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  1. Article ; Online: Does Viscosity Decoupling Guarantee Dynamic Heterogeneity? A Clue through an Excitation and Emission Wavelength-Dependent Time-Resolved Fluorescence Anisotropy Study.

    Tarif, Ejaj / Das, Nilimesh / Sen, Pratik

    The journal of physical chemistry. B

    2023  Volume 127, Issue 32, Page(s) 7162–7173

    Abstract: Traditionally, deviation from Stokes-Einstein-Debye (SED) relation in terms of viscosity dependence of medium dynamics, i.e., ...

    Abstract Traditionally, deviation from Stokes-Einstein-Debye (SED) relation in terms of viscosity dependence of medium dynamics, i.e.,
    Language English
    Publishing date 2023-08-07
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c00334
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Macromolecular crowding: how shape and interaction affect the structure, function, conformational dynamics and relative domain movement of a multi-domain protein.

    Das, Nilimesh / Sen, Pratik

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 23, Page(s) 14242–14256

    Abstract: The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders: dextran-40, Ficoll-70 and ...

    Abstract The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders: dextran-40, Ficoll-70 and PEG-35 on the structure, active-site conformational dynamics, function and relative domain movement of multi-domain human serum albumin (HSA). All the crowders used in this study have zero charges and similar sizes (at least in the dilute region) but different shapes and compositions. Some observations follow the traditional crowding theory. For example, all the crowders increased the α-helicity of HSA and hindered the conformational fluctuation dynamics. However, some observations are not in line with the expectations, such as an increase in the size of HSA with PEG-35 and uncorrelated domain movement of HSA with Ficoll-70 and PEG-35. The relative domain movement is correlated with the activity, suggesting that such moves are essential for protein function. The interaction between HSA and Ficoll-70 is proposed to be hydrophobic in nature. Overall, our results provide a somewhat systematic study of the shape-dependent macromolecular crowding effect on various protein properties and present a possible new insight into the mechanism of macromolecular crowding.
    MeSH term(s) Ficoll/chemistry ; Humans ; Macromolecular Substances/chemistry ; Molecular Conformation ; Proteins/chemistry ; Serum Albumin, Human
    Chemical Substances Macromolecular Substances ; Proteins ; Ficoll (25702-74-3) ; Serum Albumin, Human (ZIF514RVZR)
    Language English
    Publishing date 2022-06-15
    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/d1cp04842b
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  3. Article ; Online: Multifunctional Ca

    Das, Pratik / Pathak, Nimai / Modak, Pampa / Modak, Brindaban

    Journal of hazardous materials

    2021  Volume 411, Page(s) 125025

    Abstract: ... ...

    Abstract Na
    Language English
    Publishing date 2021-01-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2020.125025
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  4. Article ; Online: Associated Water Dynamics Might Be a Key Factor Affecting Protein Stability in the Crowded Milieu.

    Das, Nilimesh / Tarif, Ejaj / Dutta, Abhijit / Sen, Pratik

    The journal of physical chemistry. B

    2023  Volume 127, Issue 14, Page(s) 3151–3163

    Abstract: Over the past 20 years, the most studied and debated aspect of macromolecular crowding is how it affects protein stability. Traditionally, it is explained by a delicate balance between the stabilizing entropic effect and the stabilizing or destabilizing ... ...

    Abstract Over the past 20 years, the most studied and debated aspect of macromolecular crowding is how it affects protein stability. Traditionally, it is explained by a delicate balance between the stabilizing entropic effect and the stabilizing or destabilizing enthalpic effect. However, this traditional crowding theory cannot explain experimental observations like (i) negative entropic effect and (ii) entropy-enthalpy compensation. Herein, we provide experimental evidence that associated water dynamics plays a crucial role in controlling protein stability in the crowded milieu for the first time. We have correlated the modulation of associated water dynamics with the overall stability and its individual components. We showed that rigid associated water would stabilize the protein through entropy but destabilize it through enthalpy. In contrast, flexible associated water destabilizes the protein through entropy but stabilizes through enthalpy. Consideration of entropic and enthalpic modulation through crowder-induced distortion of associated water successfully explains the negative entropic part and entropy-enthalpy compensation. Furthermore, we argued that the relationship between the associated water structure and protein stability should be better understood by individual entropic and enthalpic components instead of the overall stability. Although a huge effort is necessary to generalize the mechanism, this report provides a unique way of understanding the relationship between protein stability and associated water dynamics, which might be a generic phenomenon and should trigger much research in this area.
    MeSH term(s) Water/chemistry ; Thermodynamics ; Entropy ; Proteins/chemistry ; Protein Stability
    Chemical Substances Water (059QF0KO0R) ; Proteins
    Language English
    Publishing date 2023-04-04
    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.2c09043
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  5. Article ; Online: A novel observation: effect of anionic gelatin nanoparticle on stromal cells.

