LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 168

Search options

  1. Article ; Online: Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations.

    Kaur, Divya / Reiss, Krystle / Wang, Jimin / Batista, Victor S / Brudvig, Gary W / Gunner, M R

    The journal of physical chemistry. B

    2024  Volume 128, Issue 10, Page(s) 2236–2248

    Abstract: At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the ...

    Abstract At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the OEC to the lumen through water channels known as the narrow or the O4 channel, broad or the Cl1 channel, and large or the O1 channel. Protein residues lining the surfaces of these channels play a critical role in stabilizing the hydrogen-bonding networks that assist in the process. We carried out an occupancy analysis to better understand the structural and possible substrate water dynamics in full PSII monomer molecular dynamics (MD) trajectories in both the S
    MeSH term(s) Molecular Dynamics Simulation ; Photosystem II Protein Complex/chemistry ; Radius/metabolism ; Oxygen/chemistry ; Water/metabolism ; Oxidation-Reduction ; Protons
    Chemical Substances Photosystem II Protein Complex ; Oxygen (S88TT14065) ; Water (059QF0KO0R) ; Protons
    Language English
    Publishing date 2024-02-20
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c05367
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: The aprotic electrochemistry of quinones.

    Prince, Roger C / Dutton, P Leslie / Gunner, M R

    Biochimica et biophysica acta. Bioenergetics

    2022  Volume 1863, Issue 6, Page(s) 148558

    Abstract: Quinones play important roles in biological electron transfer reactions in almost all organisms, with specific roles in many physiological processes and chemotherapy. Quinones participate in two-electron, two-proton reactions in aqueous solution at ... ...

    Abstract Quinones play important roles in biological electron transfer reactions in almost all organisms, with specific roles in many physiological processes and chemotherapy. Quinones participate in two-electron, two-proton reactions in aqueous solution at equilibrium near neutral pH, but protons often lag behind the electron transfers. The relevant reactions in proteins are often sequential one electron redox processes without involving protons. Here we report the aprotic electrochemistry of the two half-couples, Q/Q
    MeSH term(s) Electrochemistry ; Electron Transport ; Naphthoquinones ; Protons ; Quinones/chemistry
    Chemical Substances Naphthoquinones ; Protons ; Quinones
    Language English
    Publishing date 2022-04-09
    Publishing country Netherlands
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 60-7
    ISSN 1879-2650 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 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) 1879-2650 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618
    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.bbabio.2022.148558
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.247: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.

    Khaniya, Umesh / Mao, Junjun / Wei, Rongmei Judy / Gunner, M R

    The journal of physical chemistry. B

    2022  Volume 126, Issue 13, Page(s) 2476–2485

    Abstract: Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some ... ...

    Abstract Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The Δ
    MeSH term(s) Electron Transport ; Hydrogen-Ion Concentration ; Ligands ; Monte Carlo Method ; Muramidase/metabolism ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Protons ; Rhodobacter sphaeroides/metabolism
    Chemical Substances Ligands ; Photosynthetic Reaction Center Complex Proteins ; Protons ; Muramidase (EC 3.2.1.17)
    Language English
    Publishing date 2022-03-28
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.2c00139
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Crises drive innovation.

    Gunner, C K / Oliphant, R / Watson, A J M

    Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland

    2020  Volume 22, Issue 9, Page(s) 1195

    Keywords covid19
    Language English
    Publishing date 2020-03-30
    Publishing country England
    Document type Letter
    ZDB-ID 1440017-0
    ISSN 1463-1318 ; 1462-8910
    ISSN (online) 1463-1318
    ISSN 1462-8910
    DOI 10.1111/codi.15043
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5799: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Comparison of proton transfer paths to the Q

    Wei, Rongmei Judy / Zhang, Yingying / Mao, Junjun / Kaur, Divya / Khaniya, Umesh / Gunner, M R

    Photosynthesis research

    2022  Volume 152, Issue 2, Page(s) 153–165

    Abstract: The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the ... ...

    Abstract The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the Q
    MeSH term(s) Binding Sites ; Electron Transport ; Kinetics ; Photosynthetic Reaction Center Complex Proteins ; Protons ; Quinones ; Rhodobacter sphaeroides ; Ubiquinone
    Chemical Substances Photosynthetic Reaction Center Complex Proteins ; Protons ; Quinones ; Ubiquinone (1339-63-5)
    Language English
    Publishing date 2022-03-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1475688-2
    ISSN 1573-5079 ; 0166-8595
    ISSN (online) 1573-5079
    ISSN 0166-8595
    DOI 10.1007/s11120-022-00906-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article: Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient.

    Kaur, Divya / Khaniya, Umesh / Zhang, Yingying / Gunner, M R

    Frontiers in chemistry

    2021  Volume 9, Page(s) 660954

    Abstract: Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the ... ...

