• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.17-20
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• 2022

High-pressure (HP) NMR is a versatile tool to investigate diverse features of proteins. This technique has been particularly powerful to elucidate structural dynamics that only populates sufficiently in a pressurized condition. Amyloidogenic proteins, which are prone to aggregate and form amyloid fibrils, often maintains highly dynamic states in its native or aggregation-prone states, and HP NMR contributed much to advance our understandings of the dynamic behaviors of amyloidogenic proteins and the molecular mechanisms of their aggregation. In this mini review, we therefore summarize recent HP NMR studies on amyloid-beta (Aβ), the representative amyloidogenic intrinsically disordered protein (IDP).

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.58-62
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• 2014

Human transmembrane proteins (hTMPs) are closely related to transport, channel formation, signaling, cell to cell interaction, so they are the crucial target of modern medicinal drugs. In order to study the structure and function of these hTMPs, it is important to prepare reasonable amounts of proteins. However, their preparation is seriously difficult and time-consuming due to insufficient yields and low solubility of hTMPs. We tried to produce large amounts of Syndecan-4 transmembrane domain (Syd4-TM) that is related to the healing wounds and tumor for a long time. In this study, we performed the structure determination of Syd4-TM combining the Polarity Index at Slanted Angle (PISA) wheel pattern analysis based on $^{15}N-^1H$ 2D SAMPI-4 solid-state NMR of expressed Syd4-TM and Molecular Dynamics (MD) simulation using Discovery Studio 3.1.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

• BMB Reports
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• v.52 no.5
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• pp.304-311
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• 2019

The cytoplasmic FMR1-interacting protein family (CYFIP1 and CYFIP2) are evolutionarily conserved proteins originally identified as binding partners of the fragile X mental retardation protein (FMRP), a messenger RNA (mRNA)-binding protein whose loss causes the fragile X syndrome. Moreover, CYFIP is a key component of the heteropentameric WAVE regulatory complex (WRC), a critical regulator of neuronal actin dynamics. Therefore, CYFIP may play key roles in regulating both mRNA translation and actin polymerization, which are critically involved in proper neuronal development and function. Nevertheless, compared to CYFIP1, neuronal function and dysfunction of CYFIP2 remain largely unknown, possibly due to the relatively less well established association between CYFIP2 and brain disorders. Despite high amino acid sequence homology between CYFIP1 and CYFIP2, several in vitro and animal model studies have suggested that CYFIP2 has some unique neuronal functions distinct from those of CYFIP1. Furthermore, recent whole-exome sequencing studies identified de novo hot spot variants of CYFIP2 in patients with early infantile epileptic encephalopathy (EIEE), clearly implicating CYFIP2 dysfunction in neurological disorders. In this review, we highlight these recent investigations into the neuronal function and dysfunction of CYFIP2, and also discuss several key questions remaining about this intriguing neuronal protein.

• Proceedings of the Korean Society of Potoscience Conference
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• 2005.06a
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• pp.24-24
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• 2005

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.785-791
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• 2003

We have studied the folding mechanism of β-hairpins from proteins of 1GB1, 3AIT and 1A2P by unfolding simulations at high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the three β-hairpin structures follow different mechanism of folding. The results of unfolding simulations showed that the positions of the hydrophobic core residues influence the folding dynamics. We discussed the characteristics of different mechanisms of β-hairpin folding based on the hydrogen-bond-centric and the hydrophobic-centric models.

• Korean System Dynamics Review
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• v.11 no.3
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• pp.5-31
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• 2010

The purpose of this study is to develop a system dynamics model for growth prediction of low birth weight infants(LBWIs) based on nutrition. This growth prediction model consists of 9 modules; body weight, height, carbohydrate, protein, lipid, micronutrient, water, activity and energy module. The results of the model simulation match well with the percentiles of weights and heights of the Korean infants, also with the growth records of 55 LBWIs, under 37 weeks of gestational age, whose weights are appropriate for their gestational age. This model can be used to understand the current growth mode of LBWIs, predict the future growth of LBWIs, and be utilized as a tool for controlling the nutrient intake for the optimal growth of LBWIs in actual practice.

• Korean System Dynamics Review
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• v.6 no.1
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• pp.177-192
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• 2005

A system dynamics model is developed to investigate policies for the school-age child weights and heights. The model is based upon the system dynamic model of Soonhee lee(2003), the purpose of which was policy analysis for obese control of adult people. Although the purpose and target people are different, the main structure can be applied to in the same way. Besides the carbohydrate, protein, and fat material, the new model covers hormone and heights with new input mechanisms for foods and activities. The simulation results matches well with the average school-age children in Korea with the average inputs data (foods and activities). The model can be used for various purposes such as policy analyses, care plan for obese children, etc.

• Genomics & Informatics
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• v.19 no.4
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• pp.48.1-48.10
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• 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 ㎲ (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.

• International Journal of Industrial Entomology and Biomaterials
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• v.45 no.2
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• pp.56-69
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• 2022

Silk is a unique natural biopolymer with outstanding biocompatibility, high mechanical strength, and superior optical transparency. Due to its excellent properties, silk has been widely reported as an ideal biomaterial for several biomedical applications. Recently, fluorescent silk protein, a variant of native silk, has been reported as a biophotonic material with the potential for bioimaging and biosensing. Despite the realization of fluorescent silk, the traditional degumming process of fluorescence silk is crude and often results in fluorescence loss. The loss of fluorescent properties is attributed to the sensitivity of silk fibroin to temperature and solvent concentration during degumming. However, there is no comprehensive information on the influence of these processing parameters on fluorescence evolution and decay during fluorescent silk processing. Therefore, we conducted a spectroscopic study on fluorescence decay as a function of temperature, concentration, and duration for fluorescent silk cocoon degumming. Sodium carbonate solution was tested for degumming the fluorescent silk cocoons with different concentrations and temperatures; also, sodium carbonate solution is combined with Alcalase enzyme and triton x-100 to find optimal degumming conditions. Additionally, we conducted a molecular dynamics study to investigate the fundamental effect of temperature on the stability of the fluorescent protein. We observed degumming temperature as the prime source of fluorescent intensity reduction. From the MD study, fluorescence degradation originated from the thermal agitation of fluorescent protein Cα atoms and fluctuations of amino acid residues located in the chromophore region. Overall, degumming fluorescent silk with sodium carbonate and Alcalase enzyme solution at 25 ℃ preserved fluorescence.