• Macromolecular Research
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• v.11 no.1
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• pp.53-61
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• 2003

A molecular-thermodynamic model is developed for the salt-induced protein precipitation. The protein molecules interact through four intermolecular potentials. An equation of state is derived based on the statistical mechanical perturbation theory with the modified Chiew's equation for the fluid phase, Young's equation for the solid phase as the reference system and a perturbation based on the protein-protein effective two body potential. The equation of state provides an expression for the chemical potential of the protein. In a single protein system, the phase separation is represented by fluid-fluid equilibria. The precipitation behaviors are simulated with the partition coefficient at various salt concentrations and degree of pre-aggregation effect for the protein particles. In a binary protein system, we regard the system as a fluid-solid phase equilibrium. At equilibrium, we compute the reduced osmotic pressure-composition diagram in the diverse protein size difference and salt concentrations.

• Journal of Photoscience
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• v.10 no.1
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• pp.81-87
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• 2003

Based on structural information provided by recently reported crystal structures of rhodopsin, we present rationales for the regiospecific protein perturbation on the previously reported $\^$19/F chemical shifts of the vinyl and trifluoromethylrhodopsins and their photoproducts. The crystal structures also suggest that H-bonding is a likely cause for the earlier reported regiospecific photoisomerization of the 10-fluororhodopsins. Photoisomerization was revealed by chemical shift of the photoproducts. Additionally, possible use of 3-bond F,F coupling constants for following photoisomerization of retinal-binding proteins is discussed.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.125-131
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• 2018

Chemical shift perturbation (CSP) is a simple NMR technique for studying binding of a protein to various ligands. CSP is the only technique that can directly provide both a value for the dissociation constant and a binding site from the same set of measurements. To accurately analyze the CSP data, the exact binding mode such as multiple binding, should be carefully considered. In this review, we analyzed systematically the CSP data with multiple modes. This analysis might provide insight into the mechanism on how proteins selectively recognize their target ligands to achieve the biological function.

• Molecules and Cells
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• v.37 no.9
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• pp.672-684
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• 2014

The exact causes of cell death in Parkinson's disease (PD) remain unknown despite extensive studies on PD.The identification of signaling and metabolic pathways involved in PD might provide insight into the molecular mechanisms underlying PD. The neurotoxin 1-methyl-4-phenylpyridinium ($MPP^+$) induces cellular changes characteristic of PD, and $MPP^+$-based models have been extensively used for PD studies. In this study, pathways that were significantly perturbed in $MPP^+$-treated human neuroblastoma SH-EP cells were identified from genome-wide gene expression data for five time points (1.5, 3, 9, 12, and 24 h) after treatment. The mitogen-activated protein kinase (MAPK) signaling pathway and endoplasmic reticulum (ER) protein processing pathway showed significant perturbation at all time points. Perturbation of each of these pathways resulted in the common outcome of upregulation of DNA-damage-inducible transcript 3 (DDIT3). Genes involved in ER protein processing pathway included ubiquitin ligase complex genes and ER-associated degradation (ERAD)-related genes. Additionally, overexpression of DDIT3 might induce oxidative stress via glutathione depletion as a result of overexpression of CHAC1. This study suggests that upregulation of DDIT3 caused by perturbation of the MAPK signaling pathway and ER protein processing pathway might play a key role in $MPP^+$-induced neuronal cell death. Moreover, the toxicity signal of $MPP^+$ resulting from mitochondrial dysfunction through inhibition of complex I of the electron transport chain might feed back to the mitochondria via ER stress. This positive feedback could contribute to amplification of the death signal induced by $MPP^+$.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.265-271
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• 2004

The interaction network of protein -protein plays an important role to understand the various biological functions of cells. Currently, the high -throughput experimental techniques (two -dimensional gel electrophoresis, mass spectroscopy, yeast two -hybrid assay) provide us with the vast amount of data for protein-protein interaction at the proteome scale. In order to recognize the role of each protein in their network, the efficient bioinformatical and computational analysis methods are required. We propose a systematic and mathematical method which can analyze the protein -protein interaction network rigorously and enable us to capture the biological and physical essence of a topological character and stability of protein -protein network, and sensitivity of each protein along the biological pathway of their network. We set up a Laplacian matrix of spectral graph theory based on the protein-protein network of yeast proteome, and perform an eigenvalue analysis and apply a perturbation method on a Laplacian matrix, which result in recognizing the center of protein cluster, the identity of hub proteins around it and their relative sensitivities. Identifying the topology of protein -protein network via a Laplacian matrix, we can recognize the important relation between the biological pathway of yeast proteome and the formalism of master equation. The results of our systematic and mathematical analysis agree well with the experimental findings of yeast proteome. The biological function and meaning of each protein cluster can be explained easily. Our rigorous analysis method is robust for understanding various kinds of networks whether they are biological, social, economical...etc

