Biomedical subjects

Ben de Kruijff

Publications and source records attributed to Ben de Kruijff.

At least 37 records · Page 2Linked to original sources

PubMed2004

Molecular architecture of nanocapsules, bilayer-enclosed solid particles of Cisplatin.

Cisplatin nanocapsules represent a lipid formulation of the anticancer drug cis-diamminedichloroplatinum(II) (cisplatin) characterized by an unprecedented cisplatin-to-lipid ratio and exhibiting strongly improved cytotoxicity against tumor cells in vitro as compared to the free drug (Burger, K. N. J., et al. Nat. Med. 2002, 8, 81-84). Cisplatin nanocapsules are prepared by the repeated freezing and thawing of an equimolar dispersion of phosphatidylserine (PS) and phosphatidylcholine (PC) in a concentrated aqueous solution of cisplatin. Here, the molecular architecture of these novel nanostructures was elucidated by solid-state NMR techniques. 15N NMR and 2H NMR spectra of nanocapsules containing 15N- and 2H-labeled cisplatin, respectively, demonstrated that the core of the nanocapsules consists of solid cisplatin devoid of free water. Magic-angle spinning 15N NMR showed that approximately 90% of the cisplatin in the core is present as the dichloro species. The remaining 10% was accounted for by a newly discovered dinuclear Pt compound that was identified as the positively charged chloride-bridged dimer of cisplatin. NMR techniques sensitive to lipid organization, 31P NMR and 2H NMR, revealed that the cisplatin core is coated by phospholipids in a bilayer configuration and that the interaction between solid core and bilayer coat exerts a strong ordering effect on the phospholipid molecules. Compared to phospholipids in liposomal membranes, the motion of the phospholipid headgroups is restricted and the ordering of the acyl chains is increased, particularly in PS. The implications of these findings for the structural organization, the mechanism of formation, and the mode of action of cisplatin nanocapsules are discussed.

Antineoplastic Agents↗

PubMed2004

Resistance of Gram-positive bacteria to nisin is not determined by lipid II levels.

Lipid II is essential for nisin-mediated pore formation at nano-molar concentrations. We tested whether nisin resistance could result from different Lipid II levels, by comparing the maximal Lipid II pool in Micrococcus flavus (sensitive) and Listeria monocytogenes (relatively insensitive) and their nisin-resistant variants, with a newly developed method. No correlation was observed between the maximal Lipid II pool and nisin sensitivity, as was further corroborated by using spheroplasts of nisin-resistant and wild-type strains of M. flavus, which were equally sensitive to nisin.

Anti-Bacterial Agents↗

PubMed2004

Assembly and stability of nisin-lipid II pores.

The peptide antibiotic nisin was the first reported example of an antibiotic that kills bacteria via targeted pore formation. The specific target of nisin is Lipid II, an essential intermediate in the bacterial cell-wall synthesis. High-affinity binding of the antibiotic to Lipid II is followed by rapid permeabilization of the membrane. Here, we investigated the assembly and stability of nisin-Lipid II pore complexes by means of pyrene fluorescence and circular dichroism. We demonstrated that nisin uses all available Lipid II molecules in the membrane to form pore complexes. The pore complexes have a uniform structure and consist of 8 nisin and 4 Lipid II molecules. Moreover, the pores displayed a remarkable stability, because they were able to resist the solubilization of the membrane environment by mild detergents. Similar experiments with [N20P/M21P]nisin showed that the hinge region is essential for the assembly into stable pore complexes. The new insights were used to propose a refined model for nisin pore formation.

Amino Acid Sequence↗

PubMed2004

The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics.

The emerging antibiotics-resistance problem has underlined the urgent need for novel antimicrobial agents. Lantibiotics (lanthionine-containing antibiotics) are promising candidates to alleviate this problem. Nisin, a member of this family, has a unique pore-forming activity against bacteria. It binds to lipid II, the essential precursor of cell wall synthesis. As a result, the membrane permeabilization activity of nisin is increased by three orders of magnitude. Here we report the solution structure of the complex of nisin and lipid II. The structure shows a novel lipid II-binding motif in which the pyrophosphate moiety of lipid II is primarily coordinated by the N-terminal backbone amides of nisin via intermolecular hydrogen bonds. This cage structure provides a rationale for the conservation of the lanthionine rings among several lipid II-binding lantibiotics. The structure of the pyrophosphate cage offers a template for structure-based design of novel antibiotics.

