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  1. Article: Clustering single-cell multimodal omics data with jrSiCKLSNMF.

    Ellis, Dorothy / Roy, Arkaprava / Datta, Susmita

    Frontiers in genetics

    2023  Volume 14, Page(s) 1179439

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2023-06-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1179439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dynamic Counterion Condensation Model Decodes Functional Dynamics of RNA Pseudoknot in SARS-CoV-2: Control of Ion-Mediated Pierced Lasso Topology.

    Mainan, Avijit / Roy, Susmita

    The journal of physical chemistry letters

    2023  Volume 14, Issue 46, Page(s) 10402–10411

    Abstract: The programmed frameshifting stimulatory element, a promising drug target for COVID-19 treatment, involves a RNA pseudoknot (PK) structure. This RNA PK facilitates frameshifting, enabling RNA viruses to translate multiple proteins from a single mRNA, ... ...

    Abstract The programmed frameshifting stimulatory element, a promising drug target for COVID-19 treatment, involves a RNA pseudoknot (PK) structure. This RNA PK facilitates frameshifting, enabling RNA viruses to translate multiple proteins from a single mRNA, which is a key strategy for their rapid evolution. Overcoming the challenges of capturing large-scale structural changes of RNA under the influence of a dynamic counterion environment (K
    MeSH term(s) Humans ; RNA ; SARS-CoV-2/genetics ; Frameshifting, Ribosomal ; Nucleic Acid Conformation ; COVID-19 Drug Treatment ; COVID-19
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-11-13
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c02755
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  3. Article ; Online: Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods.

    Sarkar, Raju / Mainan, Avijit / Roy, Susmita

    Chemical communications (Cambridge, England)

    2024  Volume 60, Issue 27, Page(s) 3624–3644

    Abstract: RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge ... ...

    Abstract RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg
    MeSH term(s) RNA/chemistry ; Water/chemistry ; Computer Simulation ; Metals
    Chemical Substances RNA (63231-63-0) ; Water (059QF0KO0R) ; Metals
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc06105a
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  4. Article ; Online: Biofilm-producing antibiotic-resistant bacteria in Indian patients: a comprehensive review.

    Datta, Susmita / Nag, Soma / Roy, Dijendra Nath

    Current medical research and opinion

    2024  Volume 40, Issue 3, Page(s) 403–422

    Abstract: For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable ...

    Abstract For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable impact in the field of infectious diseases, in particular healthcare-associated infections related to indwelling devices such as catheters, implants, artificial heart valves, and prosthetic joints. Bacterial biofilm potentially adheres to any biotic or abiotic surfaces that give specific shelter to the microbial community, making them less susceptible to many antimicrobial agents and even resistant to the immune cells of animal hosts. Around thirty clinical research reports available in PUBMED have been considered to establish the occurrence of biofilm-forming bacteria showing resistance against several regular antibiotics prescribed against infection by clinicians among Indian patients. After the extensive literature review, our observation exhibits a high predominance of biofilm formation among bacteria such as
    MeSH term(s) Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Biofilms ; Bacteria ; Drug Resistance, Microbial ; Cross Infection
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-01-27
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 80296-7
    ISSN 1473-4877 ; 0300-7995
    ISSN (online) 1473-4877
    ISSN 0300-7995
    DOI 10.1080/03007995.2024.2305241
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 955: 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: Intrinsically Disordered Regions Function as a Cervical Collar to Remotely Regulate the Nodding Dynamics of SARS-CoV-2 Prefusion Spike Heads.

    Sinha, Anushree / Roy, Susmita

    The journal of physical chemistry. B

    2023  Volume 127, Issue 39, Page(s) 8393–8405

    Abstract: The SARS-CoV-2 prefusion spike heads (receptor binding domains, RBDs) frequently nod down and up to interact with host cell receptors. As the spike protein is a trimeric unit of significant size, to understand its large-scale structural dynamics ... ...