    Abstract Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
    Language English
    Publishing date 2021-06-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2021.660954
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article ; Online: Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers.

    Wei, Rongmei Judy / Khaniya, Umesh / Mao, Junjun / Liu, Jinchan / Batista, Victor S / Gunner, M R

    Photosynthesis research

    2022  Volume 156, Issue 1, Page(s) 101–112

    Abstract: Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for ... ...

    Abstract Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the Q
    MeSH term(s) Protons ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Hydrogen-Ion Concentration ; Electron Transport ; Photosynthesis ; Rhodobacter sphaeroides/metabolism
    Chemical Substances Protons ; Photosynthetic Reaction Center Complex Proteins
    Language English
    Publishing date 2022-10-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1475688-2
    ISSN 1573-5079 ; 0166-8595
    ISSN (online) 1573-5079
    ISSN 0166-8595
    DOI 10.1007/s11120-022-00973-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: The design features cells use to build their transmembrane proton gradient.

    Gunner, M R / Koder, Ronald

    Physical biology

    2017  Volume 14, Issue 1, Page(s) 13001

    Abstract: Organisms store energy from food and sunlight as an electrochemical gradient across the membranes of mitochondria, chloroplasts and bacteria. The gradient arises from differences in the concentration of protons and ions on the negative (N) and positive ( ... ...

    Abstract Organisms store energy from food and sunlight as an electrochemical gradient across the membranes of mitochondria, chloroplasts and bacteria. The gradient arises from differences in the concentration of protons and ions on the negative (N) and positive (P) sides of these membranes. This perspective describes how the proton gradient is formed. One strategy is the movement of electrons but not protons across a membrane-embedded protein from a site of proton-releasing oxidative chemistry on the P-side of the protein to a site of proton-binding reductive chemistry on the N-side. Alternately, protons are directly pumped across membrane-embedded proteins, which have gated proton transfer pathways that are opened and closed, as well as internal sites where the proton affinity varies as the protein goes through the reaction cycle. The molecules that carry out these roles are complex, utilizing non-amino acid cofactors and earth-abundant metals. However, these are also potential sources of high-energy toxic byproducts. Understanding these reactions can open the door to their rational redesign, with possible beneficial effects as far-reaching as improving the global food supply, preventing neurodegenerative diseases, and better understanding the role of metabolism in aging.
    MeSH term(s) Animals ; Cell Membrane/metabolism ; Electrochemistry ; Electron Transport ; Electrons ; Energy Metabolism ; Humans ; Hydrogen-Ion Concentration ; Membrane Proteins/metabolism ; Models, Molecular ; Oxidation-Reduction ; Proton Pumps/metabolism ; Protons ; Thermodynamics
    Chemical Substances Membrane Proteins ; Proton Pumps ; Protons
    Language English
    Publishing date 2017-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/14/1/013001
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Two Cl Ions and a Glu Compete for a Helix Cage in the CLC Proton/Cl

    Chenal, Cat / Gunner, M R

    Biophysical journal

    2017  Volume 113, Issue 5, Page(s) 1025–1036

    Abstract: The ubiquitously expressed CLC chloride transporters are involved in a great variety of physiological functions. The CLC protein fold is shared by ... ...

    Abstract The ubiquitously expressed CLC chloride transporters are involved in a great variety of physiological functions. The CLC protein fold is shared by Cl
    MeSH term(s) Anions/chemistry ; Antiporters/chemistry ; Chlorides/chemistry ; Computer Simulation ; Escherichia coli ; Escherichia coli Proteins/chemistry ; Glutamic Acid/chemistry ; Hydrogen-Ion Concentration ; Models, Molecular ; Monte Carlo Method ; Protein Binding ; Protein Structure, Secondary ; Protons ; Static Electricity ; Thermodynamics
    Chemical Substances Anions ; Antiporters ; CLC-ec1 protein, E coli ; Chlorides ; Escherichia coli Proteins ; Protons ; Glutamic Acid (3KX376GY7L)
    Language English
    Publishing date 2017-09-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2017.07.025
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 2: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Overview of the SAMPL6 pK

    Işık, Mehtap / Rustenburg, Ariën S / Rizzi, Andrea / Gunner, M R / Mobley, David L / Chodera, John D

    Journal of computer-aided molecular design

    2021  Volume 35, Issue 2, Page(s) 131–166

    Abstract: The prediction of acid dissociation constants ( ... ...

    Abstract The prediction of acid dissociation constants (pK
    MeSH term(s) Algorithms ; Computer Simulation ; Ligands ; Models, Chemical ; Molecular Structure ; Proteins/chemistry ; Software ; Solubility ; Solvents/chemistry ; Thermodynamics
    Chemical Substances Ligands ; Proteins ; Solvents
    Language English
    Publishing date 2021-01-04
    Publishing country Netherlands
    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 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-020-00362-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2625: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top