Anti-Bacterial Agents↗

PubMed2004

The selective utilization of substrates in vivo by the phosphatidylethanolamine and phosphatidylcholine biosynthetic enzymes Ept1p and Cpt1p in yeast.

In yeast, the aminoalcohol phosphotransferases Ept1p and Cpt1p catalyze the final steps in the CDP-ethanolamine and CDP-choline routes leading to phosphatidylethanolamine (PE) and phosphatidylcholine (PC), respectively. To determine how these enzymes contribute to the molecular species profiles of PE and PC in vivo, wild-type, cpt1Delta, and ept1Delta cells were pulse labeled with deuterated ethanolamine and choline. Analysis of newly synthesized PE and PC using electrospray ionization tandem mass spectrometry revealed that PE and PC produced by Ept1p and Cpt1p have different species compositions, demonstrating that the enzymes consume distinct sets of diacylglycerol species in vivo. Using the characteristic phospholipid species profiles produced by Ept1p and Cpt1p as molecular fingerprints, it was also shown that in vivo CDP-monomethylethanolamine is preferentially used as substrate by Ept1p, whereas CDP-dimethylethanolamine and CDP-propanolamine are converted by Cpt1p.

Diacylglycerol Cholinephosphotransferase↗

PubMed2004

Preparation and stability of lipid-coated nanocapsules of cisplatin: anionic phospholipid specificity.

Cisplatin nanocapsules represent a novel lipid formulation of the anti-cancer drug cis-diamminedichloroplatinum(II) (cisplatin), in which nanoprecipitates of cisplatin are coated by a phospholipid bilayer consisting of a 1:1 mixture of zwitterionic phosphatidylcholine (PC) and negatively charged phosphatidylserine (PS). Cisplatin nanocapsules are characterized by an unprecedented cisplatin-to-lipid ratio and exhibit increased in vitro cytotoxicity compared to the free drug [Nat. Med. 8, (2002) 81]. In the present study, the stability of the cisplatin nanocapsules was optimized by varying the lipid composition of the bilayer coat and monitoring in vitro cytotoxicity and the release of contents during incubations in water and in mouse serum. The release of cisplatin from the PC/PS (1:1) nanocapsules in water increased with increasing temperature with a t(1/2) of 6.5 h at 37 degrees C. At 4 degrees C, cisplatin was retained in the nanocapsules for well over 8 days. Replacement of PS by either phosphatidylglycerol or phosphatidic acid revealed that nanocapsules prepared of PS were more stable, which was found to be due to the ability of PS to form a stable cisplatin-PS coordination complex. Mouse serum had a strong destabilizing effect on the cisplatin nanocapsules. The PC/PS formulation lost over 80% of cisplatin within minutes after resuspension in serum. Incorporation of poly(ethylene glycol 2000) (PEG)-derivatized phosphatidylethanolamine and cholesterol in the bilayer coat extended the lifetime of the cisplatin nanocapsules in mouse serum to almost an hour. The results demonstrate that specificity in the interaction of cisplatin with anionic phospholipids is an important criterium for the formation and stability of cisplatin nanocapsules.

Animals↗

PubMed2004

Small alcohols destabilize the KcsA tetramer via their effect on the membrane lateral pressure.

Previously, it was shown that the tetrameric potassium channel KcsA when present in a lipid bilayer can be dissociated by trifluoroethanol [van den Brink-van der Laan, E., et al. (2004) Biochemistry 43, 4240-4250]. Here, we demonstrate that this is a general property of small alcohols. We found that small alcohols dissociate the KcsA tetramer, at a concentration that depends on their membrane affinity. Importantly, the efficiency of the alcohol-induced tetramer dissociation was found to correlate with the efficiency of both alcohol-induced bilayer leakage and acyl chain disordering. Our data suggest that the ability of small alcohols to induce KcsA tetramer dissociation and to function as anesthetics depends on their effect on the membrane lateral pressure.