    Abstract The SARS-CoV-2 prefusion spike heads (receptor binding domains, RBDs) frequently nod down and up to interact with host cell receptors. As the spike protein is a trimeric unit of significant size, to understand its large-scale structural dynamics associated with the nodding mechanism and the mutational impact on the same, we develop a topological symmetry-information-loaded coarse-grained structure-based model of a spike trimer using recent cryo-EM structural data. Our study reveals the control of two distant intrinsically disordered regions (IDRs), namely, 630 and FPPR loops, over the nodding dynamics of spike heads. We find that the order-disorder transition of IDRs becomes more evident in the variants of concern (VOCs) that are associated with the characteristic mutation, D614G, in the proximity of these IDRs. In some VOCs, the two other mutations A570D and S982A also show an integral effect. The driver mutation D614G instigates a salt-bridge disruption, altering the order-disorder dynamics of both 630 and FPPR loops and their interaction with the C-terminal domains (CTD1/CTD2). This altered connectivity in these mutants allows the two IDRs to act collectively as a "cervical collar" for the RBD, supporting various spike head postures, consistent with cryo-EM results available for specific cases. The IDRs' control over the spike structure and dynamics presents an exciting opportunity where they can be targeted as remote operational switches to artificially maneuver the nod for effective therapeutic interventions.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19 ; Protein Binding ; Mutation
    Language English
    Publishing date 2023-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c05338
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Elucidation of the structural dynamics of mutations in PHB2 protein associated with growth suppression and cancer progression.

    Khatua, Susmita / Roy, Alankar / Sen, Pritha / Ray, Sujay

    Gene

    2023  Volume 890, Page(s) 147820

    Abstract: Prohibitin is a multifunctional protein that plays an important role in numerous cellular processes. Membrane-associated mitochondrial prohibitin complex is made up of two subunits, PHB1 and PHB2 which are ubiquitously expressed and analogous to each ... ...

    Abstract Prohibitin is a multifunctional protein that plays an important role in numerous cellular processes. Membrane-associated mitochondrial prohibitin complex is made up of two subunits, PHB1 and PHB2 which are ubiquitously expressed and analogous to each other. High levels of prohibitin expression have consequently been found in esophageal cancer, endometrial adenocarcinoma, gastric cancer, hepatocellular carcinoma, breast cancer and bladder cancer. The aim of this study is to analyse two-point mutation PHB2_MT1(I → A) and PHB2_MT2(I → P), their effect on PHB2 protein and its effect on formation of mitochondrial complex. It is a residual level study, based on current experimental validation. To establish the effects of the two-point mutations, computational approaches such as molecular modelling, molecular docking, normal mode simulation, molecular dynamics simulations and MM/GBSA were used. An analysis of the energy dynamics of both unbound and complex proteins was conducted to elucidate how mutations impact the energy distribution of PHB2. Our study confirmed that the two mutations decreased the overall stability of PHB2. This was evidenced by heightened atomic fluctuations within the mutated region, accompanied by elevated deviations observed in RMSD and R
    Language English
    Publishing date 2023-09-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2023.147820
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1357: 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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  7. Article ; Online: Dynamical asymmetry exposes 2019-nCoV prefusion spike

    Roy, Susmita

    bioRxiv

    Abstract: The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric ... ...

    Abstract The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets.
    Keywords covid19
    Language English
    Publishing date 2020-04-22
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.04.20.052290
    Database COVID19

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  8. Article ; Online: Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.

    Sinha, Anushree / Sangeet, Satyam / Roy, Susmita

    ACS omega

    2023  Volume 8, Issue 26, Page(s) 23283–23304

    Abstract: Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several ... ...

    Abstract Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence-structure-function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.
    Language English
    Publishing date 2023-06-21
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c00944
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Dynamical asymmetry exposes 2019-nCoV prefusion spike

    Roy, Susmita

    bioRxiv

    Abstract: The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric ... ...

    Abstract The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets. One Sentence Summary Inter-chain-interaction driven rapid symmetry breaking strategy adopted by the prefusion trimeric spike protein likely to make 2019-nCoV highly infective.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.04.20.052290
    Database COVID19

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  10. Article ; Online: Transmissive to blackish-green NIR electrochromism in a Co(II)-based interfacial co-ordination thin film.

    Roy, Susmita / Chakraborty, Chanchal

    Chemical communications (Cambridge, England)

    2021  Volume 57, Issue 61, Page(s) 7565–7568

    Abstract: Herein, a Co(ii)-based metallo-polymer (Co-tpy-L) with a three armed non-conjugated terpyridine ligand is synthesized using solvent-solvent interfacial polymerization. The thin film exhibits durable transmissive-to-blackish green electrochromism, ... ...

    Abstract Herein, a Co(ii)-based metallo-polymer (Co-tpy-L) with a three armed non-conjugated terpyridine ligand is synthesized using solvent-solvent interfacial polymerization. The thin film exhibits durable transmissive-to-blackish green electrochromism, selectively covering both the visible and NIR regions with a moderate voltage range of -1.4 to 0 V.
    Language English
    Publishing date 2021-07-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d1cc02815d
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