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  1. Article: Renovating a double fence with or without notifying the next door and across the street neighbors: why the biogenic cytoplasmic membrane of Gram-negative bacteria display asymmetry?

    Bogdanov, Mikhail

    Emerging topics in life sciences

    2023  Volume 7, Issue 1, Page(s) 137–150

    Abstract: The complex two-membrane organization of the envelope of Gram-negative bacteria imposes an unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on the cytoplasm facing leaflet of the cytoplasmic ...

    Abstract The complex two-membrane organization of the envelope of Gram-negative bacteria imposes an unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on the cytoplasm facing leaflet of the cytoplasmic (inner) membrane (IM), across the IM and between the IM and outer membrane (OM). Balanced growth of two membranes and continuous loss of phospholipids in the periplasmic leaflet of the IM as metabolic precursors for envelope components and for translocation to the OM requires a constant supply of phospholipids in the IM cytosolic leaflet. At present we have no explanation as to why the biogenic E. coli IM displays asymmetry. Lipid asymmetry is largely related to highly entropically disfavored, unequal headgroup and acyl group asymmetries which are usually actively maintained by active mechanisms. However, these mechanisms are largely unknown for bacteria. Alternatively, lipid asymmetry in biogenic IM could be metabolically controlled in order to maintain uniform bilayer growth and asymmetric transmembrane arrangement by balancing temporally the net rates of synthesis and flip-flop, inter IM and OM bidirectional flows and bilayer chemical and physical properties as spontaneous response. Does such flippase-less or 'lipid only", 'passive' mechanism of generation and maintenance of lipid asymmetry exists in the IM? The driving force for IM asymmetry can arise from the packing requirements imposed upon the bilayer system during cell division through disproportional distribution of two negatively curved phospholipids, phosphatidylethanolamine and cardiolipin, with consistent reciprocal tendency to increase and decrease lipid order in each membrane leaflet respectively.
    MeSH term(s) Escherichia coli/chemistry ; Escherichia coli/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Phospholipids/analysis ; Phospholipids/metabolism ; Gram-Negative Bacteria/metabolism ; Escherichia coli Proteins/analysis ; Escherichia coli Proteins/metabolism
    Chemical Substances Phospholipids ; Escherichia coli Proteins
    Language English
    Publishing date 2023-03-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20230042
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  2. Article ; Online: Exploring Uniform, Dual, and Dynamic Topologies of Membrane Proteins by Substituted Cysteine Accessibility Method (SCAM™).

    Bogdanov, Mikhail

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2715, Page(s) 121–157

    Abstract: A described simple and advanced protocol for Substituted Cysteine Accessibility Method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane ... ...

    Abstract A described simple and advanced protocol for Substituted Cysteine Accessibility Method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform or identify and quantify the degree of mixed topology or establish transmembrane assembly dynamics from relatively static experimental data such as endpoint topologies of membrane proteins. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at the time by cysteine residue, and the orientation with respect to the membrane is evaluated by using a pair of membrane-impermeable non-detectable and detectable thiol-reactive labeling reagents. For the most water-exposed cysteine residues in proteins, the thiol pKa lies in the range of 8-9, and formation of cysteinyl thiolate ions is optimum in aqueous rather in a nonpolar environment. These features and the ease of specific chemical modification with thiol reagents are central to SCAM™. Membrane side-specific sulfhydryl labeling allows to discriminate "exposed, protected or dynamic" cysteines strategically "implanted" at desired positions throughout cysteine less target protein template. The strategy described is widely used to map the topology of membrane protein and establish its transmembrane dynamics in intact cells of both diderm (two-membraned) Gram-negative and monoderm (one-membraned) Gram-positive bacteria, cell-derived oriented membrane vesicles, and proteoliposomes.
    MeSH term(s) Membrane Proteins ; Cysteine ; Amino Acids ; Sulfhydryl Compounds ; Sulfhydryl Reagents
    Chemical Substances Membrane Proteins ; Cysteine (K848JZ4886) ; Amino Acids ; Sulfhydryl Compounds ; Sulfhydryl Reagents
    Language English
    Publishing date 2023-11-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3445-5_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The power and challenge of lipid (a)symmetry across the membrane and cell.

    Bogdanov, Mikhail

    Emerging topics in life sciences

    2023  Volume 7, Issue 1, Page(s) 1–6

    Abstract: Membrane asymmetry means that the two sides of membrane are structurally, physically and functionally different. Membrane asymmetry is largely related to the lipid sidedness and particularly to compositional (lipid head and acyl group) and physical ( ... ...

