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Garg M, Sharma D, Kaur G, Rawat J, Goyal B, Kumar S, Kumar R. Factor defining the effects of tetraalkylammonium chloride on stability, folding, and dynamics of horse cytochrome c. Int J Biol Macromol 2024; 276:133713. [PMID: 38986993 DOI: 10.1016/j.ijbiomac.2024.133713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
This article describes the molecular mechanism by which tetraalkylammonium chloride ([R4N]Cl: R- = methyl (Me), ethyl (Et), propyl (Pr),butyl (Bu)) modulates the stability, folding, and dynamics of cytochrome c (Cyt c). Analysis of [R4N]Cl effects on thermal/chemical denaturations, millisecond refolding/unfolding kinetics, and slow CO-association kinetics of Cyt c without and with denaturant providing some significant results: (i) [R4N]Cl decreasing the unfolding free energy estimated by thermodynamic and kinetic analysis of thermal/chemical denaturation curves and kinetic chevrons (Log kobs-[GdmCl]) of Cyt c, respectively (ii) hydrophobicity of R-group of [R4N]Cl, preferential inclusion of [R4N]Cl at the protein surface, and destabilizing enthalpic attractive interactions of [Me4N]Cl and steric entropic interactions of [Et4N]Cl,[Pr4N]Cl and [Bu4N]Cl with protein contribute to [R4N]Cl-induced decrease thermodynamic stability of Cyt c (iii) [R4N]Cl exhibits an additive effect with denaturant to decrease thermodynamic stability and refolding rates of Cyt c (iv) low concentrations of [R4N]Cl (≤ 0.5 M) constrain the motional dynamics while the higher concentrations (>0.75 M [R4N]Cl) enhance the structural-fluctuations that denture protein (v) hydrophobicity of R-group of [R4N]Cl alters the [denaturant]-dependent conformational stability, refolding-unfolding kinetics, and CO-association kinetics of Cyt c. Furthermore, the MD simulations depicted that the addition of 1.0 M of [R4N]Cl increased the conformational fluctuations in Cyt c leading to decreased structural stability in the order [Me4N]Cl < [Et4N]Cl < [Pr4N]Cl < [Bu4N]Cl consistent with the experimental results.
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Affiliation(s)
- Mansi Garg
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Academy of Scientific & Innovative Research, Chandigarh, India
| | - Gurmeet Kaur
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Jayanti Rawat
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Bhupesh Goyal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Sumit Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Rajesh Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India.
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Naidu KT, Prabhu NP. Polyols, increasing global stability of cytochrome c, destabilize the thermal unfolding intermediate. J Biomol Struct Dyn 2022; 40:11216-11228. [PMID: 34308796 DOI: 10.1080/07391102.2021.1956593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Studies on the intermediate states of proteins provide essential information on folding pathway and energy landscape of proteins. Osmolytes, known to alter the stability of proteins, might also affect the structure and energy states of folding intermediates. This was examined using cytochrome c (Cyt) as a model protein which forms a spectroscopically detectable intermediate during thermal denaturation transition. Most of the secondary structure and the native heme-ligation were intact in the intermediate state of the protein. Denaturants, urea and guanidinium hydrochloride, and ionic salt destabilizes the intermediate and drive the protein to follow two-state transition. The effect of polyol class of osmolytes, glycol, glycerol, erythritol, xylitol and sorbitol (with OH-groups two to six), on the intermediate was studied using Soret absorbance and far-UV circular dichroism. With the increasing concentration of any of the polyols, the transition-midpoint temperature (Tm) and the enthalpy change (ΔH) for native to intermediate transition were decreased. This indicated that the intermediate was destabilized by the polyols. However, the polyols increased the overall stability of the protein by increasing Tm and ΔH for intermediate to unfolded transition, except for glycol which destabilized the protein. These results show that the polyols could alter the energy state of the intermediate, and the effect of lower and higher polyols might be different on the stability and folding pathway of the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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3