Alcohols↗

PubMed2004

Photo-crosslinking analysis of preferential interactions between a transmembrane peptide and matching lipids.

In this study, a novel method is presented by which the molecular environment of a transmembrane peptide can be investigated directly. This was achieved by incorporating a photoactivatable crosslinking probe in the hydrophobic segment of a model transmembrane peptide. When this peptide was incorporated into lipid bilayers and irradiated with UV light, a covalent bond was formed between the crosslinking probe and a lipid. This crosslinking reaction could be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the resulting product could be characterized by mass spectrometry. By use of phospholipases, it was demonstrated that the peptide crosslinks to both acyl chains of the lipids. The peptide showed a clear preference to partition into fluid lipids and was excluded from lipids in the gel phase. However, when the peptide was incorporated into bilayers containing two lipid species with different acyl chain lengths, molecular sorting of the lipids around the peptide based on hydrophobic matching was not observed. It is proposed that the size of the transmembrane part plays an important role in the dynamic interactions of membrane proteins with the surrounding lipids and hence in determining whether molecular sorting can occur.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2004

Stability of KcsA tetramer depends on membrane lateral pressure.

The potassium channel KcsA forms an extremely stable tetramer. Despite this high stability, it has been shown that the membrane-mimicking solvent 2,2,2-trifluoroethanol (TFE) can induce tetramer dissociation [Valiyaveetil, F. I., et al. (2002) Biochemistry 41, 10771-7, and Demmers, J. A. A., et al. (2003) FEBS Lett. 541, 69-77]. Here we have studied the effect of TFE on the structure and oligomeric state of the KcsA tetramer, reconstituted in different lipid systems. It was found that TFE changes the secondary and tertiary structure of KcsA and that it can dissociate the KcsA tetramer in all systems used. The tetramer is stabilized by a lipid bilayer as compared to detergent micelles. The extent of stabilization was found to depend on the nature of the lipids: a strong stabilizing effect of the nonbilayer lipid phosphatidylethanolamine (PE) was observed, but no effect of the charged phoshosphatidylglycerol (PG) as compared to phosphatidylcholine (PC) was found. To understand how lipids stabilize KcsA against TFE-induced tetramer dissociation, we also studied the effect of TFE on the bilayer organization in the various lipid systems, using (31)P and (2)H NMR. The observed lipid dependency was similar as was found for tetramer stabilization: PE increased the bilayer stability as compared to PC, while PG behaved similar to PC. Furthermore, it was found that TFE has a large effect on the acyl chain ordering. The results indicate that TFE inserts primarily in the membrane interface. We suggest that the lipid bilayer stabilizes the KcsA tetramer by the lateral pressure in the acyl chain region and that this stabilizing effect increases when a nonbilayer lipid like PE is present.

Bacterial Proteins↗

PubMed2004

Uptake and remodeling of exogenous phosphatidylethanolamine in E. coli.

The fate of exogenous short-chain analogues of phosphatidylethanolamine and phosphatidylserine was studied in a deep-rough derivative of E. coli mutant strain AD93 that cannot synthesize phosphatidylethanolamine de novo. Using mass spectrometry, it was shown that dicaproyl(di 6:0)-phosphatidylethanolamine is extensively remodeled, eventually adopting the phosphatidylethanolamine species profile of the parental wild-type strain of AD93. Dicaproyl-phosphatidylserine was decarboxylated to form phosphatidylethanolamine, and yielded a species profile, which strongly resembled that of the introduced phosphatidylethanolamine. This demonstrates transport of phosphatidylserine to the cytosolic leaflet of the inner membrane. The changes of the species profile of phosphatidylethanolamine indicate that the short-chain phospholipids are most likely remodeled via two consecutive acyl chain substitutions, and at least part of this remodeling involves transport to the inner membrane.

Chromatography, Thin Layer↗

PubMed2004

Transbilayer movement of phospholipids in biogenic membranes.

