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  1. Article ; Online: The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease.

    Terse, Vishram L / Gosavi, Shachi

    Biophysical journal

    2020  Volume 120, Issue 3, Page(s) 504–516

    Abstract: In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional ...

    Abstract In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional avidity. The main protease (M
    MeSH term(s) Models, Molecular ; Peptide Hydrolases/chemistry ; Peptide Hydrolases/metabolism ; Protein Domains ; Protein Folding ; SARS-CoV-2/enzymology
    Chemical Substances Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2020-12-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.11.2277
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function.

    Terse, Vishram L / Gosavi, Shachi

    The journal of physical chemistry. B

    2018  Volume 122, Issue 49, Page(s) 11497–11507

    Abstract: Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a ... ...

    Abstract Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a C
    MeSH term(s) Humans ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Folding ; Ubiquitin/chemistry ; Ubiquitin/metabolism
    Chemical Substances Ubiquitin
    Language English
    Publishing date 2018-10-18
    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.8b07409
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Intrinsic Disorder in a Well-Folded Globular Protein.

    Mascarenhas, Nahren Manuel / Terse, Vishram L / Gosavi, Shachi

    The journal of physical chemistry. B

    2018  Volume 122, Issue 6, Page(s) 1876–1884

    Abstract: The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin ... ...

    Abstract The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding. Here, we study the folding of a single-chain variant of monellin (scMn) using simulations of an all heavy-atom structure-based model. These simulations can explain mechanistic details derived from scMn experiments performed using several different structural probes. scMn folds cooperatively in our structure-based simulations, as is also seen in experiments. We find that structure formation near the transition-state ensemble of scMn is not uniformly distributed but is localized to a hairpin-like structure which contains one strand from each chain (β2, β3). Thus, the sequence and the underlying energetics of heterodimeric monellin promote the early formation of the interchain interface (β2-β3). By studying computational scMn mutants whose "interchain" interactions are deleted, we infer that this energy distribution allows the two protein chains to remain largely disordered when this interface is not folded. From these results, we suggest that cutting the protein backbone of a globular protein between residues which lie within its folding nucleus may be one way to construct two disordered fragments which fold upon binding.
    MeSH term(s) Intrinsically Disordered Proteins/chemistry ; Molecular Dynamics Simulation ; Plant Proteins/chemistry ; Protein Folding
    Chemical Substances Intrinsically Disordered Proteins ; Plant Proteins ; monellin protein, Dioscoreophyllum cumminsii
    Language English
    Publishing date 2018--15
    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.7b12546
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rational Design of Protein-Specific Folding Modifiers.

    Das, Anirban / Yadav, Anju / Gupta, Mona / R, Purushotham / Terse, Vishram L / Vishvakarma, Vicky / Singh, Sameer / Nandi, Tathagata / Banerjee, Arkadeep / Mandal, Kalyaneswar / Gosavi, Shachi / Das, Ranabir / Ainavarapu, Sri Rama Koti / Maiti, Sudipta

    Journal of the American Chemical Society

    2021  Volume 143, Issue 44, Page(s) 18766–18776

    Abstract: Protein-folding can go ... ...

    Abstract Protein-folding can go wrong
    MeSH term(s) Models, Molecular ; Protein Conformation ; Protein Folding ; Ubiquitin/chemistry ; Ubiquitin/metabolism
    Chemical Substances Ubiquitin
    Language English
    Publishing date 2021-11-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c09611
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Intrinsic Disorder in a Well-Folded Globular Protein

    Mascarenhas, Nahren Manuel / Shachi Gosavi / Vishram L. Terse

    Journal of physical chemistry. 2018 Feb. 15, v. 122, no. 6

    2018  

    Abstract: The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin ... ...

    Abstract The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding. Here, we study the folding of a single-chain variant of monellin (scMn) using simulations of an all heavy-atom structure-based model. These simulations can explain mechanistic details derived from scMn experiments performed using several different structural probes. scMn folds cooperatively in our structure-based simulations, as is also seen in experiments. We find that structure formation near the transition-state ensemble of scMn is not uniformly distributed but is localized to a hairpin-like structure which contains one strand from each chain (β2, β3). Thus, the sequence and the underlying energetics of heterodimeric monellin promote the early formation of the interchain interface (β2-β3). By studying computational scMn mutants whose “interchain” interactions are deleted, we infer that this energy distribution allows the two protein chains to remain largely disordered when this interface is not folded. From these results, we suggest that cutting the protein backbone of a globular protein between residues which lie within its folding nucleus may be one way to construct two disordered fragments which fold upon binding.
    Keywords cutting ; energy ; models ; mutants ; physical chemistry ; protein sweeteners ; proteins ; topology
    Language English
    Dates of publication 2018-0215
    Size p. 1876-1884.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.7b12546
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Rational Design of Protein-Specific Folding Modifiers

    Das, Anirban / Yadav, Anju / Gupta, Mona / R, Purushotham / Terse, Vishram L. / Vishvakarma, Vicky / Singh, Sameer / Nandi, Tathagata / Banerjee, Arkadeep / Mandal, Kalyaneswar / Gosavi, Shachi / Das, Ranabir / Ainavarapu, Sri Rama Koti / Maiti, Sudipta

    Journal of the American Chemical Society. 2021 Nov. 01, v. 143, no. 44

    2021  

    Abstract: Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The ... ...

    Abstract Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The principle is based on constructing a “xenonucleus”, which is a prefolded peptide that mimics the folding nucleus of a protein. Using stopped-flow kinetics, NMR spectroscopy, Förster resonance energy transfer, single-molecule force measurements, and molecular dynamics simulations, we demonstrate that a xenonucleus can make the refolding of ubiquitin faster by 33 ± 5%, while variants of the same peptide have little or no effect. Our approach provides a novel method for constructing specific, genetically encodable folding catalysts for suitable proteins that have a well-defined contiguous folding nucleus.
    Keywords energy transfer ; molecular dynamics ; nuclear magnetic resonance spectroscopy ; peptides ; pharmaceutical industry ; protein folding ; ubiquitin
    Language English
    Dates of publication 2021-1101
    Size p. 18766-18776.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c09611
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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