    Patra, Shamayita / Basak, Piyali / Das, Pratik / Paul, Samrat

    Journal of biomaterials science. Polymer edition

    2023  Volume 34, Issue 18, Page(s) 2483–2497

    Abstract: Biocompatible nanoparticles are very popular in health science research. Biomolecule carriers for wound healing and tissue engineering are two main applications among many others. In many instances, these structures come in direct vicinity of cells and ... ...

    Abstract Biocompatible nanoparticles are very popular in health science research. Biomolecule carriers for wound healing and tissue engineering are two main applications among many others. In many instances, these structures come in direct vicinity of cells and govern cell behaviour and responses. In this study, gelatin nano/submicron structures were synthesized by binary nonsolvent aided coacervation (BNAC) method at pH ranging from 3 to 11 with an intention to employ in skin tissue regeneration. Effect of pH over morphology and the surface composition with respect to its ionic composition were studied. Further, the initial toxicity was assessed against peripheral blood mononuclear cells (PBMC). pH 7 was found to be the optimum for synthesis of gelatin nanoparticles (GNPs) with minimum particle size. Positive cell viability of 103.14% for GNPs synthesized at pH 7 was observed. It may be due to the minimum difference between cumulative negative and positive charge (CNCP) ratio of 1.19. Finally, effect of the gelatin nanoparticles over L929 mouse fibroblast cells was assessed through MTT assay. It has resulted in 122.77% cell viability.
    MeSH term(s) Mice ; Animals ; Gelatin/chemistry ; Leukocytes, Mononuclear ; Nanoparticles/chemistry ; Skin ; Stromal Cells
    Chemical Substances Gelatin (9000-70-8)
    Language English
    Publishing date 2023-12-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1014190-x
    ISSN 1568-5624 ; 1568-5616 ; 0920-5063
    ISSN (online) 1568-5624 ; 1568-5616
    ISSN 0920-5063
    DOI 10.1080/09205063.2023.2265129
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  6. Article: Assessment of Periodontal Health Status among the Male Adult Population with a Dual Habit of Smoking and Gutkha Chewing: A Cross-Sectional Study.

    Amaranath, Bj Janardhana / Gupta, Shruti / Kumar, Shravan / Das, Neelam / Gupta, Ira / Pratik, Shashwat

    Journal of pharmacy & bioallied sciences

    2023  Volume 15, Issue Suppl 2, Page(s) S1020–S1022

    Abstract: Aims and objective: The aim of this study was to assess the periodontal health status in subjects having dual habits of smoking and gutkha chewing among the male population of Kanpur City, Central Uttar Pradesh (UP).: Materials and methods: A total ... ...

    Abstract Aims and objective: The aim of this study was to assess the periodontal health status in subjects having dual habits of smoking and gutkha chewing among the male population of Kanpur City, Central Uttar Pradesh (UP).
    Materials and methods: A total number of 500 male subjects were included, divided into three study groups: group I-164 subjects with a dual habit of smoking and gutkha chewing, group II- 170 gutkha chewers, and group III-166 smokers. Case history, clinical examination, and the following clinical parameters were recorded-oral hygiene index (OHI-S), gingival index (GI), bleeding index, clinical attachment loss (CAL), gingival recession, and furcation involvement.
    Result: In this study, the proportion of severe CAL was maximum in dual habit (78%) followed by smokers (70.5%) and then gutkha chewers (40.0%). A significant difference was observed in the proportion of CAL status between smokers, gutkha, and dual habit cases (
    Conclusion: Overall, it was concluded that periodontal health status was found to be very poor in both smokers and gutkha chewers, but the subjects in the dual habit group were found to have extremely poor periodontal health status.
    Language English
    Publishing date 2023-07-11
    Publishing country India
    Document type Journal Article
    ZDB-ID 2573569-X
    ISSN 0975-7406 ; 0976-4879
    ISSN (online) 0975-7406
    ISSN 0976-4879
    DOI 10.4103/jpbs.jpbs_246_23
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  7. Article ; Online: Dynamic heterogeneity and viscosity decoupling: origin and analytical prediction.

    Das, Nilimesh / Sen, Pratik

    Physical chemistry chemical physics : PCCP

    2021  

    Abstract: The molecular-level structure and dynamics decide the functionality of solvent media. Therefore, a significant amount of effort is being dedicated continually over time in understanding their structural and dynamical features. One intriguing aspect of ... ...

