51
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Pontecchiani F, Simonovsky E, Wieczorek R, Barbosa N, Rowinska-Zyrek M, Potocki S, Remelli M, Miller Y, Kozlowski H. The unusual binding mechanism of Cu(II) ions to the poly-histidyl domain of a peptide found in the venom of an African viper. Dalton Trans 2015; 43:16680-9. [PMID: 25266233 DOI: 10.1039/c4dt02257b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Copper complexes of a poly-His/poly-Gly peptide (EDDHHHHHHHHHGVGGGGGGGGGG-NH2), a natural component of a snake venom, were studied by means of both experimental (thermodynamic, spectroscopic and MS) techniques and molecular dynamics (MD) simulations and density functional theory (DFT) calculations. This peptide proved to be an exceptionally effective copper chelator, forming complexes which are thermodynamically more stable than those formed by both the albumin-like ATCUN motif and several other poly-histidine protein fragments. We show that, in a poly-histidine stretch, copper seems to prefer binding to residues separated by one amino acid and that a correlation between an α-helical structure of the predicted complexes and their thermodynamic stability is observed.
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Affiliation(s)
- Fabio Pontecchiani
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17, I-44121 Ferrara, Italy.
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52
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Atsmon-Raz Y, Miller Y. Insight into Atomic Resolution of the Cross-Seeding between Tau/Mutated Tau and Amyloid-β in Neurodegenerative Diseases. Isr J Chem 2015. [DOI: 10.1002/ijch.201400162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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53
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Pellach M, Atsmon-Raz Y, Simonovsky E, Gottlieb H, Jacoby G, Beck R, Adler-Abramovich L, Miller Y, Gazit E. Spontaneous structural transition in phospholipid-inspired aromatic phosphopeptide nanostructures. ACS Nano 2015; 9:4085-4095. [PMID: 25802000 DOI: 10.1021/acsnano.5b00133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phospholipid membranes could be considered a prime example of the ability of nature to produce complex yet ordered structures, by spontaneous and efficient self-assembly. Inspired by the unique properties and architecture of phospholipids, we designed simple amphiphilic decapeptides, intended to fold in the center of the peptide sequence, with a phosphorylated serine "head" located within a central turn segment, and two hydrophobic "tails". The molecular design also included the integration of the diphenylalanine motif, previously shown to facilitate self-assembly and increase nanostructure stability. Secondary structure analysis of the peptides indeed indicated the presence of stabilized conformations in solution, with a central turn connecting two hydrophobic "tails", and interactions between the hydrophobic strands. The mechanisms of assembly into supramolecular structures involved structural transitions between different morphologies, which occurred over several hours, leading to the formation of distinctive nanostructures, including half-elliptical nanosheets and curved tapes. The phosphopeptide building blocks appear to self-assemble via a particular combination of aromatic, hydrophobic and ionic interactions, as well as hydrogen bonding, as demonstrated by proposed constructed simulated models of the peptides and self-assembled nanostructures. Molecular dynamics simulations also gave insight into mechanisms of structural transitions of the nanostructures at a molecular level. Because of the biocompatibility of peptides, the phosphopeptide assemblies allow for expansion of the library of biomolecular nanostructures available for future design and application of biomedical devices.
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Affiliation(s)
- Michal Pellach
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoav Atsmon-Raz
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Eyal Simonovsky
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Hugo Gottlieb
- ⊥Department of Chemistry, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Guy Jacoby
- ∥The Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Roy Beck
- ∥The Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Lihi Adler-Abramovich
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yifat Miller
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ehud Gazit
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- #Department of Materials Science and Engineering Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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54
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Abstract
Capping of both N- and C-terminal induce α-helix formation in Cu2+-His6 peptide.
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Affiliation(s)
- Eyal Simonovsky
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | | | - Yifat Miller
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
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55
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Wineman-Fisher V, Miller Y. Insight into the Metal Binding Sites in Amylin Aggregates. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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56
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Atsmon-Raz Y, Miller Y. Co-Aggregation of Alpha-Synuclein with Amylin(HIAPP) Leads to an Increased Risk in Type ii Diabetes Patients for Developing Parkinson's Disease. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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57
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Miller Y, Ma B, Nussinov R. Polymorphism in self-assembly of peptide-based β-hairpin contributes to network morphology and hydrogel mechanical rigidity. J Phys Chem B 2014; 119:482-90. [PMID: 25545881 PMCID: PMC4298354 DOI: 10.1021/jp511485n] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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Hydrogels are proving to be an excellent
class of materials for
biomedical applications. The molecular self-assembly of designed MAX1
β-hairpin peptides into fibrillar networks has emerged as a
novel route to form responsive hydrogels. Herein, computational modeling
techniques are used to investigate the relative arrangements of individual
hairpins within the fibrils that constitute the gel. The modeling
provides insight into the morphology of the fibril network, which
defines the gel’s mechanical properties. Our study suggests
polymorphic arrangements of the hairpins within the fibrils; however,
the relative populations and the relative conformational energies
of the polymorphic arrangements show a preference toward an arrangement
of hairpins where their turn regions are not capable of forming intermolecular
interaction. Repulsive intramolecular electrostatic interactions appear
to dictate the formation of fibrils with shorter, rather than longer,
persistent lengths. These repulsive intramolecular interactions also
disfavor the formation of fibril entanglements. Taken together, the
modeling predicts that MAX1 forms a network containing a large number
of branch points, a network morphology supported by the formation
of short fibril segments. We posit that, under static conditions,
the preferred branched structures of the MAX1 peptide assembly result
in a cross-linked hydrogel organization. At the same time, the shear
stress leads to short fibrillar structures, thus fluidic hydrogel
states.
