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Int. J. Mol. Sci., Volume 10, Issue 4 (April 2009), Pages 1419-1941

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Open AccessArticle Fluorescence Lifetime Imaging of Quantum Dot Labeled DNA Microarrays
Int. J. Mol. Sci. 2009, 10(4), 1930-1941; https://doi.org/10.3390/ijms10041930
Received: 4 March 2009 / Revised: 16 April 2009 / Accepted: 21 April 2009 / Published: 24 April 2009
Cited by 30 | PDF Full-text (394 KB) | HTML Full-text | XML Full-text
Abstract
Quantum dot (QD) labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8
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Quantum dot (QD) labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8 ns, compared to 13.3 ns obtained for spots of free QD solution, revealing that QD labels are sensitive to the spot microenvironment. Additionally, time gated detection was shown to improve the microarray image contrast ratio by 1.8, achieving femtomolar target sensitivity. Finally, lifetime multiplexing based on Qdot525 and Alexa430 was demonstrated using a single excitation-detection readout channel. Full article
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Open AccessReview Heterogeneity of Mitochondria and Mitochondrial Function within Cells as Another Level of Mitochondrial Complexity
Int. J. Mol. Sci. 2009, 10(4), 1911-1929; https://doi.org/10.3390/ijms10041911
Received: 24 March 2009 / Revised: 14 April 2009 / Accepted: 21 April 2009 / Published: 24 April 2009
Cited by 85 | PDF Full-text (1605 KB) | HTML Full-text | XML Full-text
Abstract
Beyond their fundamental role in energy metabolism, mitochondria perform a great variety of other important cellular functions. However, the interplayamong these various roles of mitochondria is still poorly understood, and the underlying mechanisms can be related to system level properties. Importantly, mitochondria localized
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Beyond their fundamental role in energy metabolism, mitochondria perform a great variety of other important cellular functions. However, the interplayamong these various roles of mitochondria is still poorly understood, and the underlying mechanisms can be related to system level properties. Importantly, mitochondria localized in different regions of a cell may display different morphology, dissimilar biochemical properties, or may differently interact with other intracellular structures. Recent advances in live imaging techniques have also revealed a functional heterogeneity of mitochondria with respect to mitochondrial redox state, membrane potential, respiratory activity, uncoupling proteins, mitochondrial ROS and calcium. An important and still unresolved question is how the heterogeneity of mitochondrial function and the regional specializations of mitochondria are mechanistically realized in the cell and to what extent this could be dependent on environmental aspects. Distinct mitochondrial subsets may also exhibit different responses to substrates and inhibitors and may vary in their sensitivity to pathology, resistance to apoptosis, oxidative stress, thus also demonstrating heterogeneous behavior. All these observations strongly suggest that the intracellular position, organization and the specific surroundings of mitochondria within the cell define their functional features, while also implying that different mitochondrial subpopulations, clusters or even single mitochondrion may execute diverse processes in a cell. The heterogeneity of mitochondrial function demonstrates an additional level of mitochondrial complexity and is a new, challenging area in mitochondrial research that potentially leads to the integration of mitochondrial bioenergetics and cell physiology with various physiological and pathophysiological implications. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics)
Open AccessArticle Overexpression of a Weed (Solanum americanum) Proteinase Inhibitor in Transgenic Tobacco Results in Increased Glandular Trichome Density and Enhanced Resistance to Helicoverpa armigera and Spodoptera litura
Int. J. Mol. Sci. 2009, 10(4), 1896-1910; https://doi.org/10.3390/ijms10041896
Received: 12 March 2009 / Revised: 17 April 2009 / Accepted: 21 April 2009 / Published: 23 April 2009
