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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: Does Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain? Clues from Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder

Das, Nilimesh / Yadav, Sandeep / Negi, Kuldeep Singh / Tarif, Ejaj / Sen, Pratik

BBA advances. 2022, v. 2

2022

Abstract: Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. ... ...

Abstract	Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. However, it is not easy to directly correlate an enzyme's dynamics and activity due to biosystems' enormous complexity. amongst many factors, structure and dynamics are two prime aspects that combinedly control the activity. Therefore, having a direct correlation between protein dynamics and activity is not straightforward. Herein, we observed and correlated the structural, functional, and dynamical responses of an industrially crucial proteolytic enzyme, bromelain with three versatile classes of chemicals: GnHCl (protein denaturant), sucrose (protein stabilizer), and Ficoll-70 (macromolecular crowder). The only free cysteine (Cys-25 at the active-site) of bromelain has been tagged with a cysteine-specific dye to unveil the structural and dynamical changes through various spectroscopic studies both at bulk and at the single molecular level. Proteolytic activity is carried out using casein as the substrate. GnHCl and sucrose shows remarkable structure-dynamics-activity relationships. Interestingly, with Ficoll-70, structure and activity are not correlated. However, microsecond dynamics and activity are beautifully correlated in this case also. Overall, our result demonstrates that bromelain dynamics in the microsecond timescale around the active-site is probably a key factor in controlling its proteolytic activity.
Keywords	active sites ; bromelains ; casein ; cysteine ; dyes ; enzyme activity ; proteolysis ; spectroscopy ; stabilizers ; sucrose
Language	English
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2667-1603
DOI	10.1016/j.bbadva.2022.100041
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Article ; Online: Subpicosecond Solvation Response and Partial Viscosity Decoupling of Solute Diffusion in Ionic Acetamide Deep Eutectic Solvents: Fluorescence Up-Conversion and Fluorescence Correlation Spectroscopic Measurements.

Subba, Navin / Tarif, Ejaj / Sen, Pratik / Biswas, Ranjit

The journal of physical chemistry. B

2020 Volume 124, Issue 10, Page(s) 1995–2005

Abstract: Fluorescence up-conversion (∼250 fs instrumental response) coupled with time correlated single photon counting measurements was performed to explore the complete Stokes shift dynamics of a dipolar solute probe, coumarin 153 (C153), in several ionic ... ...

Abstract	Fluorescence up-conversion (∼250 fs instrumental response) coupled with time correlated single photon counting measurements was performed to explore the complete Stokes shift dynamics of a dipolar solute probe, coumarin 153 (C153), in several ionic acetamide deep eutectic solvents (DESs) that contained lithium nitrate/bromide/perchlorate as electrolyte. Combined measurements near room temperature reflected a total dynamic Stokes shift of approximately 800-1100 cm
Language	English
Publishing date	2020-02-27
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.0c00061
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Article: Subpicosecond Solvation Response and Partial Viscosity Decoupling of Solute Diffusion in Ionic Acetamide Deep Eutectic Solvents: Fluorescence Up-Conversion and Fluorescence Correlation Spectroscopic Measurements

Subba, Navin / Tarif, Ejaj / Sen, Pratik / Biswas, Ranjit

Journal of physical chemistry. 2020 Feb. 17, v. 124, no. 10

2020

Abstract	Fluorescence up-conversion (∼250 fs instrumental response) coupled with time correlated single photon counting measurements was performed to explore the complete Stokes shift dynamics of a dipolar solute probe, coumarin 153 (C153), in several ionic acetamide deep eutectic solvents (DESs) that contained lithium nitrate/bromide/perchlorate as electrolyte. Combined measurements near room temperature reflected a total dynamic Stokes shift of approximately 800–1100 cm–1 and triexponential solvation response functions. Interestingly, the average rate of solvation became faster upon successive replacement of bromide by nitrate in these deep eutectics, and a subpicosecond time scale emerged in the measured solvation response when bromide was fully replaced by nitrate. Temperature dependent solute diffusion in these deep eutectics at the single molecule level, monitored by tracking the translational motion of rhodamine 6G (R6G) via fluorescence correlation spectroscopic (FCS) technique, revealed pronounced fractional viscosity dependence of the solute’s translational motion. Subsequently, this partial decoupling of solute translation was attributed to the microheterogeneous nature of these ionic DESs after examining the diffusion–viscosity relationship via the FCS measurements of R6G in several normal solvents at room temperature and in a liquid amide solvent at different temperatures.
Keywords	ambient temperature ; coumarin ; electrolytes ; fluorescence ; liquids ; lithium ; nitrates ; perchlorates ; photons ; rhodamines ; solutes ; solvation ; solvents ; spectral analysis ; spectroscopy ; viscosity
Language	English
Dates of publication	2020-0217
Size	p. 1995-2005.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.0c00061
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Article ; Online: Does Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain? Clues from Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder

Das, Nilimesh / Yadav, Sandeep / Negi, Kuldeep Singh / Tarif, Ejaj / Sen, Pratik

BBA advances

2022 Volume 2, Page(s) 100041

Abstract	Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. However, it is not easy to directly correlate an enzyme's dynamics and activity due to biosystems' enormous complexity. amongst many factors, structure and dynamics are two prime aspects that combinedly control the activity. Therefore, having a direct correlation between protein dynamics and activity is not straightforward. Herein, we observed and correlated the structural, functional, and dynamical responses of an industrially crucial proteolytic enzyme, bromelain with three versatile classes of chemicals: GnHCl (protein denaturant), sucrose (protein stabilizer), and Ficoll-70 (macromolecular crowder). The only free cysteine (Cys-25 at the active-site) of bromelain has been tagged with a cysteine-specific dye to unveil the structural and dynamical changes through various spectroscopic studies both at bulk and at the single molecular level. Proteolytic activity is carried out using casein as the substrate. GnHCl and sucrose shows remarkable structure-dynamics-activity relationships. Interestingly, with Ficoll-70, structure and activity are not correlated. However, microsecond dynamics and activity are beautifully correlated in this case also. Overall, our result demonstrates that bromelain dynamics in the microsecond timescale around the active-site is probably a key factor in controlling its proteolytic activity.
Language	English
Publishing date	2022-01-12
Publishing country	Netherlands
Document type	Journal Article
ISSN	2667-1603
ISSN (online)	2667-1603
DOI	10.1016/j.bbadva.2022.100041
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Article ; Online: Interaction and Dynamics in a Fully Biodegradable Glucose-Containing Naturally Abundant Deep Eutectic Solvent: Temperature-Dependent Time-Resolved Fluorescence Measurements.

Tarif, Ejaj / Mondal, Jayanta / Biswas, Ranjit

The journal of physical chemistry. B

2019 Volume 123, Issue 44, Page(s) 9378–9387

Abstract: A new room-temperature deep eutectic solvent (DES) composed of glucose, urea, and water has been prepared and its relaxation dynamics explored via temperature-dependent time-resolved fluorescence measurements employing hydrophilic and hydrophobic solute ... ...

Abstract	A new room-temperature deep eutectic solvent (DES) composed of glucose, urea, and water has been prepared and its relaxation dynamics explored via temperature-dependent time-resolved fluorescence measurements employing hydrophilic and hydrophobic solute probes. Differential scanning calorimetry measurements indicate a glass transition temperature (
MeSH term(s)	Biodegradation, Environmental ; Coumarins/chemistry ; Fluorescence ; Fluorescence Polarization ; Fluorescent Dyes/chemistry ; Glucose/chemistry ; Glucose/metabolism ; Hydrophobic and Hydrophilic Interactions ; Solvents/chemistry ; Solvents/metabolism ; Spectrometry, Fluorescence ; Temperature ; Urea/chemistry
Chemical Substances	Coumarins ; Fluorescent Dyes ; Solvents ; coumarin 343 ; Urea (8W8T17847W) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2019-10-25
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.9b06783
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Article: Interaction and Dynamics in a Fully Biodegradable Glucose-Containing Naturally Abundant Deep Eutectic Solvent: Temperature-Dependent Time-Resolved Fluorescence Measurements

