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  1. Book: Computational approaches for studying enzyme mechanism / Part A

    Voth, Gregory A.

    (Methods in enzymology ; volume 577)

    2016  

    Author's details edited by Gregory A. Voth
    Series title Methods in enzymology ; volume 577
    Computational approaches for studying enzyme mechanism
    Collection Computational approaches for studying enzyme mechanism
    Language English
    Size xvi, 522 Seiten, 20 ungezählte Seiten, Illustrationen, Diagramme
    Edition First edition
    Publishing country Netherlands
    Document type Book
    HBZ-ID HT019096128
    ISBN 978-0-12-805347-8 ; 0-12-805347-X
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Se 222 -577- verfügbar in Königswinter Königswinter

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  2. Book ; Collection: Computational approaches for studying enzyme mechanism

    Voth, Gregory A.

    (Methods in enzymology)

    2016  

    Author's details edited by Gregory A. Voth
    Series title Methods in enzymology
    Keywords Enzymatische Regulation ; Computersimulation ; Mathematische Modellierung
    Subject Modellierung ; Simulation ; Computer ; Simulationstechnik ; Systemsimulation ; Digitale Simulation ; Computermodell ; Rechnersimulation ; Enzymregulation ; Enzym
    Language English
    Dates of publication 2016-9999
    Publisher Elsevier Academic Press
    Publishing place Amsterdam
    Publishing country Netherlands
    Document type Book ; Collection (display volumes)
    HBZ-ID HT019066523
    Database Catalogue ZB MED Medicine, Health

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  3. Book: Computational approaches for studying enzyme mechanism / Part B

    Voth, Gregory A.

    (Methods in enzymology ; Volume 578)

    2016  

    Author's details edited by Gregory A. Voth
    Series title Methods in enzymology ; Volume 578
    Computational approaches for studying enzyme mechanism
    Collection Computational approaches for studying enzyme mechanism
    Language English
    Size xviii, 494, [24] Seiten, Illustrationen
    Edition First edition
    Publishing country Netherlands
    Document type Book
    HBZ-ID HT019066557
    ISBN 978-0-12-811107-9 ; 9780128111086 ; 0-12-811107-0 ; 0128111089
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Se 222 -578- verfügbar in Königswinter Königswinter

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  4. Article ; Online: HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex.

    Hudait, Arpa / Voth, Gregory A

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 4, Page(s) e2313737121

    Abstract: Nuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). ...

    Abstract Nuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). Notably, the central channel of the NPC appears to often accommodate and allow passage of intact HIV-1 capsid, though mechanistic details of the process remain to be fully understood. Here, we investigate the molecular interactions that operate in concert between the HIV-1 capsid and the NPC that regulate capsid translocation through the central channel. To this end, we develop a "bottom-up" coarse-grained (CG) model of the human NPC from recently released cryo-electron tomography structure and then construct composite membrane-embedded CG NPC models. We find that successful translocation from the cytoplasmic side to the NPC central channel is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel from the cytoplasmic side. The translocation dynamics is driven by maximizing the contacts between phenylalanine-glycine nucleoporins at the central channel and the capsid. For the docked intact capsids, structural analysis reveals correlated striated patterns of lattice disorder likely related to the intrinsic capsid elasticity. Uncondensed genomic material inside the docked capsid augments the overall lattice disorder of the capsid. Our results suggest that the intrinsic "elasticity" can also aid the capsid to adapt to the stress and remain structurally intact during translocation.
    MeSH term(s) Humans ; Capsid/metabolism ; HIV-1/genetics ; Nuclear Pore/metabolism ; Capsid Proteins/genetics ; Active Transport, Cell Nucleus ; Nuclear Pore Complex Proteins/metabolism ; Translocation, Genetic ; Elasticity
    Chemical Substances Capsid Proteins ; Nuclear Pore Complex Proteins
    Language English
    Publishing date 2024-01-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2313737121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: 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)

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  5. Article ; Online: Making the cut: Multiscale simulation of membrane remodeling.

    Beiter, Jeriann / Voth, Gregory A

    Current opinion in structural biology

    2024  Volume 87, Page(s) 102831

    Abstract: Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of ... ...