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Chialvo AA, Crisalle OD. Osmolyte-Induced Effects on the Hydration Behavior and the Osmotic Second Virial Coefficients of Alkyl-Substituted Urea Derivatives: Critical Assessment of Their Structure-Making/Breaking Behavior. J Phys Chem B 2021; 125:6231-6243. [PMID: 34086462 DOI: 10.1021/acs.jpcb.1c01855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We analyzed the hydration behavior of alkyl-substituted urea osmolytes in terms of their deviation from Lewis-Randall solution ideality and characterized their structure-making/breaking tendency according to a proposed solvation formalism that provides a rigorous cause-effect connection between the system microstructure and its solution thermodynamic nonidealities. After a brief introduction of the rationale behind the use of Lewis-Randall over alternative solution ideality references, we (i) assessed the effect of the nature and type of alkyl substitution on the osmolyte-induced perturbation of the solution microstructure as a function of composition, (ii) analyzed their microstructural responses to changes in temperature and pressure, and (iii) demonstrated the structure-breaking nature of urea and the magnifying behavior of its alkyl-substituted osmolytes, whose trend follows the increasingly positive deviation of the osmolyte solutions from Lewis-Randall ideality. Then, we discussed the falsifiability of a pair of frequently used conjectured structure-making/breaking criteria, supported by the derived exact relationships between the structure-making/breaking parameter, the solution thermodynamic nonideality, and the osmotic second virial coefficient of the aqueous osmolytes. Finally, we provided an outlook on how the proposed approach could guide the quest for a truly (microstructural to free energy) causative explanation for the denaturation mechanism of proteins.
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Affiliation(s)
| | - Oscar D Crisalle
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
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Effect of imidazolium based ionic liquids on CO-association dynamics and thermodynamic stability of Ferrocytochrome c. Biophys Chem 2020; 268:106497. [PMID: 33212391 DOI: 10.1016/j.bpc.2020.106497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 11/20/2022]
Abstract
Analysis of kinetic and thermodynamic parameters measured for CO-association reaction of Ferrocytochrome c (Ferrocyt c) under variable concentrations of 1-butyl-3-methylimidazolium with varying anion ([Bmim]X) (X = Cl-, I-, Br-, HSO4-) at pH 7 revealed that the low concentration of [Bmim]X (≤0.5 M) constrains the CO-association dynamics of Ferrocyt c and typically follows the order: [Bmim]HSO4 > [Bmim]Cl > [Bmim]Br > [Bmim]I. At relatively higher concentrations (>0.5), the chaotropic action of [Bmim]+ dominates which consequently increases the thermal-fluctuations responsible to denature the protein and thus accelerates the speed of CO-association reaction. Analysis of thermal denaturation curves of Ferrocyt c measured at different concentrations of [Bmim]X revealed that the [Bmim]X decreases the thermodynamic stability of protein and typically follows the order: [Bmim]I > [Bmim]Br > [Bmim]Cl > [Bmim]CH3COO > [Bmim]HSO4, demonstrating that the effect of [Bmim]X on thermodynamic stability of protein is not in accordance to Hofmeister series effect of anions because instead of increasing the kosmotropic anion carrying [Bmim]X ([Bmim]CH3COO and [Bmim]HSO4) also decreases the thermodynamic stability of protein.