Cited by 20 | PDF Full-text (902 KB) | HTML Full-text | XML Full-text
Abstract
In this study we produced transgenic tobacco plants by overexpressing a serine proteinase inhibitor gene, SaPIN2a, from the American black nightshade Solanum americanum under the control of the CaMV 35S promoter using Agrobacterium tumefaciens-mediated transformation. SaPIN2a was properly transcribed and translated as
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In this study we produced transgenic tobacco plants by overexpressing a serine proteinase inhibitor gene, SaPIN2a, from the American black nightshade Solanum americanum under the control of the CaMV 35S promoter using Agrobacterium tumefaciens-mediated transformation. SaPIN2a was properly transcribed and translated as indicated by Northern blot and Western blot analyses. Functional integrity of SaPIN2a in transgenic plants was confirmed by proteinase inhibitory activity assay. Bioassays for insect resistance showed that SaPIN2a-overexpressing transgenic tobacco plants were more resistant to cotton bollworm(Helicoverpa armigera) and tobacco cutworm(Spodoptera litura) larvae, two devastating pests of important crop plants, than the control plants. Interestingly, overexpression of SaPIN2a in transgenic tobacco plants resulted in a significant increase in glandular trichome density and a promotion of trichome branching, which could also provide an additional resistance mechanism in transgenic plants against insect pests. Therefore, SaPIN2a could be used as an alternative proteinase inhibitor for the production of insect-resistant transgenic plants. Full article
(This article belongs to the Special Issue Biotic and Abiotic Stress)
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Open AccessArticle Hereditary and Sporadic Forms of Aβ-Cerebrovascular Amyloidosis and Relevant Transgenic Mouse Models
Int. J. Mol. Sci. 2009, 10(4), 1872-1895; https://doi.org/10.3390/ijms10041872
Received: 16 January 2009 / Revised: 14 April 2009 / Accepted: 20 April 2009 / Published: 23 April 2009
Cited by 21 | PDF Full-text (437 KB) | HTML Full-text | XML Full-text
Abstract
Cerebral amyloid angiopathy (CAA) refers to the specific deposition of amyloid fibrils in the leptomeningeal and cerebral blood vessel walls, often causing secondary vascular degenerative changes. Although many kinds of peptides are known to be deposited as vascular amyloid, amyloid-β (Aβ)-CAA is the
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Cerebral amyloid angiopathy (CAA) refers to the specific deposition of amyloid fibrils in the leptomeningeal and cerebral blood vessel walls, often causing secondary vascular degenerative changes. Although many kinds of peptides are known to be deposited as vascular amyloid, amyloid-β (Aβ)-CAA is the most common type associated with normal aging, sporadic CAA, Alzheimer’s disease (AD) and Down’s syndrome. Moreover, Aβ-CAA is also associated with rare hereditary cerebrovascular amyloidosis due to mutations within the Aβ domain of the amyloid precursor protein (APP) such as Dutch and Flemish APP mutations. Genetics and clinicopathological studies on these familial diseases as well as sporadic conditions have already shown that CAA not only causes haemorrhagic and ischemic strokes, but also leads to progressive dementia. Transgenic mouse models based on familial AD mutations have also successfully reproduced many of the features found in human disease, providing us with important insights into the pathogenesis of CAA. Importantly, such studies have pointed out that specific vastopic Aβ variants or an unaltered Aβ42/Aβ40 ratio favor vascular Aβ deposition over parenchymal plaques, but higher than critical levels of Aβ40 are also observed to be anti-amyloidogenic. These data would be important in the development of therapies targeting amyloid in vessels. Full article
(This article belongs to the Special Issue Advances in Molecular Neuropathology)
Open AccessReview On the Free Energy That Drove Primordial Anabolism
Int. J. Mol. Sci. 2009, 10(4), 1853-1871; https://doi.org/10.3390/ijms10041853
Received: 26 March 2009 / Revised: 16 April 2009 / Accepted: 20 April 2009 / Published: 22 April 2009
Cited by 5 | PDF Full-text (161 KB) | HTML Full-text | XML Full-text
Abstract
A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable
