• Genomics & Informatics
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• 제9권2호
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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.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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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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• 제30권5호
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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.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.457-464
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• 2023

Proteolytic enzymes produced by filamentous fungi can degrade various fibrous and globular proteins along with other metabolites that may also find application in biotechnology. In this study, the effect of proteolytic enzymes of 22 Aspergillus strains on various proteins was investigated using protein-containing diagnostic media. Subsequently, a new parameter estimating secreted proteinases specificity towards fibrous or globular proteins without its advanced biochemical research - index of severity of proteolytic action (ISPA) - was suggested. This index determines mycozymes specificity in following manner: its value increases with greater affinity to fibrous proteins, decreases if there is higher affinity to globular proteins. ISPA value was the lowest (0.52) for Aspergillus domesticus, indicating the highest specificity to globular proteins, the highest one (1.26) for A. glaucus, whose proteinases best hydrolyzed fibrous proteins. However, the highest overall proteolytic potential was observed for Aspergillus melleus. The ability to produce acid, alkali and extracellular pigments was evaluated for all isolated strains as well.

• 한국자기공명학회논문지
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• 제21권1호
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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.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2002년도 제9회 학술 발표회 프로그램과 논문초록
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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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• 제22권5호
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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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• 제39권5호
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• pp.379-383
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• 1996

조생종 쌀인 오대벼 품종을 대상으로 종자의 배유세포에 있는 전분복합체와 단백질체의 외부형태 및 미세 구조의 특징을 광학현미경과 전자현미경으로 관찰하였다. 배유세포는 긴 막대모양으로 세로 단면이 장방형 또는 마름모형을 하고 있고, 세포벽은 $0.5\;{\mu}m$의 두께로 균질한 막상 구조물로 이루어져 있다. 또한, 세포내에는 구형 또는 타원형의 전분복합체가 치밀하게 채워져 있으며, 직경이 $18{\sim}25\;{\mu}m$로 다양한 크기로 존재하였다. 전분복합체는 12면체 또는 14면체의 중앙 전분과립을 중심으로 약 $5\;{\mu}m$ 크기의 전분과립들이 동심원상으로 2 내지 3층으로 형성되어 있다. 배유세포에서 단백질체는 호분층에서 보다 아주 드물게 관찰되었지만, 전분복합체의 주변에 인립하여 산재하고 있다. 단백질체는 직경이 약 $3\;{\mu}m$로 구형 또는 난원형의 형태를 하고 있으며 미세구조적으로 중심부는 전자밀도가 높게, 한계막의 주변부는 비교적 전자밀도가 낮게 관찰되었다.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2001년도 학술 발표회 진행표 및 논문초록
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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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• 제25권1호
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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.