• Applied Biological Chemistry
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• v.47 no.1
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• pp.33-40
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• 2004

Thermodynamic properties of ubiquitin transient folding intermediate were studied by measuring folding kinetics in varying temperatures and denaturant concentrations. Through quantitative kinetic modeling, the equilibrium constant, hence folding free energy, between unfolded state and intermediate state in several different temperatures were calculated. Using these values, the thermodynamic parameters were estimated. The heat capacity change $({\Delta}C_p)$ upon formation of folding intermediate from unfolded state were estimated to be around 80% of the overall folding reaction, indicating that ubiquitin folding intermediate is highly compact. At room temperature, the changes of enthalpy and entropy upon formation of the intermediate state were observed to be positive. The positive enthalpy change suggests that the breaking up of the highly ordered solvent structure surrounding hydrophobic side-chain upon formation of intermediate state. This positive enthalpy was compensated for by the positive entropy change of whole system so that formation of transient intermediate has negative free energy.

• Journal of Life Science
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• v.11 no.1
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• pp.43-47
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• 2001

A mutant tryptophan synthase $\alpha$-subunit, where Pro28 was replaced with Leu, tends to be expressed in recombinant E. coli. CD and fluorescence spectra of this protein indicate some changes in secondary and tertiary structure. Wild type protein was more or less affected by {TEX}$Ca^{2+}${/TEX} ion in regards of the fluorescent properties of its native, unfolded and intermediate forms, but the mutant protein was not at all. The dramatic structural changes may be related to the aggregation of this mutant protein.

• Journal of the Korean Chemical Society
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• v.58 no.6
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• pp.560-568
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• 2014

The contribution of electrostatic interactions to protein folding reaction was studied by using mutant ubiquitin with lysine to alanine mutation at residue position 29. Based on the three dimensional structure of ubiquitin, lysine 29 is located close to negatively charged glutamate 16 and aspartate 21 and considered to stabilize the native state of ubiquitin by electrostatic interactions between these residues. The equilibrium unfolding experiment showed that the native stability was decreased by about ~20% upon mutation. This observation indicates lysine 29 indeed forms electrostatic interactions with nearby residues. Folding kinetics measurements using stopped-flow device and quantitative analysis of kinetics data indicate that ubiquitin folds from unfolded state to native state via intermediate state as observed previously. This intermediate state was observed to form immediately after the initiation of folding reaction. The folding intermediate was shown to be destabilized considerably upon lysine to alanine mutation. These observations indicate that electrostatic interactions can form early stage of protein folding and hence lead the folding reaction.

• BMB Reports
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• v.41 no.1
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• pp.35-40
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• 2008

The molten globular conformation of V26A ubiquitin (valine to alanine mutation at residue 26) was studied by nuclear magnetic resonance spectroscopy in conjunction with amide hydrogen/deuterium exchange. Most of the amide protons that are involved in the native secondary structures were observed to be protected in the molten globule state with the protection factors from 1.2 to 6.7. These protection factors are about 2 to 6 orders of magnitude smaller than those of the native state. These observations indicate that V26A molten globule has native-like backbone structure with marginal stability. The comparison of amide protection factors of V26A ubiquitin molten globule state with those of initial collapsed state of the wild type ubiquitin suggests that V26A ubiquitin molten globule state is located close to unfolded state in the folding reaction coordinate. It is considered that V26A ubiquitin molten globule is useful model to study early events in protein folding reaction.

• Applied Biological Chemistry
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• v.46 no.4
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• pp.305-310
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• 2003

Hydrophobic core variant of ubiquitin appeared to have partially folded structure at pH around 2. The intrinsic tryptophan fluorescence emission maximum of this ubiquitin variant at pH 2 showed slight blue shift compare to that of unfolded state, suggesting that some residual tertiary structures remain in this solvent condition. At the same solvent condition, this ubiquitin variant binds with hydrophobic dye, 8-anilinonaphthalene-1-sulfonic acid(AMS), which is known to bind to exposed hydrophobic surface. Furthermore, far-UV circular dichroic spectrum of this ubiquitin variant in the diminished pH was remarkably different from the far-UV CD spectrum of the native state or unfolded state. Based on the molar ellipticity at 220 nm, this ubiquitin variant at pH 2 appeared to have significant amount of secondary structures. All these observations suggest that this ubiquitin variant in the diminished solvent pH has loosely folded hydrophobic core with some secondary structures, which are key features of molten globule conformation. Since molten globule has long been considered as a protein folding intermediate, it is considered that this hydrophobic core variant ubiquitin will serve as a valuable model to study protein folding process.

• Journal of Microbiology and Biotechnology
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• v.17 no.12
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• pp.2027-2032
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• 2007

[ ${\alpha}$ ]-Synuclein is the major component of Lewy bodies and responsible for the amyloid deposits observed in Parkinson's disease. Ordered filamentous aggregate formation of the natively unfolded ${\alpha}$-synuclein was investigated in vitro with the periodic ultrasonication. The ultrasonication induced the fibrillation of ${\alpha}$-synuclein, as the random structure gradually converted into a ${\beta}$-sheet structure. The resulting fibrils obtained at the stationary phase appeared heterogeneous in their size distribution, with the average length and height of $0.28\;{\mu}m{\pm}0.21\;{\mu}m$ and $5.6\;nm{\pm}1.9\;nm$, respectively. After additional extensive ultrasonication in the absence of monomeric ${\alpha}$-synuclein, the equilibrium between the fibril formation and its breakdown shifted to the disintegration of the preexisting fibrils. The resulting fragments served as nucleation centers for the subsequent seed-dependent accelerated fibrillation under a quiescent incubation condition. This self-seeding amplification process depended on the seed formation and subsequent alterations in their properties by the ultrasonication to a state that accretes the monomeric soluble protein more effectively than their reassociation of the seeds back to the original fibrils. Since many neurodegenerative disorders have been considered to be propagated via the seed-dependent amyloidosis, this study would provide a novel aspect of the significance of the seed structure and its properties leading to the acce]erated amyloid formation.

• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.3
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• pp.192-198
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• 2003

BiP, immunoglobulin binding protein, is an ER homologue of Hsp70. However, unlit other Hsp70 proteins, regulatory protein(s) for BiP has not been identified. Here, we demo strafed the presence of potential regulatory proteins for BiP using a pull -down assay. Since BiP can bind any unfolded protein, only the ATPase domain of BiP was used for the pull -down assay in order to minimize nonspecific binding. The ATPase domain was cloned to produce recombinant protein, which was then conjugated to CNBr-activated agarose. The structural conformation and ATP hydrolysis activity of the recombinant ATPase domain were similar to those of the native protein, light proteins from metabolically labeled mouse plasmacytoma cells specifically bound to the recombinant ATPase protein. The binding of these proteins was inhibited by excess amounts of free ATPase protein, and was dependent on the presence of ATP. These proteins were eluted by ADP. Of these proteins, Grp170 and BiP where identified. while the other were not identified as known ER proteins, from Western blot analyses. The presence of the ATPase-binding proteins for BiP was first demonstrated in this study, and our data suggest similar regulatory machinery for BiP may exist in the ER, as found in prokaryotes and other cellular compartments.

• Journal of the Korean Chemical Society
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• v.55 no.5
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• pp.746-750
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• 2011

Fluorescence correlation spectroscopy (FCS) is an emerging fluorescence technique used to study the dynamics of proteins on a millisecond to microsecond time scale at the single-molecule level. Solution pH-modulated protein conformational changes can be manifested by binding rate, fluorescence lifetime, and binding specificity of a probe molecule. The fluorescence lifetime of Nile red (NR) bound to apomyoglobin (apoMb) was measured to be $6{\pm}0.3$ ns, much longer than that in water solution ($2.9{\pm}0.2$ ns). As the unfolding population of apoMb increased by lowering pH of solution, the fraction for the longer lifetime of NR decreased with an increasing fraction for the shorter lifetime of NR in water. Unlike 1-anilino-8-naphthalene sulfonic acid, which has many lifetimes due to nonspecific binding to the unfolded apoMb, NR bound to apoMb possesses only a single lifetime. These results suggest that NR binds specifically to native apoMb and thus can be utilized to probe the folding/unfolding dynamics of apoMb using FCS.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.85-88
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• 2001

We scaled up a covalent immobilization system of urokinase to the activated Sepharose and used it repeatedly to cleave a fusion protein consisting of human growth hormone and GST fragment. After scale up from 6 ml to 250 ml, the column system still demonstrated basically the same performance in terms of urokinase immobilization and fusion protein cleavage. When the column was washed with 6M guanidine HCl after the cleavage reaction. the immobilized urokinase showed no activity probably because it was fully unfolded. However. as the denaturant was gradually removed from the column the immobilized urokinase fully regained its bioactivity. which indicated it was properly refolded into its native conformation as covalently attached to the solid matrix. After 20 cycles of this 'solid-phase unfolding/refolding', the immobilized urokinase maintained approx. 80% of the initial bioactivity. This method provides an efficient protocol to apply the solid-phase refolding technique to improve the longevity of immobilized enzyme columns.

• BMB Reports
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• v.35 no.2
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• pp.143-154
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• 2002

The structural and functional aspects of ervatamin B were studied in solution. Ervatamin B belongs to the $\alpha+\beta$ class of proteins. The intrinsic fluorescence emission maximum of the enzyme was at 350 nm under neutral conditions, and at 355 nm under denaturing conditions. Between pH 1.0-2.5 the enzyme exists in a partially unfolded state with minimum or no tertiary structure, and no proteolytic activity. At still lower pH, the enzyme regains substantial secondary structure, which is predominantly $\beta$-sheet conformation and shows a strong binding to 8-anilino-1-napthalene-sulfonic acid (ANS). In the presence of salt, the enzyme attains a similar state directly from the native state. Under neutral conditions, the enzyme was stable in urea, while the guanidine hydrochloride (GuHCl) induced equilibrium unfolding was cooperative. The GuHCl induced unfolding transition curves at pH 3.0 and 4.0 were non-coincidental, indicating the presence of intermediates in the unfolding pathway. This was substantiated by strong ANS binding that was observed at low concentrations of GuHCl at both pH 3.0 and 4.0. The urea induced transition curves at pH 3.0 were, however, coincidental, but non-cooperative. This indicates that the different structural units of the enzyme unfold in steps through intermediates. This observation is further supported by two emission maxima in ANS binding assay during urea denaturation. Hence, denaturant induced equilibrium unfolding pathway of ervatamin B, which differs from the acid induced unfolding pathway, is not a simple two-state transition but involves intermediates which probably accumulate at different stages of protein folding and hence adds a new dimension to the unfolding pathway of plant proteases of the papain superfamily.