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  1. Book ; Online ; E-Book: Optical Spectroscopic and Microscopic Techniques

    Sahoo, Harekrushna

    Analysis of Biological Molecules

    2022  

    Abstract: This book illustrates the significance of various optical spectroscopy and microscopy techniques, including absorption spectroscopy, fluorescence spectroscopy, infrared spectroscopy, and Raman spectroscopy for deciphering the nature of biological ... ...

    Author's details edited by Harekrushna Sahoo
    Abstract This book illustrates the significance of various optical spectroscopy and microscopy techniques, including absorption spectroscopy, fluorescence spectroscopy, infrared spectroscopy, and Raman spectroscopy for deciphering the nature of biological molecules. The content of this book chiefly focuses on (1) the principle, theory, and instrumentation used in different optical spectroscopy techniques, and (2) the application of these techniques in exploring the nature of different biomolecules (e.g., proteins, nucleic acids, enzymes, and carbohydrates). It emphasizes the structural, conformational and dynamic, and kinetic including the changes in biomolecules under a range of conditions. In closing, the book summarizes recent advances in the field of optical spectroscopic and microscopic techniques.
    Keywords Biology/Technique ; Proteins ; Molecular spectroscopy ; Biological Techniques ; Molecular Spectroscopy
    Subject code 572.36
    Language English
    Size 1 online resource (260 pages)
    Edition 1st ed. 2022.
    Publisher Springer Nature Singapore ; Imprint: Springer
    Publishing place Singapore
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 981-16-4549-3 ; 981-16-4550-7 ; 978-981-16-4549-5 ; 978-981-16-4550-1
    DOI 10.1007/978-981-16-4550-1
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    Full text online

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  2. Book: Optical Spectroscopic and Microscopic Techniques

    Sahoo, Harekrushna

    Analysis of Biological Molecules

    2022  

    Author's details Dr. Harekrushna Sahoo is currently working as an Associate Professor of Chemistry at the NIT (National Institute of Technology) in Rourkela, India. He previously served as a guest scientist at the Max-Bergmann Center (Dresden, Germany). He completed his Ph.D. at Jacobs University Bremen (Bremen, Germany) in 2006, prior to engaging in postdoctoral research at the University of Massachusetts (Amherst, USA) and Technical University Dresden (Dresden, Germany). His research chiefly focuses on using biophysical chemistry to understand the kinetics and dynamics of various types of proteins, along with the impacts of environmental stress. He has served as a reviewer for a number of international peer-reviewed and reputed journals, including Journal of Physical Chemistry B, ACS Omega, ACS Sustainable Chemistry and Engineering, Journal of Photochemistry and Photobiology, and International Journal of Biological Macromolecules. He has more than 9 years of teaching experience in General Chemistr
    Keywords Biomolecules ; Spectroscopy techniques ; microscopy ; Fluorescence ; Absorption ; Microscopy
    Language English
    Size 268 p.
    Edition 1
    Publisher Springer Nature Singapore
    Document type Book
    Note PDA Manuell_13
    Format 160 x 241 x 21
    ISBN 9789811645495 ; 9811645493
    Database PDA

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  3. Article ; Online: Sulfation of hyaluronic acid reconfigures the mechanistic pathway of bone morphogenetic protein-2 aggregation.

    Behera, Devi Prasanna / Subadini, Suchismita / Freudenberg, Uwe / Sahoo, Harekrushna

    International journal of biological macromolecules

    2024  Volume 263, Issue Pt 1, Page(s) 130128

    Abstract: Bone morphogenetic protein-2 (BMP-2) is a critical growth factor of bone extracellular matrix (ECM), pivotal for osteogenesis. Glycosaminoglycans (GAGs), another vital ECM biomolecules, interact with growth factors, affecting signal transduction. Our ... ...

