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  1. Article ; Online: Behavioral and Transcriptome Profiling of Heterozygous Rab10 Knock-Out Mice.

    Bunner, Wyatt / Wang, Jie / Cohen, Sarah / Bashtovyy, Denys / Perry, Rachel / Shookster, Daniel / Landry, Taylor / Harris, Elizabeth M / Stackman, Robert / Tran, Tuan D / Yasuda, Ryohei / Szatmari, Erzsebet M

    eNeuro

    2023  Volume 10, Issue 5

    Abstract: A central question in the field of aging research is to identify the cellular and molecular basis of neuroresilience. One potential candidate is the small GTPase, Rab10. Here, we used ... ...

    Abstract A central question in the field of aging research is to identify the cellular and molecular basis of neuroresilience. One potential candidate is the small GTPase, Rab10. Here, we used Rab10
    MeSH term(s) Mice ; Animals ; Mice, Knockout ; Alzheimer Disease/pathology ; Brain/metabolism ; Gene Expression Profiling ; Conditioning, Classical/physiology ; rab GTP-Binding Proteins/genetics ; rab GTP-Binding Proteins/metabolism
    Chemical Substances Rab10 protein, mouse (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2023-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2800598-3
    ISSN 2373-2822 ; 2373-2822
    ISSN (online) 2373-2822
    ISSN 2373-2822
    DOI 10.1523/ENEURO.0459-22.2023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Sequence conservation of apolipoprotein A-I affords novel insights into HDL structure-function.

    Bashtovyy, Denys / Jones, Martin K / Anantharamaiah, G M / Segrest, Jere P

    Journal of lipid research

    2010  Volume 52, Issue 3, Page(s) 435–450

    Abstract: We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types ... ...

    Abstract We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types in the central domain, helix 2/3 to helix 7/8. In the lipid-associating domain, helix 7 and helix 10 are the most and least conserved helixes, respectively. Furthermore, eight residues are completely conserved: P66, R83, P121, E191, and P220, and three of seven Tyr residues in human apoA-I, Y18, Y115, and Y192, are conserved. Residue Y18 appears to be important for assembly of HDL. E191-Y192 represents the only completely conserved pair of adjacent residues in apoA-I; Y192 is a preferred target for site-specific oxidative modification within atheroma, and molecular dynamic simulations suggest that the conserved pair E191-Y192 is in a solvent-exposed loop-helix-loop. Molecular dynamics testing of human apoA-I showed that M112 and M148 interact with Y115, a microenvironment unique to human apoA-I. Finally, conservation of Arg residues in the α11/3 helical wheel position 7 supports several possibilities: interactions with adjacent phospholipid molecules and/or oxidized lipids and/or binding of antioxidant enzymes through cation-π orbital interactions. We conclude that sequence alignment of apoA-I provides unique insights into apoA-I structure-function relationship.
    MeSH term(s) Amino Acid Sequence ; Animals ; Apolipoprotein A-I/chemistry ; Apolipoprotein A-I/metabolism ; Conserved Sequence ; Humans ; Lipoproteins, HDL/chemistry ; Lipoproteins, HDL/metabolism ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment
    Chemical Substances Apolipoprotein A-I ; Lipoproteins, HDL
    Language English
    Publishing date 2010-12-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 80154-9
    ISSN 1539-7262 ; 0022-2275
    ISSN (online) 1539-7262
    ISSN 0022-2275
    DOI 10.1194/jlr.R012658
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 175: Show issues Location:
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  3. Article: Sequence conservation of apolipoprotein A-I affords novel insights into HDL structure-function

    Bashtovyy, Denys / Jones, Martin K / Anantharamaiah, G.M / Segrest, Jere P

    Journal of lipid research JLR. 2011 Mar., v. 52, no. 3

    2011  

    Abstract: We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types ... ...

    Abstract We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types in the central domain, helix 2/3 to helix 7/8. In the lipid-associating domain, helix 7 and helix 10 are the most and least conserved helixes, respectively. Furthermore, eight residues are completely conserved: P66, R83, P121, E191, and P220, and three of seven Tyr residues in human apoA-I, Y18, Y115, and Y192, are conserved. Residue Y18 appears to be important for assembly of HDL. E191-Y192 represents the only completely conserved pair of adjacent residues in apoA-I; Y192 is a preferred target for site-specific oxidative modification within atheroma, and molecular dynamic simulations suggest that the conserved pair E191-Y192 is in a solvent-exposed loop-helix-loop. Molecular dynamics testing of human apoA-I showed that M112 and M148 interact with Y115, a microenvironment unique to human apoA-I. Finally, conservation of Arg residues in the α11/3 helical wheel position 7 supports several possibilities: interactions with adjacent phospholipid molecules and/or oxidized lipids and/or binding of antioxidant enzymes through cation-π orbital interactions. We conclude that sequence alignment of apoA-I provides unique insights into apoA-I structure-function relationship.
    Language English
    Dates of publication 2011-03
    Size p. 435-450.
    Publishing place American Society for Biochemistry and Molecular Biology
    Document type Article
    ZDB-ID 80154-9
    ISSN 1539-7262 ; 0022-2275
    ISSN (online) 1539-7262
    ISSN 0022-2275
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures.

