Identification of "Molten Globule"-like State in an All β-Sheet Protein

Kumar, Thallapuranam Krishnaswamy Suresh; Jayaraman, G.; Lee, C.S.; Sivaraman, Thirunavukkarasu; Lin, Wei‐Hsiang; Yu, Chung‐Shan

doi:10.1006/bbrc.1995.1221

Cited by 33 publications

(11 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on the refolding rate constants of NHs of CTX III obtained from quenched-flow H/D exchange experiments, it has been shown that the triple-stranded β-sheet was formed before the double-stranded β-sheet segment in the refolding kinetics of the protein. Moreover, it has also been demonstrated that the triple-stranded β-sheet segment of the protein was persistently found in the intermediate states identified along the acid-induced and alcohol-induced unfolding pathways of CTX III [54], [55]. To this extent, the predictions of OneG on the possible existence of two cryptic intermediates of CTX III under native conditions are consistent with the data reported from equilibrium and kinetic studies of the protein.…”

Section: Resultssupporting

confidence: 80%

OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

Tambi¹,

Sivaraman

2012

PLoS ONE

View full text Add to dashboard Cite

Understanding the relationships between conformations of proteins and their stabilities is one key to address the protein folding paradigm. The free energy change (ΔG) of unfolding reactions of proteins is measured by traditional denaturation methods and native hydrogen-deuterium (H/D) exchange methods. However, the free energy of unfolding (ΔGU) and the free energy of exchange (ΔGHX) of proteins are not in good agreement, though the experimental conditions of both methods are well matching to each other. The anomaly is due to any one or combinations of the following reasons: (i) effects of cis-trans proline isomerisation under equilibrium unfolding reactions of proteins (ii) inappropriateness in accounting the baselines of melting curves (iii) presence of cryptic intermediates, which may elude the melting curve analysis and (iv) existence of higher energy metastable states in the H/D exchange reactions of proteins. Herein, we have developed a novel computational tool, OneG, which accounts the discrepancy between ΔGU and ΔGHX of proteins by systematically accounting all the four factors mentioned above. The program is fully automated and requires four inputs: three-dimensional structures of proteins, ΔGU, ΔGU * and residue-specific ΔGHX determined under EX2-exchange conditions in the absence of denaturants. The robustness of the program has been validated using experimental data available for proteins such as cytochrome c and apocytochrome b562 and the data analyses revealed that cryptic intermediates of the proteins detected by the experimental methods and the cryptic intermediates predicted by the OneG for those proteins were in good agreement. Furthermore, using OneG, we have shown possible existence of cryptic intermediates and metastable states in the unfolding pathways of cardiotoxin III and cobrotoxin, respectively, which are homologous proteins. The unique application of the program to map the unfolding pathways of proteins under native conditions have been brought into fore and the program is publicly available at http://sblab.sastra.edu/oneg.html

show abstract

Section: Resultssupporting

confidence: 80%

OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

Tambi¹,

Sivaraman

2012

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…It is to be mentioned that the 270 nm CD band signifying the tertiary structural interactions were diminished at all concentrations of TFE (Figure 4c ). TFE has been shown to be a potential denaturant disrupting the tertiary and the quaternary structural interactions in proteins (26,27). However, the mechanism of induction of helix in proteins is still a subject of intense debate.…”

Section: Resultsmentioning

confidence: 99%

Induction of Helical Conformation in all β-sheet Proteins by Trifluoroethanol

Arunkumar

Kumar²,

Jayaraman³

et al. 1996

Journal of Biomolecular Structure and Dynamics

Self Cite

View full text Add to dashboard Cite

The effect of 2,2,2-Trifluoroethanol (TFE) on the structure of five all beta-sheet proteins, isolated from the venom of the Taiwan cobra (Naja naja atra), is studied. In all the toxins used, it is observed that significant amount of alpha-helix is induced at higher concentrations of TFE. In all these proteins, the induction of helical conformation and disruption of the tertiary structure seem to occur simultaneously. The structural transitions induced by TFE in reduced and denatured protein appear to be different from those observed in the native protein(s). In our opinion, the findings reported herein could have significant implications on research in the area of protein folding.