    Abstract Bone morphogenetic protein-2 (BMP-2) is a critical growth factor of bone extracellular matrix (ECM), pivotal for osteogenesis. Glycosaminoglycans (GAGs), another vital ECM biomolecules, interact with growth factors, affecting signal transduction. Our study primarily focused on hyaluronic acid (HA), a prevalent GAG, and its sulfated derivative (SHA). We explored their impact on BMP-2's conformation, aggregation, and mechanistic pathways of aggregation using diverse optical and rheological methods. In the presence of HA and SHA, the secondary structure of BMP-2 underwent a structured transformation, characterized by a substantial increase in beta sheet content, and a detrimental alteration, manifesting as a shift towards unstructured content, respectively. Although both HA and SHA induced BMP-2 aggregation, their mechanisms differed. SHA led to rapid amorphous aggregates, while HA promoted amyloid fibrils with a lag phase and sigmoidal kinetics. Aggregate size and shape varied; HA produced larger structures, SHA smaller. Each aggregation type followed distinct pathways influenced by viscosity and excluded volume. Higher viscosity, low diffusivity of protein and higher excluded volume In the presence of HA promotes fibrillation having size in micrometer range. Low viscosity, high diffusivity of protein and lesser excluded volume leads to amorphous aggregate of size in nanometer range.
    MeSH term(s) Hyaluronic Acid/chemistry ; Glycosaminoglycans/chemistry ; Extracellular Matrix/metabolism ; Bone Morphogenetic Protein 2/metabolism ; Chemical Phenomena ; Osteogenesis
    Chemical Substances Hyaluronic Acid (9004-61-9) ; Glycosaminoglycans ; Bone Morphogenetic Protein 2
    Language English
    Publishing date 2024-02-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.130128
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  4. Article ; Online: Probing the interaction between niobium pentoxide nanoparticles and serum albumin proteins by Spectroscopic approaches.

    Millan, Sabera / Susrisweta, Behera / Sahoo, Harekrushna

    Journal of biomolecular structure & dynamics

    2023  Volume 41, Issue 24, Page(s) 15435–15445

    Abstract: Nanoparticles (NPs) can directly or indirectly enter into the body because of their small size; then they tend to alter the conformation and function of proteins upon interaction with them. Thus, it is crucial to understand the impact of NPs in a ... ...

    Abstract Nanoparticles (NPs) can directly or indirectly enter into the body because of their small size; then they tend to alter the conformation and function of proteins upon interaction with them. Thus, it is crucial to understand the impact of NPs in a biological medium. Recently, niobium pentoxide nanoparticles (Nb
    MeSH term(s) Humans ; Nanoparticles/chemistry ; Spectrometry, Fluorescence ; Oxides ; Circular Dichroism ; Serum Albumin, Bovine/chemistry ; Protein Binding ; Thermodynamics ; Binding Sites ; Molecular Docking Simulation
    Chemical Substances niobium pentoxide (K9343U17IN) ; Oxides ; Serum Albumin, Bovine (27432CM55Q)
    Language English
    Publishing date 2023-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2188944
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Tyrosine mediated conformational change in bone morphogenetic protein - 2: Biophysical implications of protein - phytoestrogen interaction.

    Konar, Monidipa / Sahoo, Harekrushna

    International journal of biological macromolecules

    2020  Volume 150, Page(s) 727–736

    Abstract: The biophysical aspects of the binding interaction between a phytoestrogen (quercetin, QT) and bone morphogenetic protein - 2 (BMP - 2) was analyzed by various spectroscopic, calorimetric and molecular docking techniques. Interaction studies represented ... ...

    Abstract The biophysical aspects of the binding interaction between a phytoestrogen (quercetin, QT) and bone morphogenetic protein - 2 (BMP - 2) was analyzed by various spectroscopic, calorimetric and molecular docking techniques. Interaction studies represented a loss in the absorbance of protein (only the amide region) along with a prominent red shift indicating ground-state complexation which was further confirmed by quenching with significant blue shift observed from steady-state fluorescence measurements. To narrow down the involvement of aromatic residues (Tyr & Trp), synchronous fluorescence spectroscopy was employed. Both Tyr and Trp fluorescence intensity was quenched, however, shifting was noticed only in case of Tyr residues; thus, confirming the alteration in confirmation was mediated upon reduction in polarity around tyrosine residues. It was further validated by quenching studies which highlighted the existence of a buried fraction of fluorophore upon interaction. The nature of fluorescence quenching was static and the binding efficiency was low (binding constant K ~ 10
    MeSH term(s) Bone Morphogenetic Protein 2/chemistry ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Phytoestrogens/chemistry ; Protein Binding ; Quercetin/chemistry
    Chemical Substances BMP2 protein, human ; Bone Morphogenetic Protein 2 ; Phytoestrogens ; Quercetin (9IKM0I5T1E)
    Language English
    Publishing date 2020-02-12
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2020.02.113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Exploring the chemistry behind protein-glycosaminoglycan conjugate: A steady-state and kinetic spectroscopy based approach.