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A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable thermodynamic prerequisite for such a primordial anabolism is the mechanistic coupling to processes that supplied the free energy required. Here I review different sources of free energy and discuss the potential of each form having been involved in the very first anabolic reactions that were fundamental to increase molecular complexity and thus were essential for life. Full article
(This article belongs to the Special Issue Origin of Life)
Open AccessArticle Coenzyme Autocatalytic Network on the Surface of Oil Microspheres as a Model for the Origin of Life
Int. J. Mol. Sci. 2009, 10(4), 1838-1852; https://doi.org/10.3390/ijms10041838
Received: 17 February 2009 / Revised: 14 April 2009 / Accepted: 16 April 2009 / Published: 22 April 2009
Cited by 11 | PDF Full-text (115 KB) | HTML Full-text | XML Full-text
Abstract
Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored,
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Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored, and these changes enhanced autocatalysis and propagation of CLMs. Heredity started from a single kind of self-reproducing CLM, and then evolved into more complex coenzyme autocatalytic networks containing multiple kinds of CLMs. Polymerization of CLMs on the surface of microspheres and development of template-based synthesis is a potential evolutionary path towards the emergence of nucleic acids. Full article
(This article belongs to the Special Issue Origin of Life)
Open AccessArticle In Vitro Cytochrome P450 Formation of a Mono-Hydroxylated Metabolite of Zearalenone Exhibiting Estrogenic Activities: Possible Occurrence of This Metabolite in Vivo
Int. J. Mol. Sci. 2009, 10(4), 1824-1837; https://doi.org/10.3390/ijms10041824
Received: 23 March 2009 / Accepted: 16 April 2009 / Published: 21 April 2009
Cited by 25 | PDF Full-text (227 KB) | HTML Full-text | XML Full-text
Abstract
The mycoestrogen zearalenone (ZEN), as well as its reduced metabolites, which belong to the endocrine disruptor bio-molecule family, are substrates for various enzymes involved in steroid metabolism. In addition to its reduction by the steroid dehydrogenase pathway, ZEN also interacts with hepatic detoxification
[...] Read more.
The mycoestrogen zearalenone (ZEN), as well as its reduced metabolites, which belong to the endocrine disruptor bio-molecule family, are substrates for various enzymes involved in steroid metabolism. In addition to its reduction by the steroid dehydrogenase pathway, ZEN also interacts with hepatic detoxification enzymes, which convert it into hydroxylated metabolites (OH-ZEN). Due to their structures to that of estradiol, ZEN and its derived metabolites bind to the estrogen receptors and are involved in endocrinal perturbations and are possibly associated with estrogen-dependent cancers. The primary aim of this present study was to identify the enzymatic cytochrome P450 isoforms responsible for the formation of the most abundant OH-ZEN. We thus studied its in vitro formation using hepatic microsomes in a range of animal model systems including man. OH-ZEN was also recovered in liver and urine of rats treated orally with ZEN. Finally we compared the activity of ZEN and its active metabolites (α-ZAL and OH-ZEN) on estrogen receptors using HeLa ER-α and ER-β reporter cell lines as reporters. OH-ZEN estrogenic activities were revealed to be limited and not as significant as those of ZEN or α-ZAL. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle Uncovering the Properties of Energy-Weighted Conformation Space Networks with a Hydrophobic-Hydrophilic Model
Int. J. Mol. Sci. 2009, 10(4), 1808-1823; https://doi.org/10.3390/ijms10041808
Received: 14 January 2009 / Revised: 30 March 2009 / Accepted: 7 April 2009 / Published: 21 April 2009
Cited by 8 | PDF Full-text (219 KB) | HTML Full-text | XML Full-text
Abstract
The conformation spaces generated by short hydrophobic-hydrophilic (HP) lattice chains are mapped to conformation space networks (CSNs). The vertices (nodes) of the network are the conformations and the links are the transitions between them. It has been found that these networks have “small-world”
[...] Read more.