Biogenic membranes contain the enzymes that synthesize the cell's membrane lipids, of which the phospholipids are the most widespread throughout nature. Being synthesized at and inserted into the cytoplasmic leaflet of biogenic membranes, the phospholipids must migrate to the opposite leaflet to ensure balanced growth of the membrane. In this review, the current knowledge of transbilayer movement of phospholipids in biogenic membranes is summarized and the available data are compared to what is known about lipid translocation in other membranes. On the basis of this, a mechanism is proposed, in which phospholipid translocation in biogenic membranes is mediated via membrane-spanning segments of a subset of proteins, characterized by a small number of transmembrane helices. We speculate that proteins of this subset facilitate lipid translocation via the protein-lipid interface, because they display more dynamic behavior and engage in less stable protein-lipid interactions than larger membrane proteins.

Animals↗

PubMed2003

The peptide antibiotic clavanin A interacts strongly and specifically with lipid bilayers.

In this study the interaction of the antimicrobial peptide clavanin A with phosphatidylcholine bilayers is investigated by DSC, NMR, and AFM techniques. It is shown that the peptide interacts strongly and specifically with the lipids, resulting in increased order-disorder phase transition temperatures, phase separation, altered acyl chain and headgroup packing, and a drastically changed surface morphology of the bilayer. These results are interpreted in terms of clavanin-specific interactions with lipids and are discussed in the light of the different mechanisms by which clavanin A can destroy the barrier function of biological membranes.

Anti-Bacterial Agents↗

PubMed2003

The role of the abundant phenylalanines in the mode of action of the antimicrobial peptide clavanin.

Clavanin A is a special antimicrobial peptide that acts at the level of the membrane via a pH-dependent mechanism. At neutral pH, clavanin disrupts biological and model membranes in a nonspecific manner, causing efflux of large molecules. At mildly acidic conditions, however, the peptide efficiently kills bacteria by permeabilizing their membrane most likely by interacting with proteins involved in proton translocation [Biochemistry 41 (2002) 7529]. Clavanin A is unusually rich in phenylalanines with 5 out of 23 residues, which suggests that these residues are functionally important. A set of mutants, in which all Phe residues are replaced by either Ile, Leu, Trp, or Tyr was used to investigate the role of these amino acids. The antimicrobial activities of the different peptides both at neutral and low pH show that the presence of phenylalanine is not essential nor optimal, as the Trp, Leu, and Ile mutant are equally or more active than the wild-type component. In general, at neutral pH, the biological activities correlate well with the peptides' ability to interact with membrane lipids. Correspondingly, the permeabilization efficiencies of biological and model membranes of the various derivatives were found to be closely related to their ability to adopt alpha-helical structures, and follows the order 5L>5W>5I>5Y>wild type. The results suggest an important role for the Phe residues, in providing the peptide in a balanced manner with sufficient hydrophobicity, and therewith membrane affinity, as well as conformational flexibility.

Animals↗

PubMed2003

Sphingomyelin is much more effective than saturated phosphatidylcholine in excluding unsaturated phosphatidylcholine from domains formed with cholesterol.

In this study, we compared domain formation in raft-like mixtures of cholesterol and dioleoylphosphatidylcholine (DOPC) with either sphingomyelin (SM) or dipalmitoylphosphatidylcholine (DPPC). Using 2H nuclear magnetic resonance, we studied the properties of the lipid enriched in the fluid phase, DOPC. We found that acyl chain 2H-labeled DOPC is much less ordered in SM-containing mixtures than in those containing DPPC, suggesting that DOPC in the SM-containing mixture senses a lower concentration of cholesterol in its direct environment. Atomic force microscopy experiments demonstrated large differences in the size and shape of domains in the different mixtures. We propose that these various differences are a consequence of the preferential interaction of cholesterol for sphingolipids over glycerophospholipids.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2003

Interaction of the K+ channel KcsA with membrane phospholipids as studied by ESI mass spectrometry.

In this study we have used electrospray ionization mass spectrometry (ESI-MS) to investigate interactions between the bacterial K(+) channel KcsA and membrane phospholipids. KcsA was reconstituted into lipid vesicles of variable lipid composition. These vesicles were directly analyzed by ESI-MS or mixed with trifluoroethanol (TFE) before analysis. In the resulting mass spectra, non-covalent complexes of KcsA and phospholipids were observed with an interesting lipid specificity. The anionic phosphatidylglycerol (PG), and, to a lesser extent, the zwitterionic phosphatidylethanolamine (PE), which both are abundant bacterial lipids, were found to preferentially associate with KcsA as compared to the zwitterionic phosphatidylcholine (PC). These preferred interactions may reflect the differences in affinity of these phospholipids for KcsA in the membrane.

