Evidence of non-coincidence of normalized sigmoidal curves of two different structural properties for two-state protein folding/unfolding

Rahaman, Hamidur; Khan, Md. Khurshid Alam; Hassan, Md. Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

doi:10.1016/j.jct.2012.11.024

Cited by 28 publications

(12 citation statements)

References 19 publications

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“…It has been observed that all three probes gives almost identical values of these stability parameters (Table ). That is, values of measured stability parameters are independent of probe used to monitor the denaturation of a protein . Thus, the coincidence of normalized denaturation curves and similar values of stability parameters (calculated from three different probes) suggest that the GdmCl‐induced denaturation of HFE is a two‐state process.…”

Section: Discussionmentioning

confidence: 79%

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Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl‐induced denaturation study

et al. 2015

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Hemochromatosis factor E (HFE) is a member of class I MHC family and plays a significant role in the iron homeostasis. Denaturation of HFE induced by guanidinium chloride (GdmCl) was measured by monitoring changes in [θ]222 (mean residue ellipticity at 222 nm), intrinsic fluorescence emission intensity at 346 nm (F346 ) and the difference absorption coefficient at 287 nm (Δε287) at pH 8.0 and 25°C. Coincidence of denaturation curves of these optical properties suggests that GdmCl-induced denaturation (native (N) state ↔ denatured (D) state) is a two-state process. The GdmCl-induced denaturation was found reversible in the entire concentration range of the denaturant. All denaturation curves were analyzed for ΔGD0, Gibbs free energy change associated with the denaturation equilibrium (N state ↔ D state) in the absence of GdmCl, which is a measure of HFE stability. We further performed molecular dynamics simulation for 40 ns to see the effect of GdmCl on the structural stability of HFE. A well defined correlation was established between in vitro and in silico studies.

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Section: Discussionmentioning

confidence: 79%

“…At a given [GdmCl], the denatured fraction of the protein, f D was calculated using the relation

{normalf}_{D =} (y - y_{normalN}) / ({normaly}_{normalD} - y_{normalN}) = y - (a_{normalN} + b_{normalN} [GdmC 1]) / (a_{normalD} - a_{normalN}) + (b_{normalD} - b_{normalN}) [GdmC 1]

…”

Section: Experimental Partmentioning

confidence: 99%

Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl‐induced denaturation study

et al. 2015

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“…Second, each transition curve (N  X and X  D) follows a two-state mechanism. Validation of this assumption is simply the coincidence of normalized transition curve [37,71], and nearly similar values of thermodynamic parameters associated with the different transition curves monitored by different probes ([θ] 222 , F 346 and Δε 287 ) [72]. It can be easily observe from the Fig.…”

Section: Stability Parametersmentioning

confidence: 85%

“…At a given [urea], the denatured fraction of the protein, f D was calculated by using the relation [37]:…”

Section: Analysis Of Spectral Measurementsmentioning

confidence: 99%

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E

Khan

Prakash

Haque

et al. 2016

International Journal of Biological Macromolecules

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“…On the contrary, basing their arguments on theoretical grounds, Dill and Shortle (1991) have shown that the non-coincidence of sigmoidal curves of two different physical properties is also observed for a two-state protein denaturation. Recently, Rahaman et al (2013) pro- Effect of urea on C-phycoerythrin 129 vided experimental evidence that this non-coincidence is consistent with two-state denaturation behavior. In another approach for testing the two-state behavior of the urea-induced denaturation, ΔG D 0 values of the protein are measured from sigmoidal curves of different structural properties, and it is shown that this thermodynamic property is independent of techniques (probes) used to monitor the denaturation (Bolen & Yang, 2000).…”

Section: Structural and Thermodynamic Characterizationsmentioning

confidence: 88%

Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies

Anwer

Sonani

Madamwar

et al. 2013

Journal of Biomolecular Structure and Dynamics

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The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of αC-PE. To compare their stabilities, we have measured urea-induced denaturation transitions of the full length αC-PE (FL-αC-PE) and truncated αC-PE (Tr-αC-PE) followed by observing changes in absorbance at 565 nm, fluorescence at 350 and 573 nm, and circular dichroism at 222 nm as a function of [urea], the molar concentration of urea. The transition curve of each protein was analyzed for ΔG(D)(0), the value of Gibbs free energy change on denaturation (ΔG(D)) in the absence of urea; m, the slope (=∂∆G(D)/∂[urea]), and C(m), the midpoint of the denaturation curve, i.e. [urea] at which ΔG(D) = 0. A difference of about 10% in ΔG(D)(0) observed between FL-αC-PE and Tr-αC-PE, suggests that the two proteins are almost equally stable, and the natural deletion of 31 residues from the N-terminal side of the full length protein does not alter its stability. Furthermore, normalization of probes shows that the urea-induced denaturation of both the proteins is a two-state process. Folding of both structural variants (Tr-αC-PE and FL-αC-PE) of P. tenue were also studied using molecular dynamics simulations at 300 K. The results show clearly that the stability of the proteins is evenly distributed over the whole structure indicating no significant role of N-terminal residues in the stability of both proteins.

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Evidence of non-coincidence of normalized sigmoidal curves of two different structural properties for two-state protein folding/unfolding

Cited by 28 publications

References 19 publications

Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl‐induced denaturation study

Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl‐induced denaturation study

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E

Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies

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