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  1. Article ; Online: Autobiography of Ruth Nussinov.

    Nussinov, Ruth

    The journal of physical chemistry. B

    2021  Volume 125, Issue 25, Page(s) 6735–6739

    Language English
    Publishing date 2021-06-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c04719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book: Protein allostery in drug discovery

    Zhang, Jian / Nussinov, Ruth

    (Advances in experimental medicine and biology ; 1163)

    2019  

    Author's details Jian Zhang, Ruth Nussinov editors
    Series title Advances in experimental medicine and biology ; 1163
    Collection
    Language English
    Size xii, 384 Seiten, Illustrationen
    Publisher Springer
    Publishing place Singapore
    Publishing country Singapore
    Document type Book
    HBZ-ID HT020306814
    ISBN 978-981-13-8718-0 ; 9789811387197 ; 981-13-8718-4 ; 9811387192
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 3192 -1163- not available for loan Zeitschriften-Lesesaal

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  3. Article ; Online: Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance.

    Nussinov, Ruth / Jang, Hyunbum

    Annual review of pharmacology and toxicology

    2023  Volume 64, Page(s) 231–253

    Abstract: Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K- ... ...

    Abstract Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K-Ras
    MeSH term(s) Humans ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Neoplasms/drug therapy ; Paclitaxel ; Alleles ; Drug Combinations
    Chemical Substances Antineoplastic Agents ; Paclitaxel (P88XT4IS4D) ; Drug Combinations
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 196587-6
    ISSN 1545-4304 ; 0362-1642
    ISSN (online) 1545-4304
    ISSN 0362-1642
    DOI 10.1146/annurev-pharmtox-022823-113946
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions.

    Ozdemir, Emine Sila / Nussinov, Ruth

    Frontiers in oncology

    2023  Volume 13, Page(s) 1061595

    Abstract: Host-pathogen interactions (HPIs) affect and involve multiple mechanisms in both the pathogen and the host. Pathogen interactions disrupt homeostasis in host cells, with their toxins interfering with host mechanisms, resulting in infections, diseases, ... ...

    Abstract Host-pathogen interactions (HPIs) affect and involve multiple mechanisms in both the pathogen and the host. Pathogen interactions disrupt homeostasis in host cells, with their toxins interfering with host mechanisms, resulting in infections, diseases, and disorders, extending from AIDS and COVID-19, to cancer. Studies of the three-dimensional (3D) structures of host-pathogen complexes aim to understand how pathogens interact with their hosts. They also aim to contribute to the development of rational therapeutics, as well as preventive measures. However, structural studies are fraught with challenges toward these aims. This review describes the state-of-the-art in protein-protein interactions (PPIs) between the host and pathogens from the structural standpoint. It discusses computational aspects of predicting these PPIs, including machine learning (ML) and artificial intelligence (AI)-driven, and overviews available computational methods and their challenges. It concludes with examples of how theoretical computational approaches can result in a therapeutic agent with a potential of being used in the clinics, as well as future directions.
    Language English
    Publishing date 2023-02-23
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2023.1061595
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics.

    Haspel, Nurit / Jang, Hyunbum / Nussinov, Ruth

    Journal of chemical information and modeling

    2024  Volume 64, Issue 3, Page(s) 862–873

    Abstract: The Ras homologue family member A (RhoA) is a member of the Rho family, a subgroup of the Ras superfamily. RhoA interacts with the 115 kDa guanine nucleotide exchange factor (p115-RhoGEF), which assists in activation and binding with downstream effectors. ...

    Abstract The Ras homologue family member A (RhoA) is a member of the Rho family, a subgroup of the Ras superfamily. RhoA interacts with the 115 kDa guanine nucleotide exchange factor (p115-RhoGEF), which assists in activation and binding with downstream effectors. Here, we use molecular dynamics (MD) simulations and essential dynamics analysis of the inactive RhoA-GDP and active RhoA-GTP, when bound to p115-RhoGEF to decipher the mechanism of RhoA activation at the structural level. We observe that inactive RhoA-GDP maintains its position near the catalytic site on the Dbl homology (DH) domain of p115-RhoGEF through the interaction of its Switch I region with the DH domain. We further show that the active RhoA-GTP is engaged in more interactions with the p115-RhoGEF membrane-bound Pleckstrin homology (PH) domain as compared to RhoA-GDP. We hypothesize that the role of the interactions between the active RhoA-GTP and the PH domain is to help release it from the DH domain upon activation. Our results support this premise, and our simulations uncover the beginning of this process and provide structural details. They also point to allosteric communication pathways that take part in RhoA activation to promote and strengthen the interaction between the active RhoA-GTP and the PH domain. Allosteric regulation also occurs among other members of the Rho superfamily. Collectively, we suggest that in the activation process, the role of the RhoA-GTP interaction with the PH domain is to release RhoA-GTP from the DH domain after activation, making it available to downstream effectors.
    MeSH term(s) Allosteric Regulation ; Rho Guanine Nucleotide Exchange Factors ; Protein Domains ; Molecular Dynamics Simulation ; Guanosine Triphosphate/metabolism
    Chemical Substances Rho Guanine Nucleotide Exchange Factors ; Guanosine Triphosphate (86-01-1)
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01412
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design.

