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  1. Article ; Online: Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor.

    Negi, Kuldeep Singh / Das, Nilimesh / Khan, Tanmoy / Sen, Pratik

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 47, Page(s) 32602–32612

    Abstract: The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been ... ...

    Abstract The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects,
    MeSH term(s) Water/chemistry ; Proteins/chemistry ; Protein Stability ; Thermodynamics
    Chemical Substances Water (059QF0KO0R) ; Proteins
    Language English
    Publishing date 2023-12-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp03357k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Site-specific Heterogeneity of Multi-domain Human Serum Albumin and its Origin: A Red Edge Excitation Shift Study

    Das, Nilimesh / Sahu, Subhrasmita / Khan, Tanmoy / Sen, Pratik

    Photochemistry and photobiology

    2022  Volume 99, Issue 2, Page(s) 538–546

    Abstract: Conformational heterogeneity is a defining characteristic of a protein and is vital in understanding its function and folding landscape. In the present work, we interrogated the presence of conformational heterogeneity in multi-domain human serum albumin ...

    Abstract Conformational heterogeneity is a defining characteristic of a protein and is vital in understanding its function and folding landscape. In the present work, we interrogated the presence of conformational heterogeneity in multi-domain human serum albumin in a domain-specific manner using red edge excitation shift (REES) in its native state and also monitored its variation along the unfolding transition. We also looked into the origin of such conformational heterogeneity by varying the solution viscosity. We observed (1) even in the native state, the heterogeneity and dynamics of the side chain exhibit varied behaviors depending on which domain of the multi-domain human serum albumin (HSA) is being examined. (2) When the protein is in the unfolded state, the extent of REES is rendered unimportant since there is a greater quantity of free water present, in addition to the disruption of the protein's structure. (3) While the rigid protein matrix provides the rigidity of domain-I and domain-III, the rigidity of domain-II is provided by water molecules, which indicates that the role of water molecules in providing the rigidity is significant. Overall, our results provide direct evidence of the rigidity and alternate side chain packing arrangement of protein core that varies domain-wise in multi-domain HSA.
    MeSH term(s) Humans ; Serum Albumin, Human/chemistry ; Proteins ; Water ; Protein Conformation
    Chemical Substances Serum Albumin, Human (ZIF514RVZR) ; Proteins ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-10-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.13712
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1686: Show issues Location:
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  3. Article ; Online: Correlating Bromelain's activity with its structure and active-site dynamics and the medium's physical properties in a hydrated deep eutectic solvent.

    Das, Nilimesh / Khan, Tanmoy / Subba, Navin / Sen, Pratik

    Physical chemistry chemical physics : PCCP

    2021  Volume 23, Issue 15, Page(s) 9337–9346

    Abstract: Deep eutectic solvents (DESs) are emerging as new media of choice for biocatalysis due to their environmentally friendly nature, fine-tunability, and potential biocompatibility. This work deciphers the behaviour of bromelain in a ternary DES composed of ... ...

    Abstract Deep eutectic solvents (DESs) are emerging as new media of choice for biocatalysis due to their environmentally friendly nature, fine-tunability, and potential biocompatibility. This work deciphers the behaviour of bromelain in a ternary DES composed of acetamide, urea, and sorbitol at mole fractions of 0.5, 0.3, and 0.2, respectively (0.5Ac/0.3Ur/0.2Sor), with various degrees of hydration. Bromelain is an essential industrial proteolytic enzyme, and the chosen DES is non-ionic and liquid at room temperature. This provides us with a unique opportunity to contemplate protein behaviour in a non-ionic DES for the very first time. Our results infer that at a low DES concentration (up to 30% V/V DES), bromelain adopts a more compact structural conformation, whereas at higher DES concentrations, it becomes somewhat elongated. The microsecond conformational fluctuation time around the active site of bromelain gradually increases with increasing DES concentration, especially beyond 30% V/V. Interestingly, bromelain retains most of its enzymatic activity in the DES, and at some concentrations, the activity is even higher compared with its native state. Furthermore, we correlate the activity of bromelain with its structure, its active-site dynamics, and the physical properties of the medium. Our results demonstrate that the compact structural conformation and flexibility of the active site of bromelain favour its proteolytic activity. Similarly, a medium with increased polarity and decreased viscosity is favourable for its activity. The presented physical insights into how enzymatic activity depends on the protein structure and dynamics and the physical properties of the medium might provide useful guidelines for the rational design of DESs as biocatalytic media.
    Language English
    Publishing date 2021-04-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp00046b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability.

    Khan, Tanmoy / Das, Nilimesh / Negi, Kuldeep Singh / Bhowmik, Suman / Sen, Pratik

    International journal of biological macromolecules

    2023  Volume 253, Issue Pt 5, Page(s) 127100

    Abstract: Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions ... ...

    Abstract Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.
    MeSH term(s) Humans ; Solvents/chemistry ; Deep Eutectic Solvents ; Proteins ; Water/chemistry ; Molecular Conformation
    Chemical Substances Solvents ; Deep Eutectic Solvents ; Proteins ; Water (059QF0KO0R)
    Language English
    Publishing date 2023-09-29
    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.2023.127100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 2374: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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