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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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: 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: Tracking Wormlike Micelle Formation in Solution: Unique Insight through Fluorescence Correlation Spectroscopic Study

Subba, Navin / Das, Nilimesh / Sen, Pratik

Langmuir. 2022 Feb. 15, v. 38, no. 8

2022

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.
Keywords	cetyltrimethylammonium bromide ; fluorescence ; micelles ; sodium salicylate ; spectral analysis ; surfactants
Language	English
Dates of publication	2022-0215
Size	p. 2486-2494.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.1c02936
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level.

Das, Nilimesh / Sen, Pratik

The journal of physical chemistry. B

2020 Volume 124, Issue 28, Page(s) 5858–5871

Abstract: One of the main differences in the intercellular environment compared to the laboratory condition is the presence of macromolecular crowders of various compositions, sizes, and shapes. In this article, we have contemplated a systematic shape dependency ... ...

Abstract	One of the main differences in the intercellular environment compared to the laboratory condition is the presence of macromolecular crowders of various compositions, sizes, and shapes. In this article, we have contemplated a systematic shape dependency of macromolecular crowders on the thermodynamics and microsecond conformational fluctuation dynamics of protein unfolding by taking human serum albumin (HSA) as the model protein and similar-sized crowders, namely, dextran-40, ficoll-70, and PEG-35 as macromolecular crowders of different shapes, to mimic the cell environment. We observed that dextran-40 and ficoll-70 counteract the thermal denaturation and PEG-35 assists it. A complete thermodynamic analysis suggests that the stabilization by dextran-40 and ficoll-70 occurs mainly through stabilizing entropic effect, which is somewhat counteracted by the destabilizing enthalpic effect, in line with what is expected from the traditional interpretation of excluded volume and soft interaction. Surprisingly, the destabilizing effect of PEG-35 is not through unfavorable interaction but through a destabilizing entropic effect, which is opposite to the excluded volume prediction. Our speculation is that the modulation of the associated water structure due to crowder-induced distortion plays a crucial role in modulating the entropic component. Moreover, while a two-state model can approximate the overall thermal denaturation of HSA in the absence and presence of various crowders, the thermal denaturation profile of domain III of HSA involves a distinct intermediate state. The active-site dynamics of HSA are altered significantly in the presence of all the three differently shaped crowders used in the study. Rod-shaped dextran-40 and spherical ficoll-70 hinder the microsecond conformational dynamics of domain III of HSA in all states except the intermediate state. Mesh-like PEG-35 in addition to hindering the microsecond conformational dynamics shifts the intermediate state from 40 to 30 °C. Overall, our results provide new insight into deciphering the mechanism of crowder-induced changes in protein. Through our interpretation, we not only explain the unfavorable entropic contribution but also provide a physical basis to explain the entropy-enthalpy compensation.
MeSH term(s)	Ficoll ; Humans ; Macromolecular Substances ; Molecular Conformation ; Protein Unfolding ; Thermodynamics
Chemical Substances	Macromolecular Substances ; Ficoll (25702-74-3)
Language	English
Publishing date	2020-07-07
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.0c03897
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level

Das, Nilimesh / Sen, Pratik

Journal of physical chemistry. 2020 June 22, v. 124, no. 28

2020

Abstract	One of the main differences in the intercellular environment compared to the laboratory condition is the presence of macromolecular crowders of various compositions, sizes, and shapes. In this article, we have contemplated a systematic shape dependency of macromolecular crowders on the thermodynamics and microsecond conformational fluctuation dynamics of protein unfolding by taking human serum albumin (HSA) as the model protein and similar-sized crowders, namely, dextran-40, ficoll-70, and PEG-35 as macromolecular crowders of different shapes, to mimic the cell environment. We observed that dextran-40 and ficoll-70 counteract the thermal denaturation and PEG-35 assists it. A complete thermodynamic analysis suggests that the stabilization by dextran-40 and ficoll-70 occurs mainly through stabilizing entropic effect, which is somewhat counteracted by the destabilizing enthalpic effect, in line with what is expected from the traditional interpretation of excluded volume and soft interaction. Surprisingly, the destabilizing effect of PEG-35 is not through unfavorable interaction but through a destabilizing entropic effect, which is opposite to the excluded volume prediction. Our speculation is that the modulation of the associated water structure due to crowder-induced distortion plays a crucial role in modulating the entropic component. Moreover, while a two-state model can approximate the overall thermal denaturation of HSA in the absence and presence of various crowders, the thermal denaturation profile of domain III of HSA involves a distinct intermediate state. The active-site dynamics of HSA are altered significantly in the presence of all the three differently shaped crowders used in the study. Rod-shaped dextran-40 and spherical ficoll-70 hinder the microsecond conformational dynamics of domain III of HSA in all states except the intermediate state. Mesh-like PEG-35 in addition to hindering the microsecond conformational dynamics shifts the intermediate state from 40 to 30 °C. Overall, our results provide new insight into deciphering the mechanism of crowder-induced changes in protein. Through our interpretation, we not only explain the unfavorable entropic contribution but also provide a physical basis to explain the entropy–enthalpy compensation.
Keywords	active sites ; cellular microenvironment ; denaturation ; human serum albumin ; models ; prediction ; thermodynamics
Language	English
Dates of publication	2020-0622
Size	p. 5858-5871.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ISSN	1520-5207
DOI	10.1021/acs.jpcb.0c03897
Database	NAL-Catalogue (AGRICOLA)

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