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  1. Article ; Online: Writing a literature review as a class project in an upper-level undergraduate biochemistry course.

    Hati, Sanchita / Bhattacharyya, Sudeep

    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

    2024  

    Abstract: A literature review is an important part of conducting academic research. Knowing how to conduct a literature search and write a high-quality literature review is a valuable skill. Herein, the authors describe the method of introducing a literature ... ...

    Abstract A literature review is an important part of conducting academic research. Knowing how to conduct a literature search and write a high-quality literature review is a valuable skill. Herein, the authors describe the method of introducing a literature review writing exercise in an upper-level biochemistry course. Since 2020, authors have collaborated with numerous undergraduates writing literature reviews on topics in biochemistry that resulted in peer-reviewed publications. Authors believe that this unique idea of providing a course-based undergraduate research experience (CURE) to many undergraduates, especially those who otherwise do not receive collaborative research experience through traditional research paths, must be shared with other instructors.
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2039717-3
    ISSN 1539-3429 ; 1470-8175
    ISSN (online) 1539-3429
    ISSN 1470-8175
    DOI 10.1002/bmb.21814
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor.

    Hati, Sanchita / Bhattacharyya, Sudeep

    ACS omega

    2020  Volume 5, Issue 26, Page(s) 16292–16298

    Abstract: The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the ... ...

    Abstract The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus
    Keywords covid19
    Language English
    Publishing date 2020-06-23
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.0c02125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Impact of Thiol–Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor

    Sanchita Hati / Sudeep Bhattacharyya

    ACS Omega, Vol 5, Iss 26, Pp 16292-

    2020  Volume 16298

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Impact of Thiol–Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor

    Hati, Sanchita / Bhattacharyya, Sudeep

    ACS Omega

    2020  Volume 5, Issue 26, Page(s) 16292–16298

    Keywords covid19
    Language English
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Article ; Online
    ISSN 2470-1343
    DOI 10.1021/acsomega.0c02125
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Polyethylene Glycol Impacts Conformation and Dynamics of

    Liebau, Jessica / Laatsch, Bethany F / Rusnak, Joshua / Gunderson, Keegan / Finke, Brianna / Bargender, Kassandra / Narkiewicz-Jodko, Alex / Weeks, Katelyn / Williams, Murphi T / Shulgina, Irina / Musier-Forsyth, Karin / Bhattacharyya, Sudeep / Hati, Sanchita

    Biochemistry

    2024  

    Abstract: Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular ... ...

    Abstract Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor

    Hati, Sanchita / Bhattacharyya, Sudeep

    bioRxiv

    Abstract: The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which ... ...

    Abstract The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.05.07.083147
    Database COVID19

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  7. Article ; Online: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor

    Bhattacharyay, Sudeep / Hati, Sanchita

    bioRxiv

    Abstract: The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which ... ...

    Abstract The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 were investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress.
    Keywords covid19
    Language English
    Publishing date 2020-05-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.05.07.083147
    Database COVID19

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  8. Article ; Online: Polyethylene Glycol 20k. Does It Fluoresce?

    Laatsch, Bethany F / Brandt, Michael / Finke, Brianna / Fossum, Carl J / Wackett, Miles J / Lowater, Harrison R / Narkiewicz-Jodko, Alex / Le, Christine N / Yang, Thao / Glogowski, Elizabeth M / Bailey-Hartsel, Scott C / Bhattacharyya, Sudeep / Hati, Sanchita

    ACS omega

    2023  Volume 8, Issue 15, Page(s) 14208–14218

    Abstract: Polyethylene glycol (PEG) is a polyether compound commonly used in biological research and medicine because it is biologically inert. This simple polymer exists in variable chain lengths (and molecular weights). As they are devoid of any contiguous π- ... ...

    Abstract Polyethylene glycol (PEG) is a polyether compound commonly used in biological research and medicine because it is biologically inert. This simple polymer exists in variable chain lengths (and molecular weights). As they are devoid of any contiguous π-system, PEGs are expected to lack fluorescence properties. However, recent studies suggested the occurrence of fluorescence properties in non-traditional fluorophores like PEGs. Herein, a thorough investigation has been conducted to explore if PEG 20k fluoresces. Results of this combined experimental and computational study suggested that although PEG 20k could exhibit "through-space" delocalization of lone pairs of electrons in aggregates/clusters, formed via intermolecular and intramolecular interactions, the actual contributor of fluorescence between 300 and 400 nm is the stabilizer molecule, i.e., 3-
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c01124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

    Hati, Sanchita / Bhattacharyya, Sudeep

    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

    2016  Volume 44, Issue 2, Page(s) 140–159

    Abstract: A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated ... ...

    Abstract A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.
    MeSH term(s) Biochemistry/education ; Laboratories ; Models, Molecular ; Molecular Biology/education ; Protein Conformation ; Proteins/chemistry ; Proteins/physiology ; Structure-Activity Relationship ; Universities
    Chemical Substances Proteins
    Language English
    Publishing date 2016-03
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3429
    ISSN (online) 1539-3429
    DOI 10.1002/bmb.20942
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Insights into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study.

    Fossum, Carl J / Johnson, Benjamin O V / Golde, Spencer T / Kielman, Alexis J / Finke, Brianna / Smith, Macey A / Lowater, Harrison R / Laatsch, Bethany F / Bhattacharyya, Sudeep / Hati, Sanchita

    ACS omega

    2023  Volume 8, Issue 47, Page(s) 44820–44830

    Abstract: Intrinsic tryptophan fluorescence spectroscopy is an important tool for examining the effects of molecular crowding and confinement on the structure, dynamics, and function of proteins. Synthetic crowders such as dextran, ficoll, polyethylene glycols, ... ...

    Abstract Intrinsic tryptophan fluorescence spectroscopy is an important tool for examining the effects of molecular crowding and confinement on the structure, dynamics, and function of proteins. Synthetic crowders such as dextran, ficoll, polyethylene glycols, polyvinylpyrrolidone, and their respective monomers are used to mimic crowded intracellular environments. Interactions of these synthetic crowders with tryptophan and the subsequent impact on its fluorescence properties are therefore critically important for understanding the possible interference created by these crowders. In the present study, the effects of polymer and monomer crowders on tryptophan fluorescence were assessed by using experimental and computational approaches. The results of this study demonstrated that both polymer and monomer crowders have an impact on the tryptophan fluorescence intensity; however, the molecular mechanisms of quenching were different. Using Stern-Volmer plots and a temperature variation study, a physical basis for the quenching mechanism of commonly used synthetic crowders was established. The quenching of free tryptophan was found to involve static, dynamic, and sphere-of-action mechanisms. In parallel, computational studies employing Kohn-Sham density functional theory provided a deeper insight into the effects of intermolecular interactions and solvation, resulting in differing quenching modes for these crowders. Taken together, the study offers new physical insights into the quenching mechanisms of some commonly used monomer and polymer synthetic crowders.
    Language English
    Publishing date 2023-11-13
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c06006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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