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Tomášková N, Varhač R, Lysáková V, Musatov A, Sedlák E. Peroxidase activity of cytochrome c in its compact state depends on dynamics of the heme region. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1073-1083. [DOI: 10.1016/j.bbapap.2018.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
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6
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Effects of lyotropic anions on thermodynamic stability and dynamics of horse cytochrome c. Biophys Chem 2018; 240:88-97. [DOI: 10.1016/j.bpc.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/09/2018] [Accepted: 06/10/2018] [Indexed: 11/19/2022]
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Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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8
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Zhang X, Chemmalil L, Ding J, Mussa N, Li Z. Imaged capillary isoelectric focusing in native condition: A novel and successful example. Anal Biochem 2017; 537:13-19. [DOI: 10.1016/j.ab.2017.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023]
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Muneeswaran G, Kartheeswaran S, Muthukumar K, Dharmaraj CD, Karunakaran C. Effects of different solvents on the conformations of apoptotic cytochrome c: Structural insights from molecular dynamics simulation. J Mol Graph Model 2017; 76:234-241. [DOI: 10.1016/j.jmgm.2017.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/18/2017] [Accepted: 06/19/2017] [Indexed: 01/30/2023]
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Panuszko A, Bruździak P, Kaczkowska E, Stangret J. General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent. J Phys Chem B 2016; 120:11159-11169. [DOI: 10.1021/acs.jpcb.6b10119] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry,
Chemical Faculty, Gdańsk University of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
| | - Piotr Bruździak
- Department of Physical Chemistry,
Chemical Faculty, Gdańsk University of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
| | - Emilia Kaczkowska
- Department of Physical Chemistry,
Chemical Faculty, Gdańsk University of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry,
Chemical Faculty, Gdańsk University of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
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Gao Y, Yang J, Fan H, Ding Y, Ye X. Insight into the effect of methylated urea on the phase transition of aqueous solutions of poly(N
-isopropylacrylamide) by microcalorimetry: Hydrogen bonding and van der Waals interactions. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/polb.24018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yating Gao
- Department of Chemical Physics; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China; Hefei Anhui 230026 China
| | - Jinxian Yang
- Department of Chemical Physics; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China; Hefei Anhui 230026 China
| | - Haiyan Fan
- Department of Chemical Physics; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China; Hefei Anhui 230026 China
| | - Yanwei Ding
- Department of Chemical Physics; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China; Hefei Anhui 230026 China
| | - Xiaodong Ye
- Department of Chemical Physics; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China; Hefei Anhui 230026 China
- CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China; Hefei Anhui 230026 China
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Kumar R, Sharma D, Jain R, Kumar S, Kumar R. Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c. Biophys Chem 2015; 207:61-73. [DOI: 10.1016/j.bpc.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 11/25/2022]
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13
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Jain R, Kumar R, Kumar S, Chhabra R, Agarwal MC, Kumar R. Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c. Arch Biochem Biophys 2015; 585:52-63. [DOI: 10.1016/j.abb.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/26/2022]
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Sashi P, Bhuyan AK. Viscosity Dependence of Some Protein and Enzyme Reaction Rates: Seventy-Five Years after Kramers. Biochemistry 2015; 54:4453-61. [PMID: 26135219 DOI: 10.1021/acs.biochem.5b00315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kramers rate theory is a milestone in chemical reaction research, but concerns regarding the basic understanding of condensed phase reaction rates of large molecules in viscous milieu persist. Experimental studies of Kramers theory rely on scaling reaction rates with inverse solvent viscosity, which is often equated with the bulk friction coefficient based on simple hydrodynamic relations. Apart from the difficulty of abstraction of the prefactor details from experimental data, it is not clear why the linearity of rate versus inverse viscosity, k ∝ η(-1), deviates widely for many reactions studied. In most cases, the deviation simulates a power law k ∝ η(-n), where the exponent n assumes fractional values. In rate-viscosity studies presented here, results for two reactions, unfolding of cytochrome c and cysteine protease activity of human ribosomal protein S4, show an exceedingly overdamped rate over a wide viscosity range, registering n values up to 2.4. Although the origin of this extraordinary reaction friction is not known at present, the results indicate that the viscosity exponent need not be bound by the 0-1 limit as generally suggested. For the third reaction studied here, thermal dissociation of CO from nativelike cytochrome c, the rate-viscosity behavior can be explained using Grote-Hynes theory of time-dependent friction in conjunction with correlated motions intrinsic to the protein. Analysis of the glycerol viscosity-dependent rate for the CO dissociation reaction in the presence of urea as the second variable shows that the protein stabilizing effect of subdenaturing amounts of urea is not affected by the bulk viscosity. It appears that a myriad of factors as diverse as parameter uncertainty due to the difficulty of knowing the exact reaction friction and both mode and consequences of protein-solvent interaction work in a complex manner to convey as though Kramers rate equation is not absolute.
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Affiliation(s)
- Pulikallu Sashi
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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Jain R, Sharma D, Kumar S, Kumar R. Factor Defining the Effects of Glycine Betaine on the Thermodynamic Stability and Internal Dynamics of Horse Cytochrome c. Biochemistry 2014; 53:5221-35. [DOI: 10.1021/bi500356c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rishu Jain
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Deepak Sharma
- Council
of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Sandeep Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Rajesh Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
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