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Affiliation(s)
- Yifat Miller
- Department of Chemistry and ‡Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beér-Sheva 84105, Israel
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58
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Wineman-Fisher V, Atsmon-Raz Y, Miller Y. Orientations of residues along the β-arch of self-assembled amylin fibril-like structures lead to polymorphism. Biomacromolecules 2014; 16:156-65. [PMID: 25420121 DOI: 10.1021/bm501326y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amylin is an endocrine hormone peptide that consists of 37 residues and is the main component of extracellular amyloid deposits found in the pancreas of most type 2 diabetes patients. Amylin peptides are self-assembled to form oligomers and fibrils. So far, four different molecular structures of the self-assembled amylin fibrils have been observed experimentally: two ssNMR models and two crystal models. This study reveals, for the first time, that there are four self-assembled amylin forms that differ in the orientations of the side chains along the β-arch and are all derived from the two ssNMR models. The two ssNMR models are composed of these four different self-assembled forms of amylin, and the two crystal models are composed of two different self-assembled forms of amylin. This study illustrates at the atomic level the differences among the four experimental models and proposes eight new models of self-assembled amylin that are also composed of the four different self-assembled forms of amylin. Our results show polymorphism of the self-assembled fibril-like amylin, with a slight preference of some of the newly constructed models over the experimental models. Finally, we propose that two different self-assembled fibril-like forms of amylin can interact to form a new fibril-like amylin. We investigated this argument and found that some fibril-like amylin prefers to interact to form stable fibril-like structures, whereas others disfavor it. Our work provides new insights that may suggest strategies for future pharmacological studies that aim to find ways to ameliorate the interactions between polymorphic oligomers and fibrils of amylin.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
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59
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Linnewiel-Hermoni K, Motro Y, Miller Y, Levy J, Sharoni Y. Carotenoid derivatives inhibit nuclear factor kappa B activity in bone and cancer cells by targeting key thiol groups. Free Radic Biol Med 2014; 75:105-20. [PMID: 25078119 DOI: 10.1016/j.freeradbiomed.2014.07.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 07/05/2014] [Accepted: 07/19/2014] [Indexed: 11/25/2022]
Abstract
Aberrant activation of the nuclear factor kappa B (NFkB) transcription system contributes to cancer progression, and has a harmful effect on bone health. Several major components of the NFkB pathway such as IkB Kinase (IKK) and the NFkB subunits contain cysteine residues that are critical for their activity. The interaction of electrophiles with these cysteine residues results in NFkB inhibition. Carotenoids, hydrophobic plant pigments, are devoid of electrophilic groups, and we have previously demonstrated that carotenoid derivatives, but not the native compounds activate the Nrf2 transcription system. The aim of the current study was to examine whether carotenoid derivatives inhibit NFkB, and, if so, to determine the molecular mechanism underpinning the inhibitory action. We report in the present study that a mixture of oxidized derivatives, prepared by ethanol extraction from partially oxidized lycopene preparation, inhibited NFkB reporter gene activity. In contrast, the intact carotenoid was inactive. A series of synthetic dialdehyde carotenoid derivatives inhibited reporter activity as well as several stages of the NFkB pathway in both cancer and bone cells. The activity of the carotenoid derivatives depended on the reactivity of the electrophilic groups in reactions such as Michael addition to sulfhydryl groups of proteins. Specifically, carotenoid derivatives directly interacted with two key proteins of the NFkB pathway: the IKKβ and the p65 subunit. Direct interaction with IKKβ was found in an in vitro kinase assay with a recombinant enzyme. The inhibition by carotenoid derivatives of p65 transcriptional activity was observed in a reporter gene assay performed in the presence of excess p65. This inhibition action resulted, at least in part, from direct interaction of the carotenoid derivative with p65 leading to reduced binding of the protein to DNA as evidenced by electrophoretic mobility shift assay (EMSA) experiments. Importantly, we found by using mutation in key cysteine residues of both p65 and IKK that specific thiol groups are essential for NFkB inhibition by carotenoid derivatives. In conclusion, we propose that electrophilic carotenoid derivatives contribute to cancer prevention as well as bone health maintenance via the inhibition of the NFkB transcription system. Pivotal thiol groups of both IKK and p65 play a key role in this process.
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Affiliation(s)
- Karin Linnewiel-Hermoni
- Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev and Soroka Medical Center, Beer Sheva, Israel.