Tarif, Ejaj / Mondal, Jayanta / Biswas, Ranjit

Journal of physical chemistry. 2019 Oct. 10, v. 123, no. 44

2019

Abstract	A new room-temperature deep eutectic solvent (DES) composed of glucose, urea, and water has been prepared and its relaxation dynamics explored via temperature-dependent time-resolved fluorescence measurements employing hydrophilic and hydrophobic solute probes. Differential scanning calorimetry measurements indicate a glass transition temperature (Tg) of ∼236 K. Measured viscosity coefficients (η) vary from ∼600 to ∼100 cP in the temperature range 318 ≤ T/K ≤ 343 and exhibit Arrhenius-type temperature dependence with an activation energy of ∼65 kJ mol–¹. Interestingly, this DES forms a stable liquid at ∼300 K but is too viscous to be accurately measured by us below 318 K. Temperature-dependent dynamic fluorescence anisotropy measurements using hydrophobic and hydrophilic solutes of similar sizes reveal bi-exponential kinetics and Arrhenius-type temperature dependence for solute rotation times (⟨τᵣ⟩) but with significantly decreased activation energies, ∼31 kJ mol–¹ (hydrophobic) and ∼21 kJ mol–¹ (hydrophilic). Deviation from hydrodynamics is further reflected in the strong fractional viscosity dependence of ⟨τᵣ⟩: ⟨τᵣ⟩ ∝ (η/T)ᵖ with p ≈ 0.3–0.5, indicating pronounced temporal heterogeneity in the relaxation dynamics. Dynamic fluorescence Stokes shift measurements (temporal resolution ∼85 ps) produce dynamic shifts of ∼500–700 cm–¹, bi-exponential solvation energy relaxation with time constants in the range ∼0.2 ns and ∼4 ns, and estimated missing amplitudes of ∼65–75%. Impact of the density difference between a nonpolar solvent and this DES on the estimated missing amplitudes is explored via measuring the temperature-dependent densities and refractive indices of this DES. Lifetime measurements suggest considerable temperature dependence for the hydrophobic solute but no such dependence for the hydrophilic one. Excitation energy dependence of fluorescence emission of various solutes with widely different lifetimes indicates mild spatial heterogeneity for this DES.
Keywords	activation energy ; ambient temperature ; anisotropy ; biodegradability ; differential scanning calorimetry ; fluorescence ; glass transition temperature ; glucose ; hydrodynamics ; hydrophilicity ; hydrophobicity ; liquids ; physical chemistry ; refractive index ; solutes ; solvation energy ; solvents ; spatial variation ; urea ; viscosity
Language	English
Dates of publication	2019-1010
Size	p. 9378-9387.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b06783
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Article: Temperature-Dependent Dielectric Relaxation in Ionic Acetamide Deep Eutectics: Partial Viscosity Decoupling and Explanations from the Simulated Single-Particle Reorientation Dynamics and Hydrogen-Bond Fluctuations

Mukherjee, Kallol / Das, Suman / Rajbangshi, Juriti / Tarif, Ejaj / Barman, Anjan / Biswas, Ranjit

Journal of physical chemistry. 2021 Nov. 09, v. 125, no. 45

2021

Abstract: We report here temperature-dependent (293 ≤ T (K) ≤ 336) dielectric relaxation (DR) measurements of (acetamide + LiBr/NO₃–/ClO₄–) deep eutectic solvents (DESs) in the frequency window of 0.2 ≤ ν (GHz) ≤ 50 and explore, via molecular dynamics simulations, ...

Abstract	We report here temperature-dependent (293 ≤ T (K) ≤ 336) dielectric relaxation (DR) measurements of (acetamide + LiBr/NO₃–/ClO₄–) deep eutectic solvents (DESs) in the frequency window of 0.2 ≤ ν (GHz) ≤ 50 and explore, via molecular dynamics simulations, the relative roles for the collective single-particle reorientational relaxations and the H-bond dynamics of acetamide in the measured DR response. In addition, DR measurements of neat molten acetamide were performed. Recorded DR spectra of these DESs require multi-Debye fits and produce well-separated DR time scales that are spread over several picoseconds to ∼1 ns. Simulations suggest DR time scales derive contributions from both the collective reorientational (Cl(t)) relaxation and structural H-bond (CHB(t)) dynamics of acetamide. A good correlation between the measured and simulated activation energies further reveals a strong connection between the measured DR and the simulated Cl(t) and CHB(t). Average DR times exhibit a strong fractional viscosity dependence, suggesting substantial microheterogeneity in these media. Simulations of Cl(t) and CHB(t) reveal strong stretched exponential relaxations with a stretching exponent, 0.4 ≤ β ≤ 0.7. The ratio between the average reorientational correlation times of first and second ranks, ⟨τ⟩l=1/⟨τ⟩l=2, deviates appreciably from Debye’s l(l+1) law for homogeneous media. Importantly, a pronounced translation-rotation decoupling between the simulated reorientation and center-of-mass diffusion times was observed.
Keywords	hydrogen bonding ; molecular dynamics ; viscosity
Language	English
Dates of publication	2021-1109
Size	p. 12552-12567.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c07299
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Article ; Online: Temperature-Dependent Dielectric Relaxation in Ionic Acetamide Deep Eutectics: Partial Viscosity Decoupling and Explanations from the Simulated Single-Particle Reorientation Dynamics and Hydrogen-Bond Fluctuations.

Mukherjee, Kallol / Das, Suman / Rajbangshi, Juriti / Tarif, Ejaj / Barman, Anjan / Biswas, Ranjit

The journal of physical chemistry. B

2021 Volume 125, Issue 45, Page(s) 12552–12567

Abstract: We report here temperature-dependent (293 ≤ ...

Abstract	We report here temperature-dependent (293 ≤
MeSH term(s)	Acetamides ; Deep Eutectic Solvents ; Hydrogen ; Temperature ; Viscosity
Chemical Substances	Acetamides ; Deep Eutectic Solvents ; Hydrogen (7YNJ3PO35Z)
Language	English
Publishing date	2021-11-09
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.1c07299
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