The conformation spaces generated by short hydrophobic-hydrophilic (HP) lattice chains are mapped to conformation space networks (CSNs). The vertices (nodes) of the network are the conformations and the links are the transitions between them. It has been found that these networks have “small-world” properties without considering the interaction energy of the monomers in the chain, i. e. the hydrophobic or hydrophilic amino acids inside the chain. When the weight based on the interaction energy of the monomers in the chain is added to the CSNs, it is found that the weighted networks show the “scale-free” characteristic. In addition, it reveals that there is a connection between the scale-free property of the weighted CSN and the folding dynamics of the chain by investigating the relationship between the scale-free structure of the weighted CSN and the noted parameter Z score. Moreover, the modular (community) structure of weighted CSNs is also studied. These results are helpful to understand the topological properties of the CSN and the underlying free-energy landscapes. Full article
(This article belongs to the Special Issue Protein Folding 2009)
Open AccessArticle Non-Enzymatic Template-Directed Recombination of RNAs
Int. J. Mol. Sci. 2009, 10(4), 1788-1807; https://doi.org/10.3390/ijms10041788
Received: 31 March 2009 / Revised: 10 April 2009 / Accepted: 15 April 2009 / Published: 21 April 2009
Cited by 5 | PDF Full-text (714 KB) | HTML Full-text | XML Full-text
Abstract
RNA non-enzymatic recombination reactions are of great interest within the hypothesis of the "RNA world", which argues that at some stage of prebiotic life development proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task and
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RNA non-enzymatic recombination reactions are of great interest within the hypothesis of the "RNA world", which argues that at some stage of prebiotic life development proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task and the full range of catalytic roles necessary in primitive self-replicating systems. Here we report on the study of recombination reaction occuring between two 96 nucleotides (nts) fragments of RNAs under physiological conditions and governed by a short oligodeoxyribonucleotide template, partially complementary to sequences within each of the RNAs. Analysis of recombination products shows that ligation is predominantly template-directed, and occurs within the complementary complex with the template in "butt-to-butt" manner, in 1- or 3- nts bulges or in 2-3 nts internal loops. Minor recombination products formed in the template-independent manner are detected as well. Full article
(This article belongs to the Special Issue Origin of Life)
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Open AccessArticle Phenolic Compounds Protect Cultured Hippocampal Neurons against Ethanol-Withdrawal Induced Oxidative Stress
Int. J. Mol. Sci. 2009, 10(4), 1773-1787; https://doi.org/10.3390/ijms10041773
Received: 24 February 2009 / Revised: 27 March 2009 / Accepted: 15 April 2009 / Published: 20 April 2009
Cited by 6 | PDF Full-text (191 KB) | HTML Full-text | XML Full-text
Abstract
Ethanol withdrawal is linked to elevated oxidative damage to neurons. Here we report our findings on the contribution of phenolic antioxidants (17β-estradiol, p-octyl-phenol and 2,6-di-tert-butyl-4-methylphenol) to counterbalance sudden ethanol withdrawal-initiated oxidative events in hippocampus-derived cultured HT-22 cells. We showed that
[...] Read more.
Ethanol withdrawal is linked to elevated oxidative damage to neurons. Here we report our findings on the contribution of phenolic antioxidants (17β-estradiol, p-octyl-phenol and 2,6-di-tert-butyl-4-methylphenol) to counterbalance sudden ethanol withdrawal-initiated oxidative events in hippocampus-derived cultured HT-22 cells. We showed that ethanol withdrawal for 4 h after 24-h ethanol treatment provoked greater levels of oxidative damage than the preceding ethanol exposure. Phenolic antioxidant treatment either during ethanol exposure or ethanol withdrawal only, however, dose-dependently reversed cellular oxidative damage, as demonstrated by the significantly enhanced cell viability, reduced malondialdehyde production and protein carbonylation, compared to untreated cells. Interestingly, the antioxidant treatment schedule had no significant impact on the observed neuroprotection. In addition, the efficacy of the three phenolic compounds was practically equipotent in protecting HT-22 cells in spite of predictions based on an in silico study and a cell free assay of lipid peroxidation. This finding implies that free-radical scavenging may not be the sole factor responsible for the observed neuroprotection and warrants further studies to establish, whether the HT-22 line is indeed a suitable model for in vitro screening of antioxidants against EW-related neuronal damage. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
Open AccessReview Adenylate Kinase and AMP Signaling Networks: Metabolic Monitoring, Signal Communication and Body Energy Sensing
Int. J. Mol. Sci. 2009, 10(4), 1729-1772; https://doi.org/10.3390/ijms10041729
Received: 9 March 2009 / Revised: 26 March 2009 / Accepted: 2 April 2009 / Published: 17 April 2009
Cited by 151 | PDF Full-text (671 KB) | HTML Full-text | XML Full-text
Abstract
