagation of membrane tension occurs quickly in cell-attached blebs, but is largely suppressed in intact cells. The failure of tension to propagate in cells is explained by a fluid dynamical model that incorporates the flow resistance from cytoskeleton-bound transmembrane proteins. In primary endothelial cells, local increases in membrane tension lead only to local activation of mechanosensitive ion channels and to local vesicle fusion. Thus membrane tension is not a mediator of long-range intra-cellular signaling, but local variations in tension mediate distinct processes in sub-cellular domains.


Langmuir | 2018

Dendrimersomes exhibit lamellar-to-sponge phase transitions

Samantha E. Wilner; Qi Xiao; Zachary T. Graber; Samuel E. Sherman; Virgil Percec; Tobias Baumgart

Lamellar to nonlamellar membrane shape transitions play essential roles in key cellular processes, such as membrane fusion and fission, and occur in response to external stimuli, including drug treatment and heat. A subset of these transitions can be modeled by means of thermally inducible amphiphile assemblies. We previously reported on mixtures of hydrogenated, fluorinated, and hybrid Janus dendrimers (JDs) that self-assemble into complex dendrimersomes (DMSs), including dumbbells, and serve as promising models for understanding the complexity of biological membranes. Here we show, by means of a variety of complementary techniques, that DMSs formed by single JDs or by mixtures of JDs undergo a thermally induced lamellar-to-sponge transition. Consistent with the formation of a three-dimensional bilayer network, we show that DMSs become more permeable to water-soluble fluorophores after transitioning to the sponge phase. These DMSs may be useful not only in modeling isotropic membrane rearrangements of biological systems but also in drug delivery since nonlamellar delivery vehicles can promote endosomal disruption and cargo release.


Physical Chemistry Chemical Physics | 2017

Cations induce shape remodeling of negatively charged phospholipid membranes

Zachary T. Graber; Zheng Shi; Tobias Baumgart


Biophysical Journal | 2018

Lipid-Gel Model of Biological Membranes

Zheng Shi; Zachary T. Graber; Tobias Baumgart; Howard A. Stone; Adam E. Cohen


Biophysical Journal | 2018

Effect of H-Bond Donor Lipids on Phosphatidylinositol-3,4,5-Trisphosphate Ionization and Clustering

Zachary T. Graber; Joseph Thomas; Emily Johnson; Arne Gericke; Edgar E. Kooijman

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Arne Gericke

Worcester Polytechnic Institute

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Tobias Baumgart

University of Pennsylvania

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Ivan Kuzmenko

Argonne National Laboratory

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