    Abstract Membrane asymmetry means that the two sides of membrane are structurally, physically and functionally different. Membrane asymmetry is largely related to the lipid sidedness and particularly to compositional (lipid head and acyl group) and physical (lipid packing order, charge, hydration and H-bonding interactions) differences in the inner and outer leaflets of lipid bilayer. Chemically, structurally and conformationally different non-covalent bound lipid molecules are physically fluid and deformable and enable to interact dynamically to form transient arrangements with asymmetry both perpendicular and parallel to the plane of the lipid bilayer. Although biological membranes are almost universally asymmetric however the asymmetry is not absolute since only drastic difference in the number of lipids per leaflet is found and symmetric arrangements are possible. Asymmetry is thought to direct and influence many core biological functions by altering the membrane's collective biochemical, biophysical and structural properties. Asymmetric transbilayer lipid distribution is found across all lipid classes, cells and near all endomembrane compartments. Why cell membranes are (a)symmetric and adopt almost exclusively highly entropically disfavored asymmetric state?
    MeSH term(s) Cell Membrane/chemistry ; Lipid Bilayers/chemistry
    Chemical Substances Lipid Bilayers
    Language English
    Publishing date 2023-03-29
    Publishing country England
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20220088
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Preparation of Uniformly Oriented Inverted Inner (Cytoplasmic) Membrane Vesicles from Gram-Negative Bacterial Cells.

    Bogdanov, Mikhail

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2715, Page(s) 159–180

    Abstract: The complex double-membrane organization of the envelope in Gram-negative bacteria places unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on cytoplasm facing leaflet of cytoplasmic (inner) ... ...

    Abstract The complex double-membrane organization of the envelope in Gram-negative bacteria places unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on cytoplasm facing leaflet of cytoplasmic (inner) membrane (IM), across IM and between IM and outer membrane (OM). Uniformly oriented inside-out (ISO) vesicles became functional requisite for many biochemical reconstitution functional assays, vectorial proteomics, and vectorial lipidomics. Due to these demands, it is necessary to develop simple and reliable approaches for preparation of uniformly oriented IM membrane vesicles and validation of their sidedness. The uniformly ISO oriented membrane vesicles which have the cytoplasmic face of the membrane on the outside and the periplasmic side facing the sealed lumen can be obtained following intact cell disruption by a single passage through a French pressure cell (French press) at desired total pressure. Although high-pressure lysis leads to the formation of mostly inverted membrane vesicles (designated and abbreviated usually as ISO vesicles, everted or inverted membrane vesicles (IMVs)), inconclusive results are quite common. This uncertainty is due mainly by applying a different pressures, using either intact cells or spheroplasts and presence or absence of sucrose during rupture procedure. Many E. coli envelope fractionation techniques result in heterogeneity among isolated IM membrane vesicles. In part, this is due to difficulties in simple validation of sidedness of oriented membrane preparations of unknown sidedness. The sidedness of various preparations of membrane vesicles can be inferred from the orientation of residing uniformly oriented transmembrane protein. We outline the method in which the orientation of membrane vesicles can be verified by mapping of uniform or mixed topologies of essential protein E. coli protein leader peptidase (LepB) by advanced SCAM™. Although the protocol discussed in this chapter has been developed using Escherichia coli and Yersinia pseudotuberculosis, it can be directly adapted to other Gram-negative bacteria including pathogens.
    MeSH term(s) Escherichia coli ; Cell Membrane ; Membranes ; Cytoplasmic Vesicles ; Gram-Negative Bacteria
    Language English
    Publishing date 2023-11-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3445-5_10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The unusual substrate specificity of Escherichia coli cardiolipin synthase C does not require the product of the transcriptionally engaged ymdB gene.

    Sawasato, Katsuhiro / Bogdanov, Mikhail

    Biochimica et biophysica acta. Molecular and cell biology of lipids

    2024  Volume 1869, Issue 5, Page(s) 159483

    Abstract: Polycistronic transcription and translation of ymdB-clsC have been thought to be required for full activity of ClsC. The authentic initiation codon of the clsC gene is present within the open reading frame of the upstream located ymdB gene. ClsC ... ...

    Abstract Polycistronic transcription and translation of ymdB-clsC have been thought to be required for full activity of ClsC. The authentic initiation codon of the clsC gene is present within the open reading frame of the upstream located ymdB gene. ClsC translated from authentic initiation codon drives cardiolipin (CL) synthesis without transcriptionally paired YmdB. YmdB is not necessary for the substrate specificity of ClsC utilizing phosphatidylethanolamine (PE) as a co-substrate.
    Language English
    Publishing date 2024-03-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 60-7
    ISSN 1879-2618 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1879-2618 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbalip.2024.159483
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  6. Book: Prokaryotic membrane bound organelles

    Saier, Milton H. / Bogdanov, Mikhail

    4 tables

    (Journal of molecular microbiology and biotechnology ; 23,1/2)

    2013  

    Title variant Prokaryotic membrane-bound organelles
    Author's details ed. Milton H. Saier ; Mikhail Bogdanov
    Series title Journal of molecular microbiology and biotechnology ; 23,1/2
    Collection
    Language English
    Size 191 S. : Ill., graph. Darst.
    Publisher Karger
    Publishing place Basel u.a.
    Publishing country Switzerland
    Document type Book
    HBZ-ID HT017631603
    ISBN 978-3-318-02371-8 ; 3-318-02371-X
    Database Catalogue ZB MED Medicine, Health

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  7. Article: Eugene P. Kennedy's Legacy: Defining Bacterial Phospholipid Pathways and Function.