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Joseph Levy
- Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev and Soroka Medical Center, Beer Sheva, Israel
| | - Yoav Sharoni
- Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev and Soroka Medical Center, Beer Sheva, Israel
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60
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Watly J, Simonovsky E, Wieczorek R, Barbosa N, Miller Y, Kozlowski H. Insight into the coordination and the binding sites of Cu(2+) by the histidyl-6-tag using experimental and computational tools. Inorg Chem 2014; 53:6675-83. [PMID: 24905906 DOI: 10.1021/ic500387u] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
His-tags are specific sequences containing six to nine subsequent histydyl residues, and they are used for purification of recombinant proteins by use of IMAC chromatography. Such polyhistydyl tags, often used in molecular biology, can be also found in nature. Proteins containing histidine-rich domains play a critical role in many life functions in both prokaryote and eukaryote organisms. Binding mode and the thermodynamic properties of the system depend on the specific metal ion and the histidine sequence. Despite the wide application of the His-tag for purification of proteins, little is known about the properties of metal-binding to such tag domains. This inspired us to undertake detailed studies on the coordination of Cu(2+) ion to hexa-His-tag. Experiments were performed using the potentiometric, UV-visible, CD, and EPR techniques. In addition, molecular dynamics (MD) simulations and density functional theory (DFT) calculations were applied. The experimental studies have shown that the Cu(2+) ion binds most likely to two imidazoles and one, two, or three amide nitrogens, depending on the pH. The structures and stabilities of the complexes for the Cu(2+)-Ac-(His)6-NH2 system using experimental and computational tools were established. Polymorphic binding states are suggested, with a possibility of the formation of α-helix structure induced by metal ion coordination. Metal ion is bound to various pairs of imidazole moieties derived from the tag with different efficiencies. The coordination sphere around the metal ion is completed by molecules of water. Finally, the Cu(2+) binding by Ac-(His)6-NH2 is much more efficient compared to other multihistidine protein domains.
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Affiliation(s)
- Joanna Watly
- Faculty of Chemistry, University of Wroclaw , 50-383 Wroclaw, Poland
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61
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Zeytuni N, Uebe R, Maes M, Davidov G, Baram M, Raschdorf O, Friedler A, Miller Y, Schüler D, Zarivach R. Bacterial magnetosome biomineralization--a novel platform to study molecular mechanisms of human CDF-related Type-II diabetes. PLoS One 2014; 9:e97154. [PMID: 24819161 PMCID: PMC4018254 DOI: 10.1371/journal.pone.0097154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/15/2014] [Indexed: 12/20/2022] Open
Abstract
Cation diffusion facilitators (CDF) are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all organisms. CDFs were found to be involved in numerous human health conditions, such as Type-II diabetes and neurodegenerative diseases. In this work, we established the magnetite biomineralizing alphaproteobacterium Magnetospirillum gryphiswaldense as an effective model system to study CDF-related Type-II diabetes. Here, we introduced two ZnT-8 Type-II diabetes-related mutations into the M. gryphiswaldense MamM protein, a magnetosome-associated CDF transporter essential for magnetite biomineralization within magnetosome vesicles. The mutations' effects on magnetite biomineralization and iron transport within magnetosome vesicles were tested in vivo. Additionally, by combining several in vitro and in silico methodologies we provide new mechanistic insights for ZnT-8 polymorphism at position 325, located at a crucial dimerization site important for CDF regulation and activation. Overall, by following differentiated, easily measurable, magnetism-related phenotypes we can utilize magnetotactic bacteria for future research of CDF-related human diseases.
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Affiliation(s)
- Natalie Zeytuni
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - René Uebe
- Ludwig Maximillian University of Munich, Dept. Biology I, Martinsried, Germany
| | - Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Geula Davidov
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Baram
- Department of Chemistry, Ben Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oliver Raschdorf
- Ludwig Maximillian University of Munich, Dept. Biology I, Martinsried, Germany
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Yifat Miller
- Department of Chemistry, Ben Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dirk Schüler
- Ludwig Maximillian University of Munich, Dept. Biology I, Martinsried, Germany
| | - Raz Zarivach
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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62
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Wineman-Fisher V, Simkovitch R, Shomer S, Gepshtein R, Huppert D, Saif M, Kallio K, Remington SJ, Miller Y. Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A. Phys Chem Chem Phys 2014; 16:11196-208. [PMID: 24776960 DOI: 10.1039/c4cp00311j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations near the fluorescing chromophore of the green fluorescent protein (GFP) have direct effects on the absorption and emission spectra. Some mutants have significant band shifts and most of the mutants exhibit a loss of fluorescence intensity. In this study we continue our investigation of the factors controlling the excited state proton transfer (PT) process of GFP, in particular to study the effects of modifications to the key side chain Ser205 in wt-GFP, proposed to participate in the proton wire. To this aim we combined mutagenesis, X-ray crystallography, steady-state spectroscopy, time-resolved emission spectroscopy and all-atom explicit molecular dynamics (MD) simulations to study the double mutant T203V/S205A. Our results show that while in the previously described GFP double mutant T203V/S205V the PT process does not occur, in the T203V/S205A mutant the PT process does occur, but with a 350 times slower rate than in wild-type GFP (wt-GFP). Furthermore, the kinetic isotope effect in the GFP double mutant T203V/S205A is twice smaller than in the wt-GFP and in the GFP single mutant S205V, which forms a novel PT pathway. On the other hand, the crystal structure of GFP T203V/S205A does not reveal a viable proton transfer pathway. To explain PT in GFP T203V/S205A, we argue on the basis of the MD simulations for an alternative, novel proton-wire pathway which involves the phenol group of the chromophore and water molecules infrequently entering from the bulk. This alternative pathway may explain the dramatically slow PT in the GFP double mutant T203V/S205A compared to wt-GFP.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel.
