• Bulletin of the Korean Chemical Society
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• v.5 no.1
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• pp.27-32
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• 1984

To investigate the hydration effects on the conformational changes of N-pivaloly-L-prolyl-N-methyl-N'-isopropyl-L-alanin amide (PPMIA), the conformational free energy changes have been calculated by using an empirical potential function varying all the independent degrees of freedom of PPMIA backbones. It is found that cis conformers are folded by a strong intramolecular hydrogen bond involving both terminal CO and NH groups whereas trans conformers accommodate the open conformation. Conformers in the free state are proved to be less stable than in the hydrated state. The free energy changes of cis and trans PPMIA due to the hydration are -50.5 and -39.8 kcal/mole, their conformational energy changes are -52.3 and -41.0 kcal/mole, and their conformational entropy changes are -5.9 and -4.0 e.u., respectively. The free energy changes of cis PPMIA to trans PPMIA in the free and hydrated states are 5.3 and 16.0 kcal/mole, their conformational energy changes are 7.6 and 18.8 kcal/mole, and the entropy changes due to the conformational transitions correspond to 7.5 and 9.4 e.u., respectively. From these results, it is found that the bound water molecules play an important role in stabilizing the conformation of PPMIA.

• Journal of Photoscience
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• v.7 no.3
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• pp.79-86
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• 2000

Phytochromes are red and far-red light absorbing photoreceptors for photomorphogenesis in plants. The red/far wavelength reversible biliproteins are made up of two structural domains. The light-perceiving function of the photoreceptor resides in the N-terminal domain, whereas the signal transducing regulatory function is located within the C-terminal domain. The characteristic role of the phytochromes as phtosensory molecular switches is derived from the phototransformation between two distinct spectral forms, the red light absorbing Pr and the far-red light absorbing Pfr forms. The photoinduced Pr Pfr phototransformation accompanies subtle conformational changes throughout the phytochrome molecule. The conformational signals are subsequently transmitted to the C-terminal domain through various inter-domain crosstalks and induce the interaction of the activated C-terminal domain with phytochrome interacting factors. Thus the inter-domain crosstalks play critical roles in the photoactivation of the phytochromes. Posttranslational modifications, such as the phosphorylation of Ser-598, are also involved in this process through conformational changes and by modulating inter-domain signaling.

• BMB Reports
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• v.36 no.4
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• pp.359-366
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• 2003

The effects of zinc on arginine kinase and its collapsed-state intermediate were studied. Both arginine kinase and the collapsed-state intermediate were inactivated in the presence of zinc, following a biphasic kinetic course. The corresponding apparent rate constants of inactivation at different zinc concentrations and conformational changes in the presence of 0.5 mM zinc were obtained. The conformational changes of arginine kinase and the collapsed-state intermediate were followed by fluorescence spectra and circular dichroism spectra. Comparison of the results for arginine kinase and the collapsed-state intermediate showed that the collapsed-state intermediate was more susceptible to zinc, which indicated that the collapsed-state intermediate was more flexible and unstable than arginine kinase. The special structure of arginine kinase might explain these diverse phenomena.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.151-156
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• 2005

The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteins -myoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D$_2$O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.

• BMB Reports
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• v.51 no.12
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• pp.623-629
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• 2018

For mechanical force to induce changes in cellular behaviors, two main processes are inevitable; perception of the force and response to it. Perception of mechanical force by cells, or mechanosensing, requires mechanical force-induced conformational changes in mechanosensors. For this, at least one end of the mechanosensors should be anchored to relatively fixed structures, such as extracellular matrices or the cytoskeletons, while the other end should be pulled along the direction of the mechanical force. Alternatively, mechanosensors may be positioned in lipid bilayers, so that conformational changes in the embedded sensors can be induced by mechanical force-driven tension in the lipid bilayer. Responses to mechanical force by cells, or mechanotransduction, require translation of such mechanical force-induced conformational changes into biochemical signaling. For this, protein-protein interactions or enzymatic activities of mechanosensors should be modulated in response to force-induced structural changes. In the last decade, several molecules that met the required criteria of mechanosensors have been identified and proven to directly sense mechanical force. The present review introduces examples of such mechanosensors and summarizes their mechanisms of action.