• Bulletin of the Korean Chemical Society
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• v.28 no.10
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• pp.1756-1762
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• 2007

Envelope proteins of virus contain a segment of hydrophobic amino acids, called as fusion peptide, which triggers membrane fusion by insertion into membrane and perturbation of lipid bilayer structure. Potential fusion peptide sequences have been identified in the middle of L or M proteins or at the N-terminus of S protein in the envelope of human hepatitis B virus (HBV). Two 16-mer peptides representing the N-terminal fusion peptide of the S protein and the internal fusion peptide in L protein were synthesized, and their membrane disrupting activities were characterized. The internal fusion peptide in L protein showed higher activity of liposome leakage and hemolysis of human red blood cells than the N-terminal fusion peptide of S protein. Also, the membrane disrupting activity of the extracellular domain of L protein significantly increased when the internal fusion peptide region was exposed to N-terminus by the treatment of V8 protease. These results indicate that the internal fusion peptide region of L protein could activate membrane fusion when it is exposed by proteolysis.

• Macromolecular Research
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• v.11 no.4
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• pp.241-249
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• 2003

A molecular-thermodynamic model to describe the salt-induced protein precipitation is developed based on the perturbation theory. We employed the modified perturbed hard-sphere-chain (PHSC) equation of state for copolymer mixtures to take into account the pre-aggregation effect among protein particles. Hypothetical pressure-composition diagrams are computed with various size differences and salt concentrations. The precipitation behaviors are also studied for various types of pre-aggregation effect for the given systems.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.149-155
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• 2015

Acyl carrier protein is related with fatty acid biosynthesis in which specific enzymes are involved. Especially, acyl carrier protein (ACP) is the key component in the growing of fatty acid chain. ACP is the small, very acidic protein that covalently binds various intermediates of fatty acyl chain. Acylation of ACP is mediated by holo-acyl carrier protein synthase (ACPS), which transfers the 4'PP-moiety of CoA to the 36th residue Ser of apo ACP. Acyl carrier protein P (ACPP) is one of ACPs from Helicobacter plyori. The NMR structure of ACPP consists of four helices, which were reported previously. Here we show how acylation of ACPP can affect the overall structure of ACPP and figured out the contact surface of ACPP to acyl chain attached during expression of ACPP in E. coli. Based on the chemical shift perturbation data, the acylation of ACCP seems to affect the conformation of the long loop connecting helix I and helix II as well as the second short loop connecting helix II and helix III. The significant chemical shift change of Ile 54 upon acylation supports the contact of acyl chain and the second loop.

• Mass Spectrometry Letters
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• v.13 no.4
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• pp.115-124
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• 2022

Emerging evidence has shown that RNA-binding proteins (RBPs) dynamically regulate all aspects of RNA in cells and involve in major biological processes of RNA, including splicing, modification, transport, transcription and degradation. RBPs, as powerful and versatile regulatory molecule, are essential to maintain cellular homeostasis. Perturbation of RNA-protein interactions and aberration of RBPs function is associated with diverse diseases, such as cancer, autoimmune disease, and neurological disorders. Therefore, it is crucial to systematically investigate the RNA-binding proteome for understanding interactions of RNA with proteins. Thanks to the development of the mass spectrometry, a variety of proteome-wide methods have been explored to define comprehensively RNA-protein interactions in recent years and thereby contributed to speeding up the study of RNA biology. In this review, we systematically described these methods and summarized the advantages and disadvantages of each method.

• Journal of the Korean Chemical Society
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• v.47 no.5
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• pp.447-459
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• 2003

Generalized 2D correlation spectroscopy has been applied extensively to the analysis of spectral data sets obtained during the observation of a system under some external perturbation. It is used in various fields of spectroscopy including IR, Raman, UV, fluorescence, X-ray diffraction, and X-ray absorption spectroscopy (XAS) as well as chromatography. 2D hetero-spectral correlation analysis compares two completely different types of spectra obtained for a system under the same perturbation. Because of the wide range of applications of this technique, it has become one of the standard analytical techniques for the analytical chemistry, physical chemistry, biochemistry, and so on, and for studies of polymers, biomolecules, nanomaterials, etc. In this paper, we will introduce the principle of generalized 2D correlation spectroscopy and its applications that we have studied.