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63
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Zeytuni N, Uebe R, Maes M, Davidov G, Baram M, Raschdorf O, Nadav-Tsubery M, Kolusheva S, Bitton R, Goobes G, Friedler A, Miller Y, Schüler D, Zarivach R. Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain. PLoS One 2014; 9:e92141. [PMID: 24658343 PMCID: PMC3962391 DOI: 10.1371/journal.pone.0092141] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/18/2014] [Indexed: 01/25/2023] Open
Abstract
Cation diffusion facilitators (CDF) are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all domains of life. CDF's were shown to be involved in several human diseases, such as Type-II diabetes and neurodegenerative diseases. In this work, we employed a multi-disciplinary approach to study the activation mechanism of the CDF protein family. For this we used MamM, one of the main ion transporters of magnetosomes--bacterial organelles that enable magnetotactic bacteria to orientate along geomagnetic fields. Our results reveal that the cytosolic domain of MamM forms a stable dimer that undergoes distinct conformational changes upon divalent cation binding. MamM conformational change is associated with three metal binding sites that were identified and characterized. Altogether, our results provide a novel auto-regulation mode of action model in which the cytosolic domain's conformational changes upon ligand binding allows the priming of the CDF into its transport mode.
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Affiliation(s)
- Natalie Zeytuni
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - René Uebe
- Ludwig Maximillian University of Munich, Department of Biology I, Martinsried, Germany
| | - Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Geula Davidov
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Baram
- Department of Chemistry, Ben Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Oliver Raschdorf
- Ludwig Maximillian University of Munich, Department of Biology I, Martinsried, Germany
| | | | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Ronit Bitton
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, Israel
- Department of Chemical Engineering, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Yifat Miller
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, Israel
- Department of Chemical Engineering, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Dirk Schüler
- Ludwig Maximillian University of Munich, Department of Biology I, Martinsried, Germany
| | - Raz Zarivach
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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64
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Raz Y, Adler J, Vogel A, Scheidt HA, Häupl T, Abel B, Huster D, Miller Y. The influence of the ΔK280 mutation and N- or C-terminal extensions on the structure, dynamics, and fibril morphology of the tau R2 repeat. Phys Chem Chem Phys 2014; 16:7710-7. [DOI: 10.1039/c3cp54890b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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Simkovitch R, Huppert A, Huppert D, Remington SJ, Miller Y. Proton Transfer in Wild-Type GFP and S205V Mutant Is Reduced by Conformational Changes of Residues in the Proton Wire. J Phys Chem B 2013; 117:11921-31. [DOI: 10.1021/jp405698g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ron Simkovitch
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amit Huppert
- Gertner Research Center, Tel-Hashomer 52621, Israel
| | - Dan Huppert
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - S. James Remington
- Department
of Physics and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, United States
| | - Yifat Miller
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er
Sheva 84105, Israel
- Ilse
Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
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66
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Miller Y, Baram M. Investigating the Interactions between Aβ and Amylin: Insight into the Link between Alzheimer's and Type II Diabetes. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Raz Y, Rubinov B, Matmor M, Rapaport H, Ashkenasy G, Miller Y. Effects of mutations in de novo designed synthetic amphiphilic β-sheet peptides on self-assembly of fibrils. Chem Commun (Camb) 2013; 49:6561-3. [DOI: 10.1039/c3cc42879f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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68
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Raz Y, Adler J, Huster D, Haupl T, Abel B, Miller Y. The Deltak280 Mutation in the Tau Protein may Induce the Formation of Stable Abeta-Tau Aggregates in FTDP-17. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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69
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Liu X, Miller Y, Burton N, Chang J, Brown W. A randomized controlled trial assessing the effects of Tai Chi on indicators of health related qualify of life in adults with elevated blood glucose level. J Sci Med Sport 2012. [DOI: 10.1016/j.jsams.2012.11.875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Abstract
There has been a lot of speculation about the role of water in gas phase reactions involving neutrals, radicals and ions. The reaction of NO and OH has attracted a lot of attention in the past due to its relevance for ozone chemistry in the atmosphere. In the present contribution we report low temperature measurements of the recombination of OH and NO at low temperatures in Laval nozzle expansions between 300 K and 60 K. We find an increase of the bimolecular rate constant in the presence of water of up to 40%. This effect has been attributed to water molecules acting either as an efficient collider releasing energy from the intermediate (in collisions) or – which is more likely for the present experimental conditions – as a cluster partner of the reaction intermediate HONO that also dissipates energy via cluster dissociation, which can in turn both stabilize the reaction intermediate, decrease back reaction to OH and NO, and enh ance finally the overall reaction to the products. The supersaturation of water vapor in the cold Laval nozzle expansion strongly favors the formation of clusters in the nozzle throat; their exact concentration is, however, difficult to estimate due to non-equilibrium conditions. The possible role of clusters in the recombination of OH and NO is investigated using ab initio molecular dynamics calculations. Beyond the reaction intermediate HONO and intramolecular proton transfer events also transient HOON was observed in the theoretical study.