Adenylate kinase and downstream AMP signaling is an integrated metabolic monitoring system which reads the cellular energy state in order to tune and report signals to metabolic sensors. A network of adenylate kinase isoforms (AK1-AK7) are distributed throughout intracellular compartments, interstitial space and
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Adenylate kinase and downstream AMP signaling is an integrated metabolic monitoring system which reads the cellular energy state in order to tune and report signals to metabolic sensors. A network of adenylate kinase isoforms (AK1-AK7) are distributed throughout intracellular compartments, interstitial space and body fluids to regulate energetic and metabolic signaling circuits, securing efficient cell energy economy, signal communication and stress response. The dynamics of adenylate kinase-catalyzed phosphotransfer regulates multiple intracellular and extracellular energy-dependent and nucleotide signaling processes, including excitation-contraction coupling, hormone secretion, cell and ciliary motility, nuclear transport, energetics of cell cycle, DNA synthesis and repair, and developmental programming. Metabolomic analyses indicate that cellular, interstitial and blood AMP levels are potential metabolic signals associated with vital functions including body energy sensing, sleep, hibernation and food intake. Either low or excess AMP signaling has been linked to human disease such as diabetes, obesity and hypertrophic cardiomyopathy. Recent studies indicate that derangements in adenylate kinase-mediated energetic signaling due to mutations in AK1, AK2 or AK7 isoforms are associated with hemolytic anemia, reticular dysgenesis and ciliary dyskinesia. Moreover, hormonal, food and antidiabetic drug actions are frequently coupled to alterations of cellular AMP levels and associated signaling. Thus, by monitoring energy state and generating and distributing AMP metabolic signals adenylate kinase represents a unique hub within the cellular homeostatic network. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics)
Open AccessCorrection Correction: Goldbeck, R.A., et al. Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c. Int. J. Mol. Sci. 2009, 10, 1476-1499.
Int. J. Mol. Sci. 2009, 10(4), 1728; https://doi.org/10.3390/ijms10041728
Received: 16 April 2009 / Published: 17 April 2009
PDF Full-text (29 KB) | HTML Full-text | XML Full-text
Abstract
By mistake, we omitted the support from the National Institutes of Health (U.S.A.) in the Acknowledgements section in our paper recently published in Int. J. Mol. Sci. [1]. Therefore, the Acknowledgements section is revised as follows: [...] Full article
Open AccessArticle A Molecular Dynamics Simulation of the Human Lysozyme –Camelid VHH HL6 Antibody System
Int. J. Mol. Sci. 2009, 10(4), 1719-1727; https://doi.org/10.3390/ijms10041719
Received: 15 March 2009 / Revised: 9 April 2009 / Accepted: 10 April 2009 / Published: 17 April 2009
Cited by 4 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
Amyloid diseases such as Alzheimer’s and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able
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Amyloid diseases such as Alzheimer’s and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able to combat against wild-type human lysozyme for inhibiting in-vitro aggregations of the amyloidogenic variant (D67H). The present study is aimed at elucidating the unbinding mechanics between the D67H lysozyme and VHH HL6 antibody fragment by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different pulling velocities. The results of the simulation indicated that stretching forces of more than two nano Newton (nN) were required to dissociate the protein-antibody system, and the hydrogen bond dissociation pathways were computed. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessReview Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks
Int. J. Mol. Sci. 2009, 10(4), 1697-1718; https://doi.org/10.3390/ijms10041697
Received: 11 March 2009 / Revised: 7 April 2009 / Accepted: 14 April 2009 / Published: 17 April 2009
Cited by 12 | PDF Full-text (532 KB) | HTML Full-text | XML Full-text
Abstract
Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and
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Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics)
Open AccessCommunication Rupture Pathway of Phosphatidylcholine Liposomes on Silicon Dioxide
Int. J. Mol. Sci. 2009, 10(4), 1683-1696; https://doi.org/10.3390/ijms10041683
Received: 9 February 2009 / Revised: 3 April 2009 / Accepted: 10 April 2009 / Published: 17 April 2009
Cited by 39 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
We have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with asymmetric
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We have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with asymmetric lipid compositions in the outer and inner leaflets. The specific binding of neutravidin and anti-biotin to SLBs formed by liposome fusion, prior to and after equilibrated flip-flop between the upper and lower monolayers in the SLB, were then investigated. It was concluded that the lipids in the outer monolayer of the vesicle predominantly end up on the SLB side facing the SiO2 substrate, as demonstrated by having maximum 30-40% of lipids in the liposome outer monolayer orienting towards the bulk after forming the SLB. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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