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Article ; Online: Evidence of Short-Lived High-Energy Emissive State and Triplet Character of the Self-Trapped Exciton in Cs

Chatterjee, Shovon / Mukherjee, Puspal / Sen, Arghya / Sen, Pratik

The journal of physical chemistry letters

2024 Volume 15, Issue 15, Page(s) 4191–4196

Abstract: ... ...

Abstract	Cs
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.4c00511
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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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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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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
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Article ; Online: Dye-surfactant interaction in aqueous premicellar and micellar environments in the alkaline fading of di-positive methyl green carbocation

Ghosh, Dinesh C. / Sen, Pratik K. / Pal, Biswajit

Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2023 June, v. 666 p.131300-

2023

Abstract: The alkaline fading of di-positive methyl green carbocation (MeG²⁺) has been studied in different aqueous premicellar and micellar environments of anionic, cationic as well as non-ionic surfactants. Mono- and di-negative anions like halides and sulphate ... ...

Abstract	The alkaline fading of di-positive methyl green carbocation (MeG²⁺) has been studied in different aqueous premicellar and micellar environments of anionic, cationic as well as non-ionic surfactants. Mono- and di-negative anions like halides and sulphate have been found to show an inhibiting effect on the fading reaction owing to the formation of dye-anion ion-pair adduct before hydrolysis. The binding strength of the dye-anion ion-pair adduct is in the order: SO₄²⁻ > I⁻ > Br⁻ > Cl⁻ which rationalizes the same order of inhibition of the rate. A substantial change in the electronic spectra of MeG²⁺ in the presence of anionic surfactants, sodium dodecyl sulfate (SDS) and dioctyl sodium sulfosuccinate (AOT), in the pre-CMC region indicates a change in the equilibrium distribution of the two stereo isomers of the dye owing to the formation of MeG²⁺-surfactant ion-pair and ion-pair micelle. The premicellar rate inhibition of the fading reaction by SDS and AOT occurs due to the formation of 1:1 MeG²⁺-surfactant ion-pair (where ≥ 85 % of MeG²⁺ remain associated) through electrostatic interaction before hydrolysis. The cationic surfactant cetyltrimethylammonium bromide (CTAB) shows a retarding effect in the post-micellar region as the HO⁻ ion experiences both electrostatic repulsion and steric hindrance to approach the carbocation centre of the dye, embedded in the micelle. The polar hydroxyl group and the polyoxyethylene groups present in the moiety of the non-ionic surfactant Brij35 assist to increase the local concentration of HO⁻ and MeG²⁺ in the palisade layer resulting in a catalyzing effect on the fading reaction in the post CMC region. Both pre- and post-micellar rate effects have been analyzed quantitatively by different established kinetic models. Detailed calculations have been made to find out different enthalpy and entropy of activation as well as of binding in order to establish the nature of interactions between the dye MeG²⁺ and monomeric surfactant(s) /micelles as well as solvent molecules. Results of spectrophotometric and tensiometric investigations strongly support the existence of different molecular interactions in different stages of the hydrolysis reaction in the presence of surfactants.
Keywords	cationic surfactants ; cetyltrimethylammonium bromide ; dyes ; electrostatic interactions ; enthalpy ; entropy ; hydrolysis ; micelles ; moieties ; nonionic surfactants ; polyethylene glycol ; sodium ; sodium dodecyl sulfate ; solvents ; sulfates ; tensiometers ; Methyl green ; Inhibition and catalysis ; Dye-surfactant adduct ; Binding parameters
Language	English
Dates of publication	2023-06
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	1500517-3
ISSN	0927-7757
ISSN	0927-7757
DOI	10.1016/j.colsurfa.2023.131300
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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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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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Article ; Online: Tracking Wormlike Micelle Formation in Solution: Unique Insight through Fluorescence Correlation Spectroscopic Study.

Subba, Navin / Das, Nilimesh / Sen, Pratik

Langmuir : the ACS journal of surfaces and colloids

2022 Volume 38, Issue 8, Page(s) 2486–2494

Abstract: Although worm-like micelles were invented 35 years ago, its formation pathway remains unclear. Inspired by the fact that a single molecular level experiment could provide meaningful and additional information, especially in a heterogeneous subpopulation, ...

Abstract	Although worm-like micelles were invented 35 years ago, its formation pathway remains unclear. Inspired by the fact that a single molecular level experiment could provide meaningful and additional information, especially in a heterogeneous subpopulation, herein, we present a single molecular level study on the formation of wormlike micelles by cetyltrimethylammonium bromide (CTAB) and sodium salicylate (NaSal) in water. Our results indicated a coexistence of normal spherical micelles along with a big wormlike micelle in its formation path. More interestingly, we have two unique insights into the formation mechanism, which are inaccessible in ensemble averaged experiments: (i) at extremely low concentrations of the surfactant, [CTAB]/[NaSal] ∼ 0.06, the wormlike micelle attains the highest size; and (ii) the relative concentration of wormlike micelles is highest when [CTAB]/[NaSal] ∼ 2.
MeSH term(s)	Cetrimonium ; Cetrimonium Compounds/chemistry ; Micelles ; Spectrometry, Fluorescence ; Surface-Active Agents/chemistry
Chemical Substances	Cetrimonium Compounds ; Micelles ; Surface-Active Agents ; Cetrimonium (Z7FF1XKL7A)
Language	English
Publishing date	2022-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.1c02936
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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
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Article ; Online: Ultrafast Excited State Dynamics of Spatially Confined Organic Molecules.

Ramamurthy, Vaidhyanathan / Sen, Pratik / Elles, Christopher G

The journal of physical chemistry. A

2022 Volume 126, Issue 29, Page(s) 4681–4699

Abstract: This Feature Article highlights the role of spatial confinement in controlling the fundamental behavior of molecules. Select examples illustrate the value of using space as a tool to control and understand excited-state dynamics through a combination of ... ...

Abstract	This Feature Article highlights the role of spatial confinement in controlling the fundamental behavior of molecules. Select examples illustrate the value of using space as a tool to control and understand excited-state dynamics through a combination of ultrafast spectroscopy and conventional steady-state methods. Molecules of interest were confined within a closed molecular capsule, derived from a cavitand known as octa acid (OA), whose internal void space is sufficient to accommodate molecules as long as tetracene and as wide as pyrene. The free space, i.e., the space that is left following the occupation of the guest within the host, is shown to play a significant role in altering the behavior of guest molecules in the excited state. The results reported here suggest that in addition to weak interactions that are commonly emphasized in supramolecular chemistry, the extent of empty space (i.e., the remaining void space within the capsule) is important in controlling the excited-state behavior of confined molecules on ultrafast time scales. For example, the role of free space in controlling the excited-state dynamics of guest molecules is highlighted by probing the
Language	English
Publishing date	2022-07-05
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.2c03276
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