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Affiliation(s)
- Matthias Liessmann
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Leipzig, Deutschland
| | - Yifat Miller
- Ben-Gurion University of Negev, Department of Chemistry, Be er Sheva 84105, Israel
| | - Benny Gerber
- Hebrew University of Jerusalem, Department of Chemistry, Jerusalem, Israel
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Shmilovits-Ofir M, Miller Y, Gerber RB. Conformational transitions of glycine induced by vibrational excitation of the O-H stretch. Phys Chem Chem Phys 2011; 13:8715-22. [PMID: 20922237 DOI: 10.1039/c0cp01385d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.
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Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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73
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Miller Y, Ma B, Nussinov R. Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states. Biochemistry 2011; 50:5172-81. [PMID: 21506544 PMCID: PMC3109766 DOI: 10.1021/bi200400u] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Amyloid plaques and neurofibrillary tangles simultaneously accumulate in Alzheimer’s disease (AD). It is known that Aβ and tau exist together in the mitochondria; however, the interactions between Aβ oligomers and tau are controversial. Moreover, it is still unclear which specific domains in the tau protein can interact with Aβ oligomers and what could be the effect of these interactions. Herein, we examine three different Aβ–tau oligomeric complexes. These complexes present interactions of Aβ with three domains in the tau protein; all contain high β-structure propensity in their R2, R3, and R4 repeats. Our results show that, among these, Aβ oligomers are likely to interact with the R2 domain to form a stable complex with better alignment in the turn region and the β-structure domain. We therefore propose that the R2 domain can interact with soluble Aβ oligomers and consequently promote aggregation. EM and AFM images and dimensions revealed highly polymorphic tau aggregates. We suggest that the polymorphic tau and Aβ–tau aggregates may be largely due to repeat sequences which are prone to variable turn locations along the tau repeats.
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Affiliation(s)
- Yifat Miller
- Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702, USA
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74
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Parthasarathy S, Long F, Miller Y, Xiao Y, McElheny D, Thurber K, Ma B, Nussinov R, Ishii Y. Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc 2011; 133:3390-400. [PMID: 21341665 PMCID: PMC3074258 DOI: 10.1021/ja1072178] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cu(2+) binding to Alzheimer's β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimer's senile plaque and such association of Aβ with Cu(2+) triggers the production of neurotoxic reactive oxygen species (ROS) such as H(2)O(2). However, detailed binding sites and binding structures of Cu(2+) to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu(2+) binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution (13)C solid-state NMR (SSNMR) for full-length 40-residue Aβ(1-40). Selective quenching observed in (13)C SSNMR of Cu(2+)-bound Aβ(1-40) suggested that primary Cu(2+) binding sites in Aβ(1-40) fibrils include N(ε) in His-13 and His-14 and carboxyl groups in Val-40 as well as in Glu sidechains (Glu-3, Glu-11, and/or Glu-22). (13)C chemical shift analysis demonstrated no major structural changes upon Cu(2+) binding in the hydrophobic core regions (residues 18-25 and 30-36). Although the ROS production via oxidization of Met-35 in the presence of Cu(2+) has been long suspected, our SSNMR analysis of (13)C(ε)H(3)-S- in M35 showed little changes after Cu(2+) binding, excluding the possibility of Met-35 oxidization by Cu(2+) alone. Preliminary molecular dynamics (MD) simulations on Cu(2+)-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu(2+)-binding modes unique in Aβ fibril, which are realized by both intra- and intermolecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.
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Affiliation(s)
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Yifat Miller
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Kent Thurber
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda MD 20892
| | - Buyong Ma
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
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Miller Y, Ma B, Nussinov R. The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. J Am Chem Soc 2011; 133:2742-8. [PMID: 21299220 DOI: 10.1021/ja1100273] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elucidating the structure of Aβ(1-40) fibrils is of interest in Alzheimer's disease research because it is required for designing therapeutics that target Aβ(1-40) fibril formation at an early stage of the disease. M35 is a crucial residue because of its potential oxidation and its strong interactions across β-strands and across β-sheets in Aβ fibrils. Experimentally, data for the three-fold symmetry structure of the Aβ(9-40) fibril suggest formation of tight hydrophobic core through M35 interactions across the fibril axis and strong I31-V39 interactions between different cross-β units. Herein, on the basis of experimental data, we probe conformers with three-fold symmetry of the full-length Aβ(1-40). Our all-atom molecular dynamics simulations in explicit solvent of conformers based on the ssNMR data reproduced experimental observations of M35-M35 and I31-V39 distances. Our interpretation of the experimental data suggests that the observed ∼5-7 Å M35-M35 distance in the fibril three-fold symmetry structure is likely to relate to M35 interactions along the fibril axis, rather than across the fibril axis, since our measured M35-M35 distances across the fibril axis are consistently above 15 Å. Consequently, we revealed that the unique Aβ(1-40) triangular structure has a large cavity along the fibril axis and that the N-termini can assist in the stabilization of the fibril by interacting with the U-turn domains or with the C-termini domains. Our findings, together with the recent cyroEM characterization of the hollow core in Aβ(1-42) fibrils, point to the relevance of a cavity in Aβ(1-40/1-42) oligomers which should be considered when targeting oligomer toxicity.