    Páli, Tibor / Bashtovyy, Denys / Marsh, Derek

    Protein science : a publication of the Protein Society

    2006  Volume 15, Issue 5, Page(s) 1153–1161

    Abstract: The stoichiometry of the first shell of lipids interacting with a transmembrane protein is defined operationally by the population of spin-labeled lipid chains whose motion is restricted directly by the protein. Interaction stoichiometries have been ... ...

    Abstract The stoichiometry of the first shell of lipids interacting with a transmembrane protein is defined operationally by the population of spin-labeled lipid chains whose motion is restricted directly by the protein. Interaction stoichiometries have been determined experimentally for a wide range of alpha-helical integral membrane proteins by using spin-label ESR spectroscopy. Here, we determine the spatially defined number of first-shell lipids at the hydrophobic perimeter of integral membrane proteins whose 3D structure has been determined by X-ray crystallography and lipid-protein interactions characterized by spin-labeling. Molecular modeling is used to build a single shell of lipids surrounding transmembrane structures derived from the PDB. Constrained energy optimization of the protein-lipid assemblies is performed by molecular mechanics. For relatively small proteins (up to 7-12 transmembrane helices), the geometrical first shell corresponds to that defined experimentally by perturbation of the lipid-chain dynamics. For larger, multi-subunit alpha-helical proteins, the lipids perturbed directly by the protein may either exceed or be less in number than those that can be accommodated at the intramembranous perimeter. In these latter cases, the motionally restricted spin-labeled lipids can be augmented by intercalation, or can correspond to a specific subpopulation at the protein interface, respectively. For monomeric beta-barrel proteins, the geometrical lipid stoichiometry corresponds to that determined from lipid mobility for a 22-stranded barrel, but fewer lipids are motionally restricted than can be accommodated around an eight-stranded barrel. Deviations from the geometrical first shell, in the beta-barrel case, are for the smaller protein with a highly curved barrel.
    MeSH term(s) Bacterial Outer Membrane Proteins/chemistry ; Cell Membrane/metabolism ; Dimyristoylphosphatidylcholine/chemistry ; Escherichia coli Proteins/chemistry ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Membrane Fluidity ; Membrane Lipids/chemistry ; Membrane Lipids/metabolism ; Membrane Proteins/metabolism ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Receptors, Nicotinic/chemistry ; Surface Properties
    Chemical Substances Bacterial Outer Membrane Proteins ; Escherichia coli Proteins ; FhuA protein, E coli ; Lipid Bilayers ; Membrane Lipids ; Membrane Proteins ; Receptors, Nicotinic ; Dimyristoylphosphatidylcholine (U86ZGC74V5)
    Language English
    Publishing date 2006-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1110/ps.052021406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3407: Show issues Location:
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  5. Article: Structure prediction for the di-heme cytochrome b561 protein family.

    Bashtovyy, Denys / Bérczi, Alajos / Asard, Han / Páli, Tibor

    Protoplasma

    2003  Volume 221, Issue 1-2, Page(s) 31–40

    Abstract: Atomic models possessing the common structural features identified for the cytochrome b(561) (cyt b(561)) protein family are presented. A detailed and extensive sequence analysis was performed in order to identify and characterize protein sequences in ... ...