    Berezovsky, Igor N / Nussinov, Ruth

    Journal of molecular biology

    2022  Volume 434, Issue 17, Page(s) 167751

    MeSH term(s) Allosteric Regulation ; Allosteric Site ; Drug Design
    Language English
    Publishing date 2022-07-18
    Publishing country Netherlands
    Document type Editorial ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2022.167751
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    Zs.A 867: Show issues Location:
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  7. Article ; Online: Protein conformational ensembles in function: roles and mechanisms.

    Nussinov, Ruth / Liu, Yonglan / Zhang, Wengang / Jang, Hyunbum

    RSC chemical biology

    2023  Volume 4, Issue 11, Page(s) 850–864

    Abstract: ... ...

    Abstract The
    Language English
    Publishing date 2023-09-05
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2633-0679
    ISSN (online) 2633-0679
    DOI 10.1039/d3cb00114h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Cell phenotypes can be predicted from propensities of protein conformations.

    Nussinov, Ruth / Liu, Yonglan / Zhang, Wengang / Jang, Hyunbum

    Current opinion in structural biology

    2023  Volume 83, Page(s) 102722

    Abstract: Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, ...

    Abstract Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, and their mutations work by altering the relative propensities, thus the cell phenotype. Our examples include (i) inactive state variants harboring cancer driver mutations that present active state-like conformational features, as in K-Ras4B
    MeSH term(s) Humans ; Protein Conformation ; Proteins ; Neoplasms ; Phenotype
    Chemical Substances Proteins
    Language English
    Publishing date 2023-10-21
    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.2023.102722
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Editorial overview: Catalysis and regulation: The beating heart of biology.

    Nussinov, Ruth / Shirouzu, Mikako

    Current opinion in structural biology

    2021  Volume 71, Page(s) iii–v

    MeSH term(s) Biology ; Catalysis
    Language English
    Publishing date 2021-10-09
    Publishing country England
    Document type Editorial
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2021.09.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Cell cycle progression mechanisms: slower cyclin-D/CDK4 activation and faster cyclin-E/CDK2.

    Zhang, Wengang / Liu, Yonglan / Jang, Hyunbum / Nussinov, Ruth

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Dysregulation of cyclin-dependent kinases (CDKs) impacts cell proliferation, driving cancer. Here, we ask why the cyclin-D/CDK4 complex governs cell cycle progression through the longer G1 phase, whereas cyclin-E/CDK2 regulates the short G1/S phase ... ...

    Abstract Dysregulation of cyclin-dependent kinases (CDKs) impacts cell proliferation, driving cancer. Here, we ask why the cyclin-D/CDK4 complex governs cell cycle progression through the longer G1 phase, whereas cyclin-E/CDK2 regulates the short G1/S phase transition. We consider the experimentally established high-level bursting of cyclin-E, and sustained duration of elevated cyclin-D expression in the cell, available experimental cellular and structural data, and comprehensive explicit solvent molecular dynamics simulations to provide the mechanistic foundation of the distinct activation scenarios of cyclin-D/CDK4 and cyclin-E/CDK2 in the G1 phase and G1/S transition of the cell cycle, respectively. These lead us to propose slower activation of cyclin-D/CDK4 and rapid activation of cyclin-E/CDK2. Importantly, we determine the mechanisms through which this occurs, offering innovative CDK4 drug design considerations. Our insightful mechanistic work addresses the compelling cell cycle regulation question and illuminates the distinct activation speeds in the G1 versus G1/S phases, which are crucial for cell function.
    Language English
    Publishing date 2023-08-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.16.553605
    Database MEDical Literature Analysis and Retrieval System OnLINE

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