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Affiliation(s)
- Yifat Miller
- Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, Maryland 21702, USA
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Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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78
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Aβ Amyloid Organization: Insight into Aβ Aggregation. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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79
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Miller Y, Thomas JL, Kemp DD, Finlayson-Pitts BJ, Gordon MS, Tobias DJ, Gerber RB. Structure of Large Nitrate−Water Clusters at Ambient Temperatures: Simulations with Effective Fragment Potentials and Force Fields with Implications for Atmospheric Chemistry. J Phys Chem A 2009; 113:12805-14. [DOI: 10.1021/jp9070339] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Jennie L. Thomas
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Daniel D. Kemp
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Barbara J. Finlayson-Pitts
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Mark S. Gordon
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Douglas J. Tobias
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - R. Benny Gerber
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel, Department of Chemistry and AirUCI, University of California, Irvine, California 92697-2025, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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80
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Miller Y, Finlayson-Pitts BJ, Gerber RB. Ionization of N2O4in Contact with Water: Mechanism, Time Scales and Atmospheric Implications. J Am Chem Soc 2009; 131:12180-5. [DOI: 10.1021/ja900350g] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry, and The Fritz Haber Research Center, Hebrew University, Jerusalem 91904, Israel, and Department of Chemistry, University of California, Irvine, California 92697-2025
| | - Barbara J. Finlayson-Pitts
- Department of Physical Chemistry, and The Fritz Haber Research Center, Hebrew University, Jerusalem 91904, Israel, and Department of Chemistry, University of California, Irvine, California 92697-2025
| | - R. Benny Gerber
- Department of Physical Chemistry, and The Fritz Haber Research Center, Hebrew University, Jerusalem 91904, Israel, and Department of Chemistry, University of California, Irvine, California 92697-2025
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81
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Link O, Vöhringer-Martinez E, Lugovoj E, Liu Y, Siefermann K, Faubel M, Grubmüller H, Gerber RB, Miller Y, Abel B. Ultrafast phase transitions in metastable water near liquid interfaces. Faraday Discuss 2009; 141:67-79; discussion 81-98. [DOI: 10.1039/b811659h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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82
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Wolf I, Shapira A, Giniger R, Miller Y, Gerber R, Cheshnovsky O. Critical Size for Intracluster Proton Transfer from Water to an Anion. Angew Chem Int Ed Engl 2008; 47:6272-4. [DOI: 10.1002/anie.200800542] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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83
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Wolf I, Shapira A, Giniger R, Miller Y, Gerber R, Cheshnovsky O. Critical Size for Intracluster Proton Transfer from Water to an Anion. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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84
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Abstract
Recombination events of a proton with NO3- at (H2O)8 clusters are studied by molecular dynamics, using "on-the-fly" reliable ab initio MP2 potentials. The main findings are: (1) the lifetime of the ions is less than 1.2 picoseconds; (2) the recombination step invariably involves H3O+, not H5O2+; and (3) an essentially unique transition-state structure of H3O+/NO3- for recombination is found in all cases. Proton migration involves both H3O+ and H5O2+ species: Grotthuss and other mechanisms contribute.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem, 91904, Israel
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85
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Kamboures MA, Raff JD, Miller Y, Phillips LF, Finlayson-Pitts BJ, Gerber RB. Complexes of HNO3 and NO3− with NO2 and N2O4, and their potential role in atmospheric HONO formation. Phys Chem Chem Phys 2008; 10:6019-32. [DOI: 10.1039/b805330h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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86
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Miller Y, Gerber RB. Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O: hydrogen-hopping and photodissociation processes. J Am Chem Soc 2007; 128:9594-5. [PMID: 16866489 DOI: 10.1021/ja062890+] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photochemical processes of sulfuric acid (H2SO4) and sulfuric acid monohydrate (H2SO4-H2O) following overtone excitation of the OH stretching mode are studied by classical trajectory simulations using the semiempirical PM3 potential suface in "on the fly" calculations. The main results are the following: (1) In the excitation of H2SO4 to the fifth OH-stretch overtone, hopping of the H atom between oxygen atoms is found to take place in 22% of the trajectories, only once during simulations of 400 ps. (2) All the trajectories for H2SO4 show a rapid cis-trans isomerization. (3) The photolysis of H2SO4 into SO3 + H2O takes place in 5% of the trajectories on a time scale of approximately 9 ps. (4) Only low overtone levels of H2SO4-H2O have sufficiently long lifetimes to be spectroscopically relevant. Excitation to these OH stretching overtones is found to result in the dissociation of the cluster. H hopping or dissociation of H2SO4 does not take place.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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87
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Miller Y, Chaban GM, Zhou J, Asmis KR, Neumark DM, Gerber RB. Vibrational spectroscopy of (SO42−)∙(H2O)n clusters, n=1–5: Harmonic and anharmonic calculations and experiment. J Chem Phys 2007; 127:094305. [PMID: 17824737 DOI: 10.1063/1.2764074] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n<or=5.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel
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88
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Miller Y, Chaban GM, Finlayson-Pitts BJ, Gerber RB. Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O. J Phys Chem A 2007; 110:5342-54. [PMID: 16623461 DOI: 10.1021/jp0559940] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in "on-the-fly" simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO, isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these OH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.