• BMB Reports
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• v.39 no.5
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• pp.530-536
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• 2006

Thermal conformational changes of human serum albumin (HSA) in phosphate buffer, 10 mM at pH = 7 are investigated using differential scanning calorimetric (DSC), circular dichroism (CD) and UV spectroscopic methods. The results indicate that temperature increment from $25^{\circ}C$ to $55^{\circ}C$ induces reversible conformational changes in the structure of HSA. Conformational change of HSA are shown to be a three-step process. Interestingly, melting temperature of the last domain is equal to the maximum value of fever in pathological conditions, i.e. $42^{\circ}C$. These conformational alterations are accompanied by a mild alteration of secondary structures. Study of HSA-SDS (sodium dodecyl sulphate) interaction at $45^{\circ}C$ and $35^{\circ}C$ reveals that SDS affects the HSA structure at least in three steps: the first two steps result in more stabilization and compactness of HSA structure, while the last one induces the unfolding of HSA. Since HSA has a more affinity for SDS at $45^{\circ}C$ compared to $35^{\circ}C$, It is suggested that the net negative charge of HSA is decreased in fever, which results in the decrease of HSA-associated cations and plasma osmolarity, and consequently, heat removal via the increase in urine volume.

• BMB Reports
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• v.28 no.6
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• pp.546-551
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• 1995

The conformation studies of myelin P2 protein and two of its major peptides were carried out using circular dichroism and fluorescence spectroscopy in water and in lipid environments. Significant conformational changes occur when the protein or peptides were bound to gangliosides. Similar effects were also found in trifluoroethanol solutions. The conformational features of P2 protein and its major peptides were discussed in relation to the environmental changes and the disease-inducing effects.

• BMB Reports
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• v.42 no.3
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• pp.166-171
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• 2009

Hsp70s assist in the process of protein folding through nucleotide-controlled cycles of substrate binding and release by alternating from an ATP-bound state in which the affinity for substrate is low to an ADP-bound state in which the affinity for substrate is high. It has been long recognized that the two-domain structure of Hsp70 is critical for these regulated interactions. Therefore, it is important to obtain information about conformational changes in the relative positions of Hsp70 domains caused by nucleotide binding. In this study, analytical ultracentrifugation and dynamic light scattering were used to evaluate the effect of ADP and ATP binding on the conformation of the human stress-induced Hsp70.1 protein. The results of these experiments showed that ATP had a larger effect on the conformation of Hsp70 than ADP. In agreement with previous biochemical experiments, our results suggest that conformational changes caused by nucleotide binding are a consequence of the movement in position of both nucleotide- and substrate-binding domains.

• Mass Spectrometry Letters
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• v.10 no.4
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• pp.117-122
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• 2019

This study demonstrated the sensitivity of electron capture dissociation mass spectrometry (ECD-MS) to probe subtle conformational changes in gaseous melittin ions induced by the substitution of an amino acid. ECD-MS was performed for triply and quadruply-protonated melittin and its variants obtained by a single amino acid substitution, namely, D-Pro14, Pro14Ala, and Leu13Ala. Although native triply-protonted melittin showed only a few peptide backbone cleavage products, the D-Pro14 and Pro14Ala variants exhibited extensive backbone fragments, suggesting the occurrence of a significant structural or conformational change induced by a single amino acid substitution at Pro14. On the contrary, the substitution at Leu13, namely Leu13Ala (+3), did not cause significant changes in the ECD backbone fragmentation pattern. Thus, the sensitivity of ECD-MS is demonstrated to be good enough to probe the aforementioned conformational change in melittin.

• Bulletin of the Korean Chemical Society
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• v.8 no.1
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• pp.39-45
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• 1987

Daunomycin, an anthracycline antibiotic, has been found to inhibit virus multiplication and shows considerable activity against tumors. Its activity may be varied by conformational changes of daunomycin. The conformational changes are come from the pucker of D-ring and variation of environments. We have carried out conformational analyses by using empirical potential function. We found that when daunomycin is hydrated or bound to $Mg^{2+}$ ion, the minimum conformer of each state is altered from ${\alpha}$ conformer to ${\beta}$ conformer through the pathway having four local minima. Our calculated results are in good agreements with those of X-ray crystallography and biological experiments, in which metal ion inhibits the binding of daunomycin to DNA.