    Abstract Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of membrane-bound organelles, much less an entire cell. Therefore, multiscale modeling approaches are often necessary to build a comprehensive picture of the interplay of these factors, and have provided critical insights into our understanding of membrane dynamics. Here, we review computational methods for studying membrane remodeling, as well as passive and active examples of protein-driven membrane remodeling. As the field advances towards the modeling of key aspects of organelles and whole cells - an increasingly accessible regime of study - we summarize here recent successes and offer comments on future trends.
    Language English
    Publishing date 2024-05-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2024.102831
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3206: 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)

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  6. Article ; Online: How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?

    Chen, Sijia / Voth, Gregory A

    The journal of physical chemistry. B

    2023  Volume 127, Issue 5, Page(s) 1264–1275

    Abstract: The room temperature ionic liquid (RTIL) air-liquid interface plays an important role in many applications. Herein, we present molecular dynamics simulation results for the air-liquid interface of a common RTIL, 1-butyl-3-methylimidazolium bis( ... ...

    Abstract The room temperature ionic liquid (RTIL) air-liquid interface plays an important role in many applications. Herein, we present molecular dynamics simulation results for the air-liquid interface of a common RTIL, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, [C
    Language English
    Publishing date 2023-01-26
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.2c07981
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules.

    Beckett, Daniel / Voth, Gregory A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within β-tubulin. ... ...

    Abstract Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within β-tubulin. Hydrolysis is favored in the MT lattice compared to free heterodimer with an experimentally observed rate increase of 500 to 700 fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP-state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive QM/MM simulations with transition-tempered metadynamics free energy sampling of compacted and expanded inter-dimer complexes, as well as free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.
    Significance statement: Microtubules (MTs) are large and dynamic components of the eukaryotic cytoskeleton with the ability to stochastically convert from a polymerizing to a depolymerizing state and vice-versa. Depolymerization is coupled to the hydrolysis of guanosine-5'-triphosphate (GTP), which is orders of magnitude faster in the MT lattice than in free tubulin heterodimers. Our results computationally ascertain the catalytic residue contacts in the MT lattice that accelerate GTP hydrolysis compared to the free heterodimer as well as confirm that a compacted MT lattice is necessary for hydrolysis while a more expanded lattice is unable to form the necessary contacts and thereby hydrolyze GTP.
    Language English
    Publishing date 2023-05-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.01.538927
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding.

    Banerjee, Puja / Voth, Gregory A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-gRNA interactions play a crucial role in the multimerization process, which is ...

    Abstract During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-gRNA interactions play a crucial role in the multimerization process, which is yet to be fully understood. We have performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model (hENM) applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to impact mainly the SP1 domain of the 18-mer and the MA-CA linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the NC domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, as well as regulates the dynamic organization of the local membrane region itself.
    Significance: Gag(Pr
    Language English
    Publishing date 2023-08-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.16.553549
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces.

    Jin, Jaehyeok / Voth, Gregory A

    The journal of physical chemistry letters

    2023  Volume 14, Issue 6, Page(s) 1354–1362

    Abstract: Systematic bottom-up coarse-graining (CG) of molecular systems provides a means to explore different coupled length and time scales while treating the molecular-scale physics at a reduced level. However, the configuration dependence of CG interactions ... ...

    Abstract Systematic bottom-up coarse-graining (CG) of molecular systems provides a means to explore different coupled length and time scales while treating the molecular-scale physics at a reduced level. However, the configuration dependence of CG interactions often results in CG models with limited applicability for exploring the parametrized configurations. We propose a statistical mechanical theory to design CG interactions across different configurations and conditions. In order to span wide ranges of conformational space, distinct classical CG free energy surfaces for characteristic configurations are identified using molecular collective variables. The coupling interaction between different CG free energy surfaces can then be systematically determined by analogy to quantum mechanical approaches describing coupled states. The present theory can accurately capture the underlying many-body potentials of mean force in the CG variables for various order parameters applied to liquids, interfaces, and in principle proteins, uncovering the complex nature underlying the coupling interaction and imparting a new protocol for the design of predictive multiscale models.
    Language English
    Publishing date 2023-02-02
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c03844
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Elucidating the Molecular Mechanism of CO

    Yoon, Bohak / Voth, Gregory A

    Journal of the American Chemical Society

    2023  Volume 145, Issue 29, Page(s) 15663–15667

    Abstract: Amino acid ionic liquids have received increasing attention as ideal candidates for the ... ...

    Abstract Amino acid ionic liquids have received increasing attention as ideal candidates for the CO
    Language English
    Publishing date 2023-07-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.3c03613
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 4' 55/32: Show issues
    Z 7.3: Show issues

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