• 한국정보통신학회논문지
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• 제22권1호
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• pp.26-32
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• 2018

단백질의 이차구조는 단백질의 진화, 구조, 기능을 연구하는데 중요한 정보이다. 단백질 서열 정보만을 이용하여 단백질의 이차 구조를 예측하는 분야에 심층 학습 방법들이 최근 들어 활발히 적용되고 있다. 이러한 방법에서 널리 사용되는 입력은 단백질 서열을 변환하여 만들어진 단백질 프로파일이다. 본 논문에서는 효과적인 단백질 프로파일을 얻기 위하여 단백질 서열 탐색 방법으로 PSI-BLAST와 더불어서 HHblits를 사용하였다. 단백질 프로파일의 구성에 사용되는 상동 단백질 서열을 결정하기 위한 유사도 문턱치와 상동 단백질 서열 정보를 반복적으로 사용하는 회수를 조절하였다. 합성곱 신경망과 순환 신경망을 사용하여 단백질 이차구조를 예측하였는데, 진화적 정보를 한번만 추가하여 만들어진 단백질 프로파일이 효과적이었다.

• 대한기계학회논문집A
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• 제30권7호
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• pp.841-848
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• 2006

Many researchers are developing computational prediction methods for protein tertiary structures to get much more information of protein. These methods are very attractive on the aspects of breaking technologies of computer hardware and simulation software. One of the computational methods for the prediction is a fragment assembly method which shows good ab initio predictions at several cases. There are many barriers, however, in conventional fragment assembly methods. Argues on protein energy functions and global optimization to predict the structures are in progress fer example. In this study, a new prediction method for protein structures is proposed. The proposed method mainly consists of two parts. The first one is a fragment assembly which uses very shot fragments of representative proteins and produces a prototype of a given sequence query of amino acids. The second one is a global optimization which folds the prototype and makes the only protein structure. The goodness of the proposed method is shown through numerical experiments.

• 한국정보통신학회논문지
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• 제19권12호
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• pp.3011-3016
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• 2015

단백질의 삼차원 구조를 단백질의 국부적 구조인 단백질 조각의 일차원적 나열로 표현하면, 단백질 구조의 분석, 모델링, 탐색, 예측 등에 효과적으로 응용될 수 있다. 본 논문에서는 자연 상태의 단백질 구조를 정확하게 나타낼 수 있는 단백질 조각 라이브러리를 구성하기 위하여, 대규모 단백질 구조 자료를 이용 할 수 있는 거리 척도들의 효과적인 조합을 조사하였다. 단백질 조각 라이브러리를 구성하기 위해 군집화를 사용하였다. 초기 군집화 단계에서는 가장 계산량이 작은 내부 알파탄소간 거리를 사용하였고, 군집의 확장단계에서는 내부 알파탄소간 거리, 비네-코시거리와 평균 제곱근 오차를 조합하여 사용하였다. 제안한 거리 척도의 조합으로 대규모 자료를 이용하여 단백질 조각 라이브러리를 구성하였다. 구성된 라이브러리를 사용하여 단백질 구조를 나타내는 실험에서 작은 평균 제곱근 오차가 발생함을 확인하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1381-1388
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• 2019

Objective: The aims of this study were to reveal the magnitude of the differences in protein structures at a cellular level as well as protein utilization and availability among soybean meal (SBM), canola meal (CM), and rapeseed meal (RSM) as feedstocks in China. Methods: Experiments were designed to compare the three different types of feedstocks in terms of: i) protein chemical profiles; ii) protein fractions partitioned according to Cornell Net Carbohydrate and Protein System; iii) protein molecular structures and protein second structures; iv) special protein compounds-amino acid (AA); v) total digestible protein and energy values; vi) in situ rumen protein degradability and intestinal digestibility. The protein second structures were measured using FT/IR molecular spectroscopy technique. A summary chemical approach in National Research Council (NRC) model was applied to analyze truly digestible protein. Results: The results showed significant differences in both protein nutritional profiles and protein structure parameters in terms of ${\alpha}-helix$, ${\beta}-sheet$ spectral intensity and their ratio, and amide I, amide II spectral intensity and their ratio among SBM, CM, and RSM. SBM had higher crude protein (CP) and AA content than CM and RSM. For dry matter (DM), SBM, and CM had a higher DM content compared with RSM (p<0.05), whereas no statistical significance was found between SBM and CM (p = 0.28). Effective degradability of CP and DM did not demonstrate significant differences among the three groups (p>0.05). Intestinal digestibility of rumen undegradable protein measured by three-step in vitro method showed that there was significant difference (p = 0.05) among SBM, CM, and RSM, which SBM was the highest and RSM was the lowest with CM in between. NRC modeling results showed that digestible CP content in SBM was significantly higher than that of CM and RSM (p<0.05). Conclusion: This study suggested that SBM and CM contained similar protein value and availability for dairy cattle, while RSM had the lowest protein quality and utilization.

• BMB Reports
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• 제29권4호
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• pp.380-385
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• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• 통합자연과학논문집
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• 제10권2호
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• pp.74-77
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• 2017

Bradykinin receptor B2 (B2R) is a GPCR protein which binds with the inflammatory mediator hormone bradkynin. Kallidin, a decapeptide, also signals through this receptor. B2R is crucial in the cross-talk between renin-angiotensin system (RAS) and the kinin-kallikrein system (KKS) and in many processes including vasodilation, edema, smooth muscle spasm and pain fiber stimulation. Thus the structural study of the receptor becomes important. We have predicted the peptide structures of Bradykinin and Kallidin from their amino acid sequences and the structures were docked with the receptor structure. The results obtained from protein-protein docking could be helpful in studying the B2R structural features and in the pathophysiology in various diseases related to it.