    Abstract The molecular-level structure and dynamics decide the functionality of solvent media. Therefore, a significant amount of effort is being dedicated continually over time in understanding their structural and dynamical features. One intriguing aspect of solvent structure and dynamics is heterogeneity. In these systems, the dynamics follow , where p is the measure of viscosity decoupling. We analytically predicted that in such cases, the Stokes-Einstein relationship is modified to due to microdomain formation, and the second term on the right-hand side leads to viscosity decoupling. We validated our prediction by estimating the p values of a few solvents, and they matched well with the literature. Overall, we believe that our approach gives a simple yet unique physical picture to help us understand the heterogeneity of solvent media.
    Language English
    Publishing date 2021-07-20
    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/d1cp01804c
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  8. 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
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  9. Article: Atypical Presentation of Periosteal Chondroma of the Talus in a 9-Year-Old Boy: A Case Report.

    Bhavani, Prashant / Dwidmuthe, Samir / Shahare, Pratik / Roy, Mainak / Das, Deepanjan / Math, Suhas Aradhya Bhikshavarthi

    Journal of orthopaedic case reports

    2024  Volume 14, Issue 3, Page(s) 73–77

    Abstract: Introduction: ?Introduction: Periosteal chondromas are rare, slow-growing, benign cartilaginous tumors arising from the cortical surface of the bone, beneath the periosteal membrane. Typically affect young males, the most common site being the proximal ... ...

    Abstract Introduction: ?Introduction: Periosteal chondromas are rare, slow-growing, benign cartilaginous tumors arising from the cortical surface of the bone, beneath the periosteal membrane. Typically affect young males, the most common site being the proximal humerus. There have been no reported cases of periosteal chondroma of the talus in the literature.
    Case report: A 9-year-old Indian boy presented with a 1.5-year history of atraumatic right ankle pain and swelling, exacerbated by walking, with limited dorsiflexion. Physical examination revealed a firm, painless swelling on the anterior ankle's talar region, accompanied by equinus deformity. Radiography displayed osseous masses on the anterior talus. Magnetic resonance imaging indicated well-defined osseous growths originating from the talus's anterior aspect, likely osteochondromas, with adjacent osseous fragments in the tibiotalar joint, suggestive of loose bodies, supporting a clinical diagnosis of synovial chondromatosis. Surgical excision revealed whitish, hard, irregular tissue, confirmed as periosteal chondroma on histopathology. After 6 months, the patient is pain-free with unrestricted movement and no clinical or radiological signs of recurrence.
    Conclusion: This case report presents a unique instance of previously unreported talus periosteal chondroma, adding novelty to medical literature. It details the diagnostic challenges and its intricacies. It provides a comprehensive overview of clinical presentation, imaging and histopathological findings, differentials and provisional diagnosis, surgical approach, and post-operative outcomes. The successful surgical management, along with the specific details of the surgical procedure (anteromedial approach, excision, and curettage), adds practical insights for orthopedic surgeons and contributes to the existing knowledge on treatment strategies for talus periosteal chondroma. This report will serve as an excellent educational resource.
    Language English
    Publishing date 2024-03-15
    Publishing country India
    Document type Case Reports
    ZDB-ID 2658169-3
    ISSN 2250-0685
    ISSN 2250-0685
    DOI 10.13107/jocr.2024.v14.i03.4292
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  10. Article ; Online: Development of a New Methodology for Dearomative Borylation of Coumarins and Chromenes and Its Applications to Synthesize Boron-Containing Retinoids.

    Das, Bhaskar C / Yadav, Pratik / Das, Sasmita / Saito, Mariko / Evans, Todd

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 3

    Abstract: Dearomative borylation of coumarins and chromenes via conjugate addition represents a relatively unexplored and challenging task. To address this issue, herein, we report a new and general copper (I) catalyzed dearomative borylation process to synthesize ...

    Abstract Dearomative borylation of coumarins and chromenes via conjugate addition represents a relatively unexplored and challenging task. To address this issue, herein, we report a new and general copper (I) catalyzed dearomative borylation process to synthesize boron-containing oxacycles. In this report, the borylation of coumarins, chromones, and chromenes comprising functional groups, such as esters, nitriles, carbonyls, and amides, has been achieved. In addition, the method generates different classes of potential boron-based retinoids, including the ones with oxadiazole and anthocyanin motifs. The borylated oxacycles can serve as suitable intermediates to generate a library of compounds.
    MeSH term(s) Benzopyrans ; Boron ; Coumarins ; Copper ; Amides
    Chemical Substances Benzopyrans ; Boron (N9E3X5056Q) ; Coumarins ; Copper (789U1901C5) ; Amides
    Language English
    Publishing date 2023-01-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28031052
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    Zs.MO 81: Show issues

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