    Abstract Atomic models possessing the common structural features identified for the cytochrome b(561) (cyt b(561)) protein family are presented. A detailed and extensive sequence analysis was performed in order to identify and characterize protein sequences in this family of transmembrane electron transport proteins. According to transmembrane helix predictions, all sequences contain 6 transmembrane helices of which 2-6 are located closely in the same regions of the 26 sequences in the alignment. A mammalian ( Homo sapiens) and a plant ( Arabidopsis thaliana) sequence were selected to build 3-dimensional structures at atomic detail using molecular modeling tools. The main structural constraints included the 2 pairs of heme-ligating His residues that are fully conserved in the family and the lipid-facing sides of the helices, which were also very well conserved. The current paper proposes 3-dimensional structures which to our knowledge are the first ones for any protein in the cyt b(561) family. The highly conserved His residues anchoring the two hemes on the cytoplasmic side and noncytoplasmic side of the membrane are in all proteins located in the transmembrane helices 2, 4 and 3, 5, respectively. Several highly conserved amino acids with aromatic side chain are identified between the two heme ligation sites. These residues may constitute a putative transmembrane electron transport pathway. The present study demonstrates that the structural features in the cyt b(561) family are well conserved at both the sequence and the protein level. The central 4-helix core represents a transmembrane electron transfer architecture that is highly conserved in eukaryotic species.
    MeSH term(s) Amino Acid Sequence ; Arabidopsis/genetics ; Cytochrome b Group/chemistry ; Cytochrome b Group/genetics ; Electron Transport ; Heme/chemistry ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Chemical ; Molecular Sequence Data ; Protein Structure, Tertiary ; Structure-Activity Relationship
    Chemical Substances Cytochrome b Group ; cytochrome b561 (11130-51-1) ; Heme (42VZT0U6YR)
    Language English
    Publishing date 2003-05
    Publishing country Austria
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 123809-7
    ISSN 1615-6102 ; 0033-183X
    ISSN (online) 1615-6102
    ISSN 0033-183X
    DOI 10.1007/s00709-002-0065-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2366: Show issues Location:
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  6. Article: The ntrPR operon of Sinorhizobium meliloti is organized and functions as a toxin-antitoxin module.

    Bodogai, Monica / Ferenczi, Szilamér / Bashtovyy, Denys / Miclea, Paul / Papp, Péter / Dusha, Ilona

    Molecular plant-microbe interactions : MPMI

    2006  Volume 19, Issue 7, Page(s) 811–822

    Abstract: The chromosomal ntrPR operon of Sinorhizobium meliloti encodes a protein pair that forms a toxin-antitoxin (TA) module, the first characterized functional TA system in Rhizobiaceae. Similarly to other bacterial TA systems, the toxin gene ntrR is preceded ...

    Abstract The chromosomal ntrPR operon of Sinorhizobium meliloti encodes a protein pair that forms a toxin-antitoxin (TA) module, the first characterized functional TA system in Rhizobiaceae. Similarly to other bacterial TA systems, the toxin gene ntrR is preceded by and partially overlaps with the antitoxin gene ntrP. Based on protein homologies, the ntrPR operon belongs to the vapBC family of TA systems. The operon is negatively autoregulated by the NtrPNtrR complex. Promoter binding by NtrP is weak; stable complex formation also requires the presence of NtrR. The N-terminal part of NtrP is responsible for the interaction with promoter DNA, whereas the C-terminal part is required for protein-protein interactions. In the promoter region, a direct repeat sequence was identified as the binding site of the NtrPNtrR complex. NtrR expression resulted in the inhibition of cell growth and colony formation; this effect was counteracted by the presence of the antitoxin NtrP. These results and our earlier observations demonstrating a less effective downregulation of a wide range of symbiotic and metabolic functions in the ntrR mutant under microoxic conditions and an increased symbiotic efficiency with the host plant alfalfa suggest that the ntrPR module contributes to adjusting metabolic levels under symbiosis and other stressful conditions.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; DNA Footprinting ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Operon/genetics ; Sinorhizobium meliloti/drug effects ; Sinorhizobium meliloti/genetics ; Sinorhizobium meliloti/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins
    Language English
    Publishing date 2006-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 743331-1
    ISSN 1943-7706 ; 0894-0282
    ISSN (online) 1943-7706
    ISSN 0894-0282
    DOI 10.1094/MPMI-19-0811
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3530: Show issues Location:
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  7. Article ; Online: Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations.

    Catte, Andrea / Patterson, James C / Bashtovyy, Denys / Jones, Martin K / Gu, Feifei / Li, Ling / Rampioni, Aldo / Sengupta, Durba / Vuorela, Timo / Niemelä, Perttu / Karttunen, Mikko / Marrink, Siewert Jan / Vattulainen, Ilpo / Segrest, Jere P

    Biophysical journal

    2007  Volume 94, Issue 6, Page(s) 2306–2319

    Abstract: Spheroidal high-density lipoprotein (HDL) particles circulating in the blood are formed through an enzymatic process activated by apoA-I, leading to the esterification of cholesterol, which creates a hydrophobic core of cholesteryl ester molecules in the ...