show abstract

“…The CTX III and SNTX are extensively characterized proteins from TFT superfamily of snake venoms in terms of structures, folding and dynamics (Kumar et al, 1995;Sivaraman et al, 1996Sivaraman et al, , 1997Sivaraman et al, , 1998Sivaraman et al, , 1999b. Moreover, thermodynamic stabilities of the proteins have also been examined at molecular-and as well at residue-level resolutions in similar solution conditions (Sivaraman et al, 1999c(Sivaraman et al, , 2000.…”

Section: Simulations On Ctx III and Sntx At Different Temperaturesmentioning

confidence: 99%

“…Structural stabilities and folding of the CTX III and SNTX characterized using variety of biophysical Unfolding stabilities of two structurally similar proteins 2041 methods have been documented in the literature (Kumar et al, 1995;Sivaraman, 1999;Sivaraman et al, 1996Sivaraman et al, , 1997Sivaraman et al, , 1998Sivaraman et al, , 1999aSivaraman et al, , 1999bSivaraman et al, , 2000. Temperature-and guanidine hydrochloride-induced denaturation of the proteins have been probed at pH 3.2 using circular dichroism techniques: free energy of unfolding (ΔG U ) of the CTX III and SNTX were estimated to be 4.9 and 2.3 kcal/mol, respectively, from the chemical denaturation of the proteins; the CTX III and SNTX were shown to be fully unfolded at 363 K under the solution conditions described above with T m values of 343 and 333 K, respectively, from thermal denaturation of the proteins (Sivaraman et al, 1999c(Sivaraman et al, , 2000.…”

Section: 'Cn Network' Hypothesis and Unfolding Stabilities Of The Ctxmentioning

confidence: 99%

“…In these connections, figuring out residues that are essential for structural integrities and as well residues essential for functional activities of proteins are indispensable to manipulate stabilities and activities of those proteins through protein-engineering strategies from the view of biotechnological and biomedical industries standpoints (Brannigan & Wilkinson, 2002;Leisola & Turunen, 2007;Marcheschi, Gronenberg, & Liao, 2013;Shaw, 1987). Structure, folding and stabilities of cardiotoxin III (CTX III) and short-neurotoxin (SNTX or CBTX, cobrotoxin) belonging to three-finger toxin (TFT) superfamily of snake venom of Naja naja atra (Taiwan cobra) have been well characterized at molecular resolutions and as well at residue-level resolutions (Chang, Lu, Lin, & Yu, 2006;Kumar et al, 1995;Sivaraman, Kumar, & Yu, 1999a;Sivaraman et al, 1999b;Sivaraman, Kumar, Chang, Lin, & Yu, 1998;Sivaraman, Kumar, Jayaraman, Han & Yu, 1997;Sivaraman, Kumar, & Yu, 1996). The proteins are homologous, have similar 3D folds but exhibit drastically different unfolding stabilities and biological functions.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations

Gorai

Prabhavadhni

Sivaraman

2014

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Unfolding stabilities of two homologous proteins, cardiotoxin III and short-neurotoxin (SNTX) belonging to three-finger toxin (TFT) superfamily, have been probed by means of molecular dynamics (MD) simulations. Combined analysis of data obtained from steered MD and all-atom MD simulations at various temperatures in near physiological conditions on the proteins suggested that overall structural stabilities of the two proteins were different from each other and the MD results are consistent with experimental data of the proteins reported in the literature. Rationalization for the differential structural stabilities of the structurally similar proteins has been chiefly attributed to the differences in the structural contacts between C- and N-termini regions in their three-dimensional structures, and the findings endorse the 'CN network' hypothesis proposed to qualitatively analyse the thermodynamic stabilities of proteins belonging to TFT superfamily of snake venoms. Moreover, the 'CN network' hypothesis has been revisited and the present study suggested that 'CN network' should be accounted in terms of 'structural contacts' and 'structural strengths' in order to precisely describe order of structural stabilities of TFTs.

show abstract

Identification of "Molten Globule"-like State in an All β-Sheet Protein

Cited by 33 publications

References 0 publications

OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

Induction of Helical Conformation in all β-sheet Proteins by Trifluoroethanol

Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations

Contact Info

Product

Resources

About