• Journal of the Korean Magnetic Resonance Society
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• v.9 no.2
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• pp.74-92
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• 2005

The high resolution solution structure of MCP-3 was determined using multinuclear, multidimensional NMR spectroscopy with an expressed and $^{13}C-\;and\;^{15}N-labeled$ protein. The MCP-3 has a typical chemokine fold including 3 anti-parallel $\beta-sheets$, and a C-terminal helix, but it exists as a monomer in solution under the conditions where the structure was determined (2 mM, pH 5.1 at $30^{\circ}C$). Based on the structure and the amino acid sequence compared to other chemokines we propose that Ile20 and Leu25 in MCP-3 play key roles in the formation of N-loop (residues between the $2^{nd}$ cysteine and the I sheet) which has been implicated as a determinant of chemokine specificity. Additional receptor binding surface is supplied by the 40s loop (residues between the 2 and the 3 sheet) and the binding interface of the acidic N-terminal region of chemokine receptor to MCP-3 would resemble the dimerization interface of CC type dimer.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.5
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• pp.414-418
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• 2004

A 'minimally complex problem set' for ab initio protein Structure prediction has been proposed. As well as consisting of non-redundant and crystallographically determined high-resolution protein structures, without disulphide bonds, modified residues, unusual connectivities and heteromolecules, it is more importantly a collection of protein structures. with a high probability of being the same in the crystal form as in solution. To our knowledge, this is the first attempt at this kind of dataset. Considering the lattice constraint in crystals, and the possible flexibility in solution of crystallographically determined protein structures, our dataset is thought to be the safest starting points for an ab initio protein structure prediction study.

• BMB Reports
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• v.42 no.11
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• pp.697-704
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• 2009

Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.

• Journal of the Korean Magnetic Resonance Society
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• v.15 no.1
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• pp.80-89
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• 2011

3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences.

• Applied Microscopy
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• v.47 no.3
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• pp.160-164
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• 2017

Electron crystallography has been used as the one of powerful tool for studying the structure of biological macromolecules at high resolution which is sufficient to provide details of intramolecular and intermolecular interactions at near-atomic level. Previously it commonly uses two-dimensional crystals that are periodic arrangement of biological molecules, however recent studies reported a novel technical approach to electron crystallography of three-dimensional crystals, called micro electron-diffraction (MicroED) which involves placing the irregular and small sized protein crystals in a transmission electron microscope to determine the atomic structure. In here, we review the advances in electron crystallography techniques with several recent studies. Furthermore, we discuss the future direction of this structural approach.

• BMB Reports
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• v.31 no.4
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• pp.307-327
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• 1998

Cytochrome c peroxidase (CcP) is a yeast mitochondrial enzyme which catalyzes the reduction of hydrogen peroxide to water using two equivalents of ferrocytochrome c. The CcP/cytochrome c system has many features which make it a very useful model for detailed investigation of heme protein structure/function relationships including activation of hydrogen peroxide, protein-protein interactions, and long-range electron transfer. Both CcP and cytochrome c are single heme, single subunit proteins of modest size. High-resolution crystallographic structures of both proteins, of one-to-one complexes of the two proteins, and a number of active-site mutants are available. Site-directed mutagenesis studies indicate that the distal histidine in CcP is primarily responsible for rapid utilization of hydrogen peroxide implying significantly different properties of the distal histidine in the peroxidases compared to the globins. CcP and cytochrome c bind to form a dynamic one-to-one complex. The binding is largely electrostatic in nature with a small, unfavorable enthalpy of binding and a large positive entropy change upon complex formation. The cytochrome c-binding site on CcP has been mapped in solution by measuring the binding affinities between cytochrome c and a number of CcP surface mutations. The binding site for cytochrome c in solution is consistent with the crystallographic structure of the one-to-one complex. Evidence for the involvement of a second, low-affinity cytochrome c-binding site on CcP in long-range electron transfer between the two proteins is reviewed.

• Journal of the Korean Magnetic Resonance Society
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• v.3 no.2
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• pp.100-108
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• 1999

Cop protein is the transcription repressor protein in rolling circle replication plasmid. With antisense RNA, Cop protein controls the copy number of plasmid. Cop family proteins have been found in various plasmids. Among Cop family proteins, Cop studied in this paper consists of 55 amino acids (Mw. 6,400), and was known to have trimer structure. Since no structural facts are elucidated, we have carried out preliminary experiments aimed at the elucidation of its three dimensional structure. The secondary structure of Cop is studied by CD and NMR. To solve the aggregation of Cop at high concentration, we tested various detergents and salts. The addition of detergents and salts could not solve the aggregation problem. However, we found that concentration is important in solving the aggregation problem. We knew that 0.18mM in 50mM potassium phosphate without any other ingredients is maximum concentration not to aggregate. Wa also investigated the pH dependence of Cop protein, and knew that Cop protein is more stable in acid state. At various temperatures, 15N-1H HSQC spectra were measured in order to find the optimal experimental condition. To enhance the peak resolution, 3D NOESY-HSQC spectrum is acquired. Since there are NOE peaks in the NH-NH region, we knew that Cop protein has $\alpha$-helical content, which was also confirmed by CD.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.147-161
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• 2012

Human melanocortin-4 receptor (hMC4R) among MC-Rs, expressed in the brain, is in charge of the control on energy homeostasis and food intake. The structure and function of human MC4R have been studied to understand their essential function and roles. To investigate the structure and function, it is necessary to prepare sufficient amounts of proteins. However, their expression and purification is demanding and time-consuming due to their innate insoluble and toxic properties. The heterozygous mutations of hMC4R, exchange of Asp 90 to Asn located in second transmembrane, cause severe obesity in human. To obtain purified hMC4R wt-TM2 for structural studies, it was first over-expressed and purified by fast protein liquid chromatography (FPLC) and then solution NMR studies were performed to get high-resolution spectra. In here, we established optimized purification scheme to get more purified target peptide.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.86-87
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• 2000

Protein folding is a fundamental problem in structural bioinformatics and so numerous studies have been devoted to the subject. As the most common regular secondary conformation in proteins, helix has been an important ingredient of the protein folding problem. In particular, alanine based polypeptides are widely studied to identify the helix folding process in that the aianine amino acid is known to have one of the highest helix propensities. In principle, intrinsic helix propensities can be obtained from gas-phase measurements where solvent effect is absent. Hudgins et al. studied alanine-based peptides in vacuo using high-resolution ion mobility measurement technique. It was reported that introduction of a single Iysine at the C terminus resulted in the formation of very stable, monomeric polyalanine helices. We also have investigated helix formation in vacuo with different terminal charge conditions; we have found a new type of helix motif, To the best of our knowledge, this type of helix conformation has not been characterized before and we name it as I-helix.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.103-110
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• 2012

Membrane proteins play a essential role in the biological systems and it is not easy to handle a membrane protein for its structural study. Solid-state NMR (ssNMR) can be a good tool to investigate the structures and dynamics of membrane proteins. In ssNMR, Magic Angle Spinning (MAS) and Cross Polarization (CP) can be utilized to reduce the line-broadening, leading to high resolution and sensitivity in the spectrum. ssNMR, if combined with other spectroscopic methods, can provide us a enough knowledge on structures and dynamics of membrane proteins in biological condition.