• Genomics & Informatics
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• v.9 no.2
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• pp.74-78
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• 2011

Numerous restraints and simplifications have been developed for methods that anticipate protein structure to reduce the colossal magnitude of possible conformational states. In this study, we investigated if globularity is a general characteristic of proteins and whether they can be applied as a valid constraint in protein structure simulations with approximated measurements (Gb-index). Unexpectedly, most of the proteins showed strong structural globularity (i.e., mode of approximately 76% similarity to the perfect globe) with only a few percent of proteins being outliers. Small proteins tended to be significantly non-globular ($R^2$=0.79) and the minimum Gb-index showed a logarithmic increase with the increase in protein size ($R^2$=0.62), strongly implying that the non-globular characteristics might be more acceptable for smaller proteins than larger ones. The strong perfect globe-like character and the relationship between small size and the loss of globular structure of a protein may imply that living organisms have mechanisms to aid folding into the globular structure to reduce irreversible aggregation. This also implies the possible mechanisms of diseases caused by protein aggregation, including some forms of trinucleotide repeat expansion-mediated diseases.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.21-21
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• 2011

A series of Quasi-Elastic Neutron Scattering (QENS) experiments helps us to understand the single-particle (hydrogen atom) dynamics of a globular protein and its hydration water and strong coupling between them. We also performed Molecular Dynamics (MD) simulations on a realistic model of the hydrated hen-egg Lysozyme powder having two proteins in the periodic box. We found the existence of a Fragile-to-Strong dynamic Crossover (FSC) phenomenon in hydration water around a protein occurring at TL=$225{\pm}5K$ by analyzing Intermediate Scattering Function (ISF). On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the High Density Liquid (HDL) form, a more fluid state, to predominantly the Low Density Liquid (LDL) form, a less fluid state, derived from the existence of a liquid?liquid critical point at an elevated pressure. We showed experimentally and confirmed theoretically that this sudden switch in the mobility of the hydration water around a protein triggers the dynamic transition (so-called glass transition) of the protein, at a temperature TD=220 K. Mean Square Displacement (MSD) is the important factor to show that the FSC is the key to the strong coupling between a protein and its hydration water by suggesting TL${\fallingdotseq}$TD. MD simulations with TIP4P force field for water were performed to understand hydration level dependency of the FSC temperature. We added water molecules to increase hydration level of the protein hydration water, from 0.30, 0.45, 0.60 and 1.00 (1.00 is the bulk water). These confirm the existence of the FSC and the hydration level dependence of the FSC temperature: FSC temperature is decreased upon increasing hydration level. We compared the hydration water around Lysozyme, B-DNA and RNA. Similarity among those suggests that the FSC and this coupling be universal for globular proteins, biopolymers.

• BMB Reports
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• v.30 no.5
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• pp.346-351
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• 1997

The maximum adsorption/desorption conditions and the adsorption mechanism of globular proteins to vaccine adjuvants were determined. The maximum adsorption ratio of protein to the $Al^{3+}$ content of aluminum oxyhydroxide and the optimal adsorption pH are 2:1 (${\mu}g:{\mu}g$) for bovine serum albumin (BSA) at pH 6.0 and 2.5:1 (${\mu}g:{\mu}g$) for immunoglobulin G (IgG) at pH 7.0, respectively. The maximum adsorption ratio onto aluminum phosphate gel was 1.5:1 (${\mu}g$ Protein:${\mu}g$ $Al^{3+}$) at pH 5.0 for both BSA and IgG. Adsorption of the native globular proteins, BSA and IgG, to aluminum oxyhydroxide and aluminum phosphate gel was reversible as a function of pH. Complete desorption of these proteins from aluminum phosphate gel was observed at alkaline pH, whereas only 80~90% removal from aluminum oxyhydroxide was achieved with alkaline pH and 50 mM phosphate buffer. We conclude that electrostatic and hydrogen bonding interactions between the native proteins and adjuvants are important binding mechanisms for adsorption, and that the surface charge of the protein and the colloid components control the maximum adsorption conditions.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.1
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• pp.26-30
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• 2017

Dynamic properties of proteins can present key information on protein-ligand and protein-protein interaction. Despite their usefulness, the properties of protein dynamics have not been obtained easily due to protein stability and short-term measurement. Here, it is shown that combined method for analysis of dynamical properties. It utilizes predicted order parameter and NMR relaxation data such as $T_1$, $T_2$, and heteronuclear NOE. The suggested method could be used to know the flexibility of protein roughly without precise dynamical parameters such as order parameters through model-free analysis.