    Konar, Monidipa / Sahoo, Harekrushna

    Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

    2020  Volume 242, Page(s) 118726

    Abstract: The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, ... ...

    Abstract The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, fluorescence and circular dichroism). The absorbance in peptide region and fluorescence intensity of BMP - 2 was quenched in presence of CS; thus, confirming the formation of a ground-state complex. As there was an increase in Stern-Volmer constant observed as a function of temperature, idea of dynamic quenching was established. However, the negligible changes in lifetime indicated static quenching; thus, making the process a combination of static-dynamic quenching. Basically, the protein - glycan interaction was driven by entropy of the system and mediated by hydrophobic interactions. Secondary structure (CD spectroscopy) of native protein was significantly affected (intensity became more negative) in presence of CS, thus, introducing more compactness in the protein. CS infused thermal and chemical stability into BMP - 2 via alteration in its conformation. The rate of association was inversely proportional to concentration of quencher (CS), which confirmed the correlation between large size (~ 5 times the size of protein) and structural complexity of CS with fewer binding sites present in BMP - 2. The rate of association in presence of urea, suggested a decrease in association rate as a function of urea concentration for 15 μM CS. Experimental evidences suggested an interaction between protein and glycan mediated by hydrophobic interactions, which deciphers structural, thermal and chemical stability into protein.
    MeSH term(s) Binding Sites ; Circular Dichroism ; Glycosaminoglycans ; Kinetics ; Protein Binding ; Protein Structure, Secondary ; Spectrometry, Fluorescence ; Thermodynamics
    Chemical Substances Glycosaminoglycans
    Language English
    Publishing date 2020-07-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 210413-1
    ISSN 1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
    ISSN (online) 1873-3557
    ISSN 0370-8322 ; 0584-8539 ; 1386-1425
    DOI 10.1016/j.saa.2020.118726
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  7. Article: Tyrosine mediated conformational change in bone morphogenetic protein – 2: Biophysical implications of protein – phytoestrogen interaction

    Konar, Monidipa / Sahoo, Harekrushna

    International journal of biological macromolecules. 2020 May 01, v. 150

    2020  

    Abstract: The biophysical aspects of the binding interaction between a phytoestrogen (quercetin, QT) and bone morphogenetic protein – 2 (BMP – 2) was analyzed by various spectroscopic, calorimetric and molecular docking techniques. Interaction studies represented ... ...

    Abstract The biophysical aspects of the binding interaction between a phytoestrogen (quercetin, QT) and bone morphogenetic protein – 2 (BMP – 2) was analyzed by various spectroscopic, calorimetric and molecular docking techniques. Interaction studies represented a loss in the absorbance of protein (only the amide region) along with a prominent red shift indicating ground-state complexation which was further confirmed by quenching with significant blue shift observed from steady-state fluorescence measurements. To narrow down the involvement of aromatic residues (Tyr & Trp), synchronous fluorescence spectroscopy was employed. Both Tyr and Trp fluorescence intensity was quenched, however, shifting was noticed only in case of Tyr residues; thus, confirming the alteration in confirmation was mediated upon reduction in polarity around tyrosine residues. It was further validated by quenching studies which highlighted the existence of a buried fraction of fluorophore upon interaction. The nature of fluorescence quenching was static and the binding efficiency was low (binding constant K ~ 10−2 M). Mechanistically, the involvement of van der Waals and hydrogen bonding interaction was confirmed from both van't Hoff plot and molecular docking studies. Secondary structure and thermal stability of the protein was not significantly affected by quercetin. All these investigations confirmed a significant effect on the structure and conformation of BMP – 2 in presence of quercetin which might serve as a potential therapeutic for the treatment of osteoporosis in postmenopausal women.
    Keywords absorbance ; bone morphogenetic proteins ; calorimetry ; computer simulation ; fluorescence ; fluorescence emission spectroscopy ; fluorescent dyes ; hydrogen bonding ; plant estrogens ; quercetin ; thermal stability ; tyrosine ; van der Waals forces
    Language English
    Dates of publication 2020-0501
    Size p. 727-736.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2020.02.113
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach.