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Affiliation(s)
- Y Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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89
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Ramazan KA, Wingen LM, Miller Y, Chaban GM, Gerber RB, Xantheas SS, Finlayson-Pitts BJ. New Experimental and Theoretical Approach to the Heterogeneous Hydrolysis of NO2: Key Role of Molecular Nitric Acid and Its Complexes. J Phys Chem A 2006; 110:6886-97. [PMID: 16722704 DOI: 10.1021/jp056426n] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although heterogeneous chemistry on surfaces in the troposphere is known to be important, there are currently only a few techniques available for studying the nature of surface-adsorbed species as well as their chemistry and photochemistry under atmospheric conditions of 1 atm pressure and in the presence of water vapor. We report here a new laboratory approach using a combination of long path Fourier transform infrared spectroscopy (FTIR) and attenuated total reflectance (ATR) FTIR that allows the simultaneous observation and measurement of gases and surface species. Theory is used to identify the surface-adsorbed intermediates and products, and to estimate their relative concentrations. At intermediate relative humidities typical of the tropospheric boundary layer, the nitric acid formed during NO2 heterogeneous hydrolysis is shown to exist both as nitrate ions from the dissociation of nitric acid formed on the surface and as molecular nitric acid. In both cases, the ions and HNO3 are complexed to water molecules. Upon pumping, water is selectively removed, shifting the NO(3-)-HNO3(H2O)y equilibria toward more dehydrated forms of HNO3 and ultimately to nitric acid dimers. Irradiation of the nitric acid-water film using 300-400 nm radiation generates gaseous NO, while irradiation at 254 nm generates both NO and HONO, resulting in conversion of surface-adsorbed nitrogen oxides into photochemically active NO(x). These studies suggest that the assumption that deposition or formation of nitric acid provides a permanent removal mechanism from the atmosphere may not be correct. Furthermore, a potential role of surface-adsorbed nitric acid and other species formed during the heterogeneous hydrolysis of NO2 in the oxidation of organics on surfaces, and in the generation of gas-phase HONO on local to global scales, should be considered.
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Affiliation(s)
- K A Ramazan
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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90
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Keith R, Miller Y, Kelly K, Hirsch F, Kittelson J, Jackson M, Metsinger V, Franklin W, Bunn P, Geraci M. PD-056 Clinical update on the phase II trial of oral iloprost in the chemoprevention of lung cancer in high risk patients. Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)80389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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91
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Miller Y, Keith R, Hirsch F, Dempsey E, Franklin W, Kennedy T. P-265 Natural history of untreated endobronchial carcinoma in situ. Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)80759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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92
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Miller Y, Hyun D, Blatchford P, Lewis M, Keith R, Kennedy T, Franklin W, Kittelson J, Hirsch F. P-264 Ki67 proliferation index in endobronchial biopsies: Associationwith lung cancer, airflow obstruction and smoking history. Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)80758-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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93
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Franklin W, Sugita M, Haney J, Miller Y, Keith R, Mitchell J, Hirsch F, Kennedy T, Bemis L. P-245 245 Detection of RNA biomarkers in sputum of lung cancer patientsand high risk smokers. Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)80739-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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94
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Merrick D, Sugita M, Hirsch F, Keith R, Miller Y, Coldren C, Lapadat R, Witta S, Geraci M, Franklin W. O-049 Affymetrix gene expression profiles in premalignant bronchialmucosa. Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)80181-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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95
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Miller Y, Chaban GM, Gerber RB. Ab Initio Vibrational Calculations for H2SO4 and H2SO4·H2O: Spectroscopy and the Nature of the Anharmonic Couplings. J Phys Chem A 2005; 109:6565-74. [PMID: 16834003 DOI: 10.1021/jp058110l] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H2SO4) and of sulfuric acid monohydrate cluster (H2SO4 x H2O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H2SO4 and H2SO4 x H2O.