• Proceedings of the Korean Biophysical Society Conference
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• 2002.06b
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• pp.30-30
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• 2002

The native forms of common globular proteins are in their most stable state but the native forms of plasma serpins (serine protease inhibitors) show high-energy state interactions. The high-energy state strain of a ${\alpha}$$_1$-antitrypsin, a prototype serpin, is distributed throughout the whole molecule, but the strain that regulates the function directly appears to be localized in the region where the reactive site loop is inserted during complex formation with a target protease.(omitted)

• Biomolecules & Therapeutics
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• v.22 no.5
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• pp.384-389
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• 2014

Adiponectin, an adipokine predominantly secreted from adipose tissue, exhibits diverse biological responses, including metabolism of glucose and lipid, and apoptosis in cancer cells. Recently, adiponectin has been shown to modulate autophagy as well. While emerging evidence has demonstrated that autophagy plays a role in the modulation of proliferation and apoptosis of cancer cells, the role of autophagy in apoptosis of cancer cell caused by adiponectin has not been explored. In the present study, we demonstrated that globular adiponectin (gAcrp) induces both apoptosis and autophagy in human hepatoma cell line (HepG2 cells) and breast cancer cells (MCF-7), as evidenced by increase in caspase-3 activity, Bax, microtubule-associated protein light chain 3-II (LC3 II) protein levels, and autophagosome formation. Interestingly, gene silencing of LC3B, an autophagy marker, significantly enhanced gAcrp-induced apoptosis in both HepG2 and MCF-7 cell lines, whereas induction of autophagy by rapamycin, an mTOR inhibitor, significantly prevented gAcrp-induced apoptosis in hepatoma cells HepG2. Furthermore, modulation of autophagy produced similar effects on gAcrp-induced Bax expression in HepG2 cells. These results implicate that induction of autophagy plays a regulatory role in adiponectin-induced apoptosis of cancer cells, and thus inhibition of autophagy would be a novel promising target to enhance the efficiency of cancer cell apoptosis by adiponectin.

• Applied Biological Chemistry
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• v.39 no.5
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• pp.379-383
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• 1996

The ultrastructure of the compound starch granules and the protein bodies of Odaebyeo rice of early matured variety were examined by light microscope and electron microscope. The endosperm cell appealed rectangular or octangular shape on the cross section. The thickness of cell wall containing of membraneous materials was about $0.5\;{\mu}m$ in diameter. The starch cell was filled compactly with globular or oval shaped compound starch granules with the size of $20{\sim}25\;{\mu}m$ in diameter. The compound starch granules were consisted of central core starch granule and concentrical $2{\sim}3$ layers of starch granules. The average thickness of the starch granules were about $5\;{\mu}m$. Most protein bodies were found in the aleurone layer The globular protin bodies were scattered near the compound starch granules and $2.5{\sim}3\;{\mu}m$ in diameter. The protein bodies composed of central electron dense materials and peripheral electron loose materials in limiting membrane.

• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.21-21
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• 2001

PDZ domains are molecular-recognition elements that mediate protein-protein interactions. The PDZ domain was discovered originally as a common motif present in three structurally related proteins： PSD-95 (postsynaptic density protein), Dlg (discs-large protein) and ZQ-1 (zonula occludens-1). The PDZ domain is globular domain, containing about 80-100 amino acids, and a conserved motif with two alpha helices and six beta strands. Most of them bind selectively to the C-termini of the interacting proteins at the complexes of signaling molecules and membrane associated receptors.(omitted)

• Applied Microscopy
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• v.25 no.1
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• pp.15-29
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• 1995

Legumin was purified from the endosperm cells of the ginseng seed and analyzed its characteristics. Distributional patterns of the legumin in the endosperm cells were identified using the immunocytochemical method. Legumin was glycoprotein composed of two subunits, molecular weights about 33,000 and 25,000 respectively. The molecular shape of purified legumin stained negatively seems to have hexagonal structure about 10 nm in size. It was localized at the rER, dictyosomes, and in the vacuoles at the early developing stage. Legumin was glycosylated in the dictyosomes and transported from the dictyosomes to the vacuoles. Legumin was accumulated into the central vacuole via the dictyosomes while the endosperm cells were developing. The armorphous proteins containing legumin were scattered randomly within the central vacuoles, which were aggregated together and became gradually spherical shape. Legumin was distributed within the globular protein bodies in the endosperm cells of matured seed. However legumin was not found in the globoids located in the protein bodies.

• BMB Reports
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• v.42 no.7
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• pp.411-417
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• 2009

Transcriptional activation domain (TAD) in virion protein 16 (VP16) of herpes simplex virus does not have any globular structure, yet exhibits a potent transcriptional activity. In order to probe the structural basis for the transcriptional activity of VP16 TAD, we have used NMR spectroscopy to investigate its detailed structural features. Results show that an unbound VP16 TAD is not merely "unstructured" but contains four short motifs (residues 424-433, 442-446, 465-467 and 472-479) with transient structural order. Pre-structured motifs in other intrinsically unfolded proteins (IUPs) were shown to be critically involved in target protein binding. The 472-479 motif was previously shown to bind to $hTAF_{II}31$, whereas the $hTAF_{II}31$-binding ability of other motifs found in this study has not been addressed. The VP16 TAD represents another IUP whose pre-structured motifs mediate promiscuous binding to various target proteins.