    Abstract Spheroidal high-density lipoprotein (HDL) particles circulating in the blood are formed through an enzymatic process activated by apoA-I, leading to the esterification of cholesterol, which creates a hydrophobic core of cholesteryl ester molecules in the middle of the discoidal phospholipid bilayer. In this study, we investigated the conformation of apoA-I in model spheroidal HDL (ms-HDL) particles using both atomistic and coarse-grained molecular dynamics simulations, which are found to provide consistent results for all HDL properties we studied. The observed small contribution of cholesteryl oleate molecules to the solvent-accessible surface area of the entire ms-HDL particle indicates that palmitoyloleoylphosphatidylcholines and apoA-I molecules cover the hydrophobic core comprised of cholesteryl esters particularly well. The ms-HDL particles are found to form a prolate ellipsoidal shape, with sizes consistent with experimental results. Large rigid domains and low mobility of the protein are seen in all the simulations. Additionally, the average number of contacts of cholesteryl ester molecules with apoA-I residues indicates that cholesteryl esters interact with protein residues mainly through their cholesterol moiety. We propose that the interaction of annular cholesteryl oleate molecules contributes to apoA-I rigidity stabilizing and regulating the structure and function of the ms-HDL particle.
    MeSH term(s) Animals ; Apolipoprotein A-I/chemistry ; Biophysics/methods ; Cholesterol/chemistry ; Computer Simulation ; Humans ; Lipid Bilayers/chemistry ; Lipoproteins, HDL/chemistry ; Liver/metabolism ; Models, Biological ; Molecular Conformation ; Phosphatidylcholines/chemistry ; Protein Structure, Tertiary ; Solvents ; Surface Properties
    Chemical Substances Apolipoprotein A-I ; Lipid Bilayers ; Lipoproteins, HDL ; Phosphatidylcholines ; Solvents ; Cholesterol (97C5T2UQ7J)
    Language English
    Publishing date 2007-12-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1529/biophysj.107.115857
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study.

    Catte, Andrea / Patterson, James C / Jones, Martin K / Jerome, W Gray / Bashtovyy, Denys / Su, Zhengchang / Gu, Feifei / Chen, Jianguo / Aliste, Marcela P / Harvey, Stephen C / Li, Ling / Weinstein, Gilbert / Segrest, Jere P

    Biophysical journal

    2006  Volume 90, Issue 12, Page(s) 4345–4360

    Abstract: ApoA-I is a uniquely flexible lipid-scavenging protein capable of incorporating phospholipids into stable particles. Here we report molecular dynamics simulations on a series of progressively smaller discoidal high density lipoprotein particles produced ... ...

    Abstract ApoA-I is a uniquely flexible lipid-scavenging protein capable of incorporating phospholipids into stable particles. Here we report molecular dynamics simulations on a series of progressively smaller discoidal high density lipoprotein particles produced by incremental removal of palmitoyloleoylphosphatidylcholine via four different pathways. The starting model contained 160 palmitoyloleoylphosphatidylcholines and a belt of two antiparallel amphipathic helical lipid-associating domains of apolipoprotein (apo) A-I. The results are particularly compelling. After a few nanoseconds of molecular dynamics simulation, independent of the starting particle and method of size reduction, all simulated double belts of the four lipidated apoA-I particles have helical domains that impressively approximate the x-ray crystal structure of lipid-free apoA-I, particularly between residues 88 and 186. These results provide atomic resolution models for two of the particles produced by in vitro reconstitution of nascent high density lipoprotein particles. These particles, measuring 95 angstroms and 78 angstroms by nondenaturing gradient gel electrophoresis, correspond in composition and in size/shape (by negative stain electron microscopy) to the simulated particles with molar ratios of 100:2 and 50:2, respectively. The lipids of the 100:2 particle family form minimal surfaces at their monolayer-monolayer interface, whereas the 50:2 particle family displays a lipid pocket capable of binding a dynamic range of phospholipid molecules.
    MeSH term(s) Apolipoprotein A-I/chemistry ; Apolipoprotein A-I/ultrastructure ; Computer Simulation ; Crystallography/methods ; Lipoproteins, HDL/chemistry ; Lipoproteins, HDL/ultrastructure ; Models, Chemical ; Models, Molecular ; Motion ; Protein Conformation
    Chemical Substances Apolipoprotein A-I ; Lipoproteins, HDL
    Language English
    Publishing date 2006-06-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1529/biophysj.105.071456
    Database MEDical Literature Analysis and Retrieval System OnLINE

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