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Affiliation(s)
- Y Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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96
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Varella-Garcia M, Schulte AP, Kittelson J, Zeng C, Miller Y, Franklin WA, Hirsch FR. Evaluation of chromosomal aneusomy in bronchial epithelium of smokers as a marker for lung cancer risk. J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.7184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - A. P. Schulte
- University of Colorado Health Sciences Center, Denver, CO
| | - J. Kittelson
- University of Colorado Health Sciences Center, Denver, CO
| | - C. Zeng
- University of Colorado Health Sciences Center, Denver, CO
| | - Y. Miller
- University of Colorado Health Sciences Center, Denver, CO
| | - W. A. Franklin
- University of Colorado Health Sciences Center, Denver, CO
| | - F. R. Hirsch
- University of Colorado Health Sciences Center, Denver, CO
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97
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Kuschel A, Lübke A, Köppe E, Miller Y, Hahlweg K, Sanders MR. Häufigkeit psychischer Auffälligkeiten und Begleitsymptome bei drei- bis sechsjährigen Kindern: Ergebnisse der Braunschweiger Kindergartenstudie. Zeitschrift für Kinder- und Jugendpsychiatrie und Psychotherapie 2004; 32:97-106. [PMID: 15181785 DOI: 10.1024/1422-4917.32.2.97] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Zusammenfassung: Fragestellung: Im Rahmen der Braunschweiger Kindergartenstudie wurde die Häufigkeit psychischer Auffälligkeiten und Begleitsymptome bei Kindern im Alter zwischen 3 und 6 Jahren untersucht. Methode: Die Untersuchung wurde im November 1998 in allen städtischen Kindertagesstätten Braunschweigs mit einer leicht modifizierten Version des Elternfragebogens über das Verhalten von Kindern und Jugendlichen/CBCL 4-18 durchgeführt. Von N = 809 Kindern liegen Elterneinschätzungen vor. Ergebnisse: Die Prävalenzraten für psychische Störungen bei Kindergartenkindern liegen zwischen 0,5% und 5,0%, wobei in dieser Altersgruppe Aggressives Verhalten, Aufmerksamkeitsprobleme und Soziale Probleme am häufigsten auftreten. Es werden außerdem Komorbiditätsraten für die einzelnen Syndromskalenpaare der CBCL berichtet. Diskussion: Abschließend werden die vorliegenden Ergebnisse mit anderen Untersuchungen verglichen und Implikationen vor allem für die Prävention kindlicher Verhaltensauffälligkeiten diskutiert.
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Affiliation(s)
- A Kuschel
- Institut für Psychologie, Technischen Universität Braunschweig
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98
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Miller Y, Fredj E, Harvey JN, Gerber RB. Ultraviolet Spectroscopy of Large Water Clusters: Model and Calculations for (H2O)n, for n = 8, 11, 20, 40, and 50. J Phys Chem A 2004. [DOI: 10.1021/jp030678b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Y. Miller
- Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, Computer Science Department, Jerusalem College of TechnologyMachon Lev, Jerusalem 91160, Israel, School of Chemistry, University of Bristol, Bristol BS8 1TS, England, and Department of Chemistry, University of California, Irvine, California 92697-2025
| | - E. Fredj
- Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, Computer Science Department, Jerusalem College of TechnologyMachon Lev, Jerusalem 91160, Israel, School of Chemistry, University of Bristol, Bristol BS8 1TS, England, and Department of Chemistry, University of California, Irvine, California 92697-2025
| | - J. N. Harvey
- Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, Computer Science Department, Jerusalem College of TechnologyMachon Lev, Jerusalem 91160, Israel, School of Chemistry, University of Bristol, Bristol BS8 1TS, England, and Department of Chemistry, University of California, Irvine, California 92697-2025
| | - R. B. Gerber
- Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, Computer Science Department, Jerusalem College of TechnologyMachon Lev, Jerusalem 91160, Israel, School of Chemistry, University of Bristol, Bristol BS8 1TS, England, and Department of Chemistry, University of California, Irvine, California 92697-2025
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99
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Gay K, Baughman W, Miller Y, Jackson D, Whitney CG, Schuchat A, Farley MM, Tenover F, Stephens DS. The emergence of Streptococcus pneumoniae resistant to macrolide antimicrobial agents: a 6-year population-based assessment. J Infect Dis 2000; 182:1417-24. [PMID: 11023465 DOI: 10.1086/315853] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2000] [Revised: 06/23/2000] [Indexed: 11/03/2022] Open
Abstract
From 1994 through 1999, the available isolates (4148 isolates) from active population-based surveillance of invasive pneumococcal disease in metropolitan Atlanta were serotyped and were tested for antimicrobial susceptibility. Macrolide-resistant isolates were studied for the presence of ermAM (a ribosomal methylase gene), mefE (a macrolide efflux gene), and tetM (the class M tetracycline resistance gene). Macrolide resistance increased from 16% of all invasive isolates in 1994 to 32% in 1999. Of the macrolide-resistant pneumococcal isolates studied, 99% contained genomic copies of mefE or ermAM. Isolates with ermAM were mainly serotypes 6B, 23F, 14, or 19F and contained tetM; mefE-associated isolates were predominantly serotypes 14, 6A, or 19F, and most did not contain tetM. The frequency of the ermAM-mediated phenotype in invasive Streptococcus pneumoniae remained stable over the 6-year surveillance. However, the mefE-mediated phenotype increased from 9% in 1994 to 26% of all isolates in 1999 and was noted in new serotypes. By 1999, 93% of the mefE-containing strains had minimum inhibitory concentrations >/=8 microgram/mL. Dissemination of the mefE determinant accounted for the rapid increase in the rate of macrolide resistance in our S. pneumoniae population.
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Affiliation(s)
- K Gay
- Departments of Medicine and of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
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100
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Kelly K, Dempsey E, Kennedy T, Miller Y, Franklin W, Prindiville S, Holte J, Bunn P. Preliminary results from a phase II trial evaluating 13 cis-retinoic acid with or without alpha tocopherol or observation in patients at high risk for lung cancer. Lung Cancer 2000. [DOI: 10.1016/s0169-5002(00)80788-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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