Bacterial Proteins↗

PubMed2003

Translocation of phospholipids is facilitated by a subset of membrane-spanning proteins of the bacterial cytoplasmic membrane.

The mechanism by which phospholipids are transported across biogenic membranes, such as the bacterial cytoplasmic membrane, is unknown. We hypothesized that this process is mediated by the presence of the membrane-spanning segments of inner membrane proteins, rather than by dedicated flippases. In support of the hypothesis, it was demonstrated that transmembrane alpha-helical peptides, mimicking the membrane-spanning segments, mediate flop of 2-6-(7-nitro-2,1,3-benzoxadiazol-4-yl) aminocaproyl (C6-NBD)-phospholipids (Kol, M. A., de Kroon, A. I., Rijkers, D. T., Killian, J. A., and de Kruijff, B. (2001) Biochemistry 40, 10500-10506). Here the dithionite reduction assay was used to measure transbilayer equilibration of C6-NBD-phospholipids in proteoliposomes, composed of Escherichia coli phospholipids and a subset of bacterial membrane proteins. It is shown that two well characterized integral proteins of the bacterial cytoplasmic membrane, leader peptidase and the potassium channel KcsA, induce phospholipid translocation, most likely by their transmembrane domains. In contrast, the ATP-binding cassette transporter from the E. coli inner membrane MsbA, a putative lipid flippase, did not mediate phospholipid translocation, irrespective of the presence of ATP. OmpT, an outer membrane protein from E. coli, did not facilitate flop either, demonstrating specificity of protein-mediated phospholipid translocation. The results are discussed in the light of phospholipid transport across the E. coli inner membrane.

Bacterial Proteins↗

PubMed2003

Lipid II is an intrinsic component of the pore induced by nisin in bacterial membranes.

The peptidoglycan layers surrounding bacterial membranes are essential for bacterial cell survival and provide an important target for antibiotics. Many antibiotics have mechanisms of action that involve binding to Lipid II, the prenyl chain-linked donor of the peptidoglycan building blocks. One of these antibiotics, the pore-forming peptide nisin uses Lipid II as a receptor molecule to increase its antimicrobial efficacy dramatically. Nisin is the first example of a targeted membrane-permeabilizing peptide antibiotic. However, it was not known whether Lipid II functions only as a receptor to recruit nisin to bacterial membranes, thus increasing its specificity for bacterial cells, or whether it also plays a role in pore formation. We have developed a new method to produce large amounts of Lipid II and variants thereof so that we can address the role of the lipid-linked disaccharide in the activity of nisin. We show here that Lipid II is not only the receptor for nisin but an intrinsic component of the pore formed by nisin, and we present a new model for the pore complex that includes Lipid II.

Membrane Lipids↗

PubMed2003

The two biosynthetic routes leading to phosphatidylcholine in yeast produce different sets of molecular species. Evidence for lipid remodeling.

Phosphatidylcholine (PC), a major lipid class in the membranes of eukaryotes, is synthesized either via the triple methylation of phosphatidylethanolamine (PE) or via the CDP-choline route. To investigate whether the two biosynthetic routes contribute differently to the steady-state profile of PC species, i.e., PC molecules with specific acyl chain compositions, the pools of newly synthesized PC species were monitored by labeling Saccharomyces cerevisiae with deuterated precursors of the two routes, (methyl-D3)-methionine and (D13)-choline, respectively. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) revealed that the two PC biosynthetic pathways yield different sets of PC species, with the CDP-choline route contributing most to the molecular diversity. Moreover, yeast was shown to be capable of remodeling PC by acyl chain exchange at the sn-1 position of the glycerol backbone. Remodeling was found to be required to generate the steady-state species distribution of PC. This is the first study demonstrating a functional difference between the two biosynthetic routes in yeast.

Acylation↗