    Dowhan, William / Bogdanov, Mikhail

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 666203

    Abstract: In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells ... ...

    Abstract In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells and
    Language English
    Publishing date 2021-03-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.666203
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  8. Article ; Online: Mapping of Membrane Protein Topology by Substituted Cysteine Accessibility Method (SCAM™).

    Bogdanov, Mikhail

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1615, Page(s) 105–128

    Abstract: A described simple and advanced protocol for the substituted-cysteine accessibility method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane ... ...

    Abstract A described simple and advanced protocol for the substituted-cysteine accessibility method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform topology or identify and quantify the degree of mixed topology. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at a time by cysteine residue, and the orientation with respect to the membrane is evaluated using a pair of membrane-impermeable nondetectable and detectable thiol-reactive labeling reagents.
    MeSH term(s) Amino Acid Substitution ; Amino Acids/chemistry ; Cysteine/chemistry ; Escherichia coli/genetics ; Gene Expression ; Immunoprecipitation ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Models, Molecular ; Mutagenesis, Site-Directed ; Plasmids/genetics ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Solubility ; Staining and Labeling
    Chemical Substances Amino Acids ; Membrane Proteins ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7033-9_9
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  9. Article: On the lipid dependence of bacterial mechanosensitive channel gating in situ.

    Britt, Madolyn / Sawasato, Katsuhiro / Moller, Elissa / Kidd, Gerald / Bogdanov, Mikhail / Sukharev, Sergei

    bioRxiv : the preprint server for biology

    2024  

    Abstract: For bacterial mechanosensitive channels acting as turgor-adjusting osmolyte release valves, membrane tension is the primary stimulus driving opening transitions. Because tension is transmitted through the surrounding lipid bilayer, it is possible that ... ...

    Abstract For bacterial mechanosensitive channels acting as turgor-adjusting osmolyte release valves, membrane tension is the primary stimulus driving opening transitions. Because tension is transmitted through the surrounding lipid bilayer, it is possible that the presence or absence of different lipid species may influence the function of these channels. In this work, we characterize the lipid dependence of chromosome-encoded MscS and MscL in E. coli strains with genetically altered lipid composition. We use two previously generated strains that lack one or two major lipid species (PE, PG, or CL) and engineer a third strain that is highly enriched in CL due to the presence of hyperactive cardiolipin synthase ClsA. We characterize the functional behavior of these channels using patch-clamp and quantify the relative tension midpoints, closing rates, inactivation depth, and the rate of recovery back to the closed state. We also measure the osmotic survival of lipid-deficient strains, which characterizes the functional consequences of lipid-mediated channel function at the cell level. We find that the opening and closing behavior of MscS and MscL tolerate the absence of specific lipid species remarkably well. The lack of cardiolipin (CL), however, reduces the active MscS population relative to MscL and decreases the closing rate, slightly increasing the propensity of MscS toward inactivation and slowing the recovery process. The data points to the robustness of the osmolyte release system and the importance of cardiolipin for the adaptive behavior of MscS.
    Language English
    Publishing date 2024-01-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.22.576706
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Impact Behavior and Residual Strength of PEEK/CF-Laminated Composites with Various Stacking Sequences.

    Eremin, Alexander V / Burkov, Mikhail V / Bogdanov, Alexey A / Kononova, Anastasia A / Lyubutin, Pavel S

    Polymers

    2024  Volume 16, Issue 5

    Abstract: Carbon fiber-reinforced composites are popular due to their high strength and light weight; thus, the structures demonstrate high performance and specific strength. However, these composites are susceptible to impact damage. The objective of this ... ...

    Abstract Carbon fiber-reinforced composites are popular due to their high strength and light weight; thus, the structures demonstrate high performance and specific strength. However, these composites are susceptible to impact damage. The objective of this research was to study the behavior of carbon fiber-reinforced laminates based on a polyetheretherketone (PEEK) matrix with six stacking sequences under static and impact loading. Four-point bending, short-beam bending, drop weight impact, and compression after impact tests were carried out. The results were complemented with digital shearography to estimate the damaged areas. Finite element modeling served to assess the failure mechanisms, such as fiber and matrix failure, in different layers due to tension of compression. Three behavior pattern of layups under drop-weight impact were found: (i)-energy redistribution due to mostly linear behavior (like a trampoline) and thus lower kinetic energy absorption for damage initiation, (ii)-moderate absorption of energy with initiation and propagation of concentrated damage with depressed redistribution of energy in the material, (iii)-moderate energy absorption with good redistribution due to initiation of small, dispersed damage. The results can be used to predict the mechanical behavior of composites with different stacking sequences in materials for proper structural design.
    Language English
    Publishing date 2024-03-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527146-5
    ISSN 2073-4360 ; 2073-4360
    ISSN (online) 2073-4360
    ISSN 2073-4360
    DOI 10.3390/polym16050717
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