    Subadini, Suchismita / Bera, Krishnendu / Hritz, Jozef / Sahoo, Harekrushna

    Colloids and surfaces. B, Biointerfaces

    2021  Volume 202, Page(s) 111696

    Abstract: The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly ... ...

    Abstract The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
    MeSH term(s) Circular Dichroism ; Kinetics ; Polyethylene Glycols ; Protein Denaturation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Retinoic Acid
    Chemical Substances Receptors, Retinoic Acid ; retinoic acid binding protein I, cellular ; Polyethylene Glycols (3WJQ0SDW1A)
    Language English
    Publishing date 2021-03-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1500523-9
    ISSN 1873-4367 ; 0927-7765
    ISSN (online) 1873-4367
    ISSN 0927-7765
    DOI 10.1016/j.colsurfb.2021.111696
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  9. Article ; Online: Coumarin-Based Noncytotoxicity Fluorescent Dye for Tracking Actin Protein in In-Vivo Imaging.

    Nayak, Pratuysha / Bag, Janmejaya / Padhan, Subrata Kumar / Sahoo, Harekrushna / Sahu, Satya Narayan / Mishra, Monalisa

    Chemical research in toxicology

    2023  Volume 36, Issue 6, Page(s) 926–933

    Abstract: ... ...

    Abstract Drosophila
    MeSH term(s) Humans ; Animals ; Drosophila melanogaster/genetics ; Actins ; Fluorescent Dyes/pharmacology ; Coumarins/pharmacology ; Larva
    Chemical Substances Actins ; Fluorescent Dyes ; Coumarins
    Language English
    Publishing date 2023-06-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639353-6
    ISSN 1520-5010 ; 0893-228X
    ISSN (online) 1520-5010
    ISSN 0893-228X
    DOI 10.1021/acs.chemrestox.3c00051
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  10. Article ; Online: Phosphate and sulphate-mediated structure and stability of bone morphogenetic protein - 2 (BMP - 2): A spectroscopy enabled investigation.

    Konar, Monidipa / Sahoo, Harekrushna

    International journal of biological macromolecules

    2019  Volume 135, Page(s) 1123–1133

    Abstract: Impact of different monovalent and divalent cationic salts of sulphates and phosphates on conformation and stability of BMP - 2 was unraveled by absorbance, fluorescence and circular dichroism (CD) spectroscopy. Increase in absorbance of protein confirms ...

    Abstract Impact of different monovalent and divalent cationic salts of sulphates and phosphates on conformation and stability of BMP - 2 was unraveled by absorbance, fluorescence and circular dichroism (CD) spectroscopy. Increase in absorbance of protein confirms the ground-state complexation between salt and BMP - 2. Phosphate salts, with the exception of sodium phosphate quenched the fluorescence intensity. The nature of quenching was static, as revealed by temperature-dependent fluorescence studies (Stern-Volmer constant (K
    MeSH term(s) Bone Morphogenetic Protein 2/chemistry ; Phosphates/chemistry ; Protein Conformation ; Protein Stability ; Spectrometry, Fluorescence ; Spectrum Analysis ; Sulfates/chemistry ; Thermodynamics
    Chemical Substances BMP2 protein, human ; Bone Morphogenetic Protein 2 ; Phosphates ; Sulfates
    Language English
    Publishing date 2019-06-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2019.06.015
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