• Molecules and Cells
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• 제24권3호
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• pp.437-440
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• 2007

$OGL-20P^T$-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain $OGL-20P^T$, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of $OGL-20P^T$-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily ${\alpha}$-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.28-31
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• 2000

We describe a hidden Markov model, HMMTIR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear HMMs used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the database, and achieves a great reduction in parameters by representing overlapping motifs in a much more compact form. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.6% and backbone torsion angles better than any previously reported method, and predicts the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction. HMMSTR has been incorporated into a public, fully-automated protein structure prediction server.

• BMB Reports
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• 제44권2호
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• 한국자기공명학회논문지
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• 제17권1호
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• pp.59-66
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• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.

• 인터넷정보학회논문지
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• 제16권2호
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• pp.117-125
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• 2015

단백질 기능을 규명하는 단백질 구조 정보는 단백질 의약품의 약효를 증진시키고, 개발을 단축시키는데 큰 영향을 미친다. 따라서 단백질의 구조를 효과적으로 분석하기 위한 단백질 가시화에 대한 연구가 증가하고 있다. 하지만 단백질 가시화에 대한 연구가 단백질의 구조를 예측하거나 렌더링의 속도를 향상시키는 것을 중심으로 이뤄지고 있으며, 단백질 가시화 형태에 따른 정보 전달 효용성에 대한 연구는 미비한 실정이다. 본 연구는 단백질 의약품에 대한 효율적인 정보 서비스의 사전 연구로써 단백질 1, 2차구조 혼합가시화 형태별 정보표현적합도를 분석하였다. 단백질 1, 2차구조 혼합가시화 형태는 대표적 가시화 서비스인 Chimera, PDB, Cn3D와 기존 가시화 서비스의 문제점을 개선한 단백질 1, 2차구조 혼합가시화 형태를 대상으로 하였다. 정보표현적합도를 구하기 위한 정보요인은 피험자 분석 결과를 바탕으로 단백질 1차구조, 아미노산 위치, 단백질 2차구조, 단백질 2차구조 비율정보로 구분하였으며, 피험자는 단백질 의약품 업계종사기간이 5년 이상인 전문가 집단을 대상으로 하였다. 그 결과 단백질 1, 2차구조 혼합가시화형태별 정보표현적합도에는 유의미한 차이가 있었으며, 가시화 형태별 정보 전달 효용성에 차이가 있음을 입증할 수 있었다.

• 한국식품과학회지
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• 제31권6호
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• pp.1488-1494
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• 1999

감마선 조사가 상업적 등급의 SPI와 WPC의 SDS-PAGE 헝태와 이차구조 함량, 용해도 등 이화학적 변화에 미치는 영향을 조사하였다. 감마선이 조사된 SPI와 WPC의 SDS-PAGE 형태은 SPI 용액의 경우 5 kGy 이상 조사에서 단백질의 degraded pattern과 아울러 중합이 나타난 반면에 WPC 용액에서는 단백질이 절단된 형태로 나타났다. 반면에 감마선이 조사된 SPI와 WPC 분말의 경우 분자량 분포에는 큰 변화가 없었다. Circular dichroism 연구에서 감마선이 조사된 SPI와 WPC용액의 이차구조의 변화는 감마선 조사에 의하여 단백질의 구조 변화를 나타내는 random coil함량이 증가하였다. 또한, SPI와 WPC 분말의 경우에는 감마선 조사에 의한 용해도의 차이가 있었다.

• 한국자기공명학회논문지
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• 제13권2호
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• pp.117-125
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• 2009

HP0062 is an 86 residue hypothetical protein from Helicobacter pylori strain 26695. HP0062 was identified ESAT-6/WXG100 superfamily protein based on structure and sequence alignment and also contains leucine zipper domain sequence. Here, we report the sequence-specific backbone resonance assignment of HP0062. About 97.7% of all $^1H_N,\;^{15}N,\;^{13}C_{\alpha},\;^{13}C_{\beta}\;and\;^{13}C=O$ resonances were assigned unambiguously. We could predict the secondary structure of HP0062 by analyzing the deviation of the $^{13}C_{alpha}\;and\;^{13}C_{\beta}$ chemical shifts from their respective random coil values. Secondary structure prediction shows that HP0062 consist of two ${\alpha}$-helices. This study is a prerequisite for determining the solution structure of HP0062 and can be used for the study on interaction between HP0062 and DNA and other Helicobacter pylori proteins.

• BMB Reports
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• 제33권2호
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• pp.133-137
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• 2000

To elucidate the effect of oxygen radicals on the molecular properties of proteins, the secondary and tertiary structure and molecular weight size of BSA and ${\beta}$-lactoglobulin were examined after irradiation of proteins at various doses. Gamma-irradiation of protein solutions caused the disruption of the ordered structure of protein molecules as well as degradation, cross-linking, and aggregation of the polypeptide chains. As a model system, BSA and ${\beta}$-lactoglobulin were used as a typical ${\alpha}$-helical and a ${\beta}$-sheet structure protein, respectively. A circular dichroism study showed that the increase of radiation decreased the ordered structure of proteins with a concurrent increase of aperiodic structure content. Fluorescence spectroscopy indicated that irradiation quenched the emission intensity excited at 280 nm. SDS-PAGE and a gel permeation chromatography study indicated that radiation caused initial fragmentation of proteins resulting in a subsequent aggregation due to cross-linking of protein molecules.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.250-261
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• 2004

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is introduced. This method utilizes secondary structure prediction information and fragment assembly. The secondary structure prediction of proteins is performed with the PREDICT method which uses PSI-BLAST to generate profiles and a distance measure in the pattern space. In order to predict the tertiary structure of a protein sequence, we assemble fragments in the fragment library constructed as a byproduct of PREDICT. The tertiary structure is obtained by minimizing the potential energy using the conformational space annealing method which enables one to sample diverse low lying minima of the energy function. We apply PROFESY for prediction of some proteins with known structures, which shows good performances. We also participated in CASP5 and applied PROFESY to new fold targets for blind predictions. The results were quite promising, despite the fact that PROFESY was in its early stage of development. In particular, the PROFESY result is the best for the hardest target T0161.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.