• 한국정보컨버전스학회:학술대회논문집
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• 한국정보컨버전스학회 2008년도 International conference on information convergence
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• pp.39-42
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• 2008

G protein-coupled receptor(GPCR) family is a cell membrane protein, and plays an important role in a signaling mechanism which transmits external signals through cell membranes into cells. Now, it is estimated that there may be about 800-1000 GPCRs in a human genome. But, GPCRs each are known to have various complex control mechanisms and very unique signaling mechanisms. GPCRs are involved in maintaining homeostasis of various human systems including an endocrine system or a neural system and thus, disorders in activity control of GPCRs are thought to be the major source of cardiovascular disorders, metabolic disorders, degenerative disorders, carcinogenesis and the like. As more than 60% of currently marketed therapeutic agents target GPCRs, the GPCR field has been actively explored in the pharmaceutical industry. Structural features, and class and subfamily of GPCRs are well known by function, and accordingly, the most fundamental work in studies identifying the previous GPCRs is to classify the GPCRs with given protein sequences. Studies for classifying previously identified GPCRs more easily with mathematical models have been mainly going on. Considering that secondary sequences of proteins, namely, secondary binding structures of amino acids constituting proteins are closely related to functions, the present paper does not place the focus on primary sequences of proteins as previously practiced, but instead, proposes a method to transform primary sequences into secondary structures and compare the secondary structures, and then detect an unknown GPCR assumed to have a same function in databases of previously identified GPCRs.

• EDISON SW 활용 경진대회 논문집
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• 제6회(2017년)
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• pp.16-26
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• 2017

Auxin response factor (ARF) and Aux/IAA transcriptional repressor family proteins play a major role in auxin's signalling process. Using the GALAXY protein modelling programs, monomer, dimer and oligomer structures of Aux/IAA17 and ARF5 protein were predicted based on the known experimental structures. By analysing the proposed complex structures, key interacting residues on binding site could be determined, and further suggestions for experimental studies were made.

• Interdisciplinary Bio Central
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• 제1권2호
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• pp.8.1-8.6
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• 2009

Introduction: It is a challenge to design a protein score function which stabilizes the native structures of many proteins simultaneously. The coarse-grained description of proteins to construct the pairwise-contact score function usually ignores the backbone directionality of protein structures. We propose a new two-body score function which stabilizes all native states of 1,006 proteins simultaneously. This two-body score function differs from the usual pairwise-contact functions in that it considers two adjacent amino acids at two ends of each peptide bond with the backbone directionality from the N-terminal to the C-terminal. The score is a corresponding propensity for a directional alignment of two adjacent amino acids with their local environments. Results and Discussion: We show that the construction of a directional adjacency-score function was achieved using 1,006 training proteins with the sequence homology less than 30%, which include all representatives of different protein classes. After parameterizing the local environments of amino acids into 9 categories depending on three secondary structures and three kinds of hydrophobicity of amino acids, the 32,400 adjacency-scores of amino acids could be determined by the perceptron learning and the protein threading. These could stabilize simultaneously all native folds of 1,006 training proteins. When these parameters are tested on the new distinct 382 proteins with the sequence homology less than 90%, 371 (97.1%) proteins could recognize their native folds. We also showed using these parameters that the retro sequence of the SH3 domain, the B domain of Staphylococcal protein A, and the B1 domain of Streptococcal protein G could not be stabilized to fold, which agrees with the experimental evidence.

• Animal Bioscience
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• 제34권5호
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• pp.855-866
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• 2021

Objective: Performance and physiological responses of dairy calves may change by using extruded soybean meal (ESBM) instead of common soybean meal (SBM) in starter feed. The aims of the current study were i) to determine the effect of extrusion processing of SBM on protein electrophoretic size, fourier transform infrared spectroscopy (FTIR) structures and Cornell Net Carbohydrate and Protein System (CNCPS) protein subfractions and ii) to determine the effect of substitution of SBM with ESBM in starter feed of Holstein heifer calves during pre and post-weaning on performance, nutrient digestibility, and blood metabolites. Methods: The SBM was substituted with ESBM at the level of 0%, 25%, 50%, 75%, and 100% (dry matter [DM] basis). Fifty heifer calves (initial body weight 40.3±0.63 kg) were used for the study. After birth, animals were fed colostrum for 3 days and then they were fed whole milk until weaning. Animals had free access to starter feed and water during the study. Results: Extrusion of SBM decreased electrophoretic protein size and increased rapidly degradable true protein fraction, changed FTIR protein and amide II region. With increasing level of ESBM in the diet, starter intake increased quadratically during the pre-weaning period (p<0.05) and body weight, DM intake and average daily gain increased linearly during the post-weaning and the whole study period (p<0.05). Tbe DM and crude protein digestibilities at week 14 and blood glucose and beta hydroxybutyric acid increased linearly in calves as the level of ESBM increased in the diet (p<0.05). Conclusion: Dairy calves performance and physiological responses were sensitive to SBM protein characteristics including electrophoretic size, FTIR structures and CNCPS protein fractions.