• Food Science of Animal Resources
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• v.42 no.6
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• pp.915-927
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• 2022

Recently, protein-fortified milk powders are being widely consumed in Korea to prevent sarcopenia, and the demand for high-protein food powders is continuously increasing in the Korean market. However, spray-dried milk proteins have poor flowability and wettability owing to their fine particle sizes and high inter-particle cohesive forces. Fluidized bed agglomeration is widely used to improve the instant properties of food powders. This study investigated the effect of fluidized bed agglomeration on whey protein isolate (WPI)-fortified skim milk powder (SMP) at different SMP/WPI ratios. The fluidized bed process increased the particle size distribution, and agglomerated particles with grape-like structures were observed in the SEM images. As the size increased, the Carr index (CI) and Hausner ratio (HR) values of the agglomerated WPI-fortified SMP particles exhibited excellent flowability (CI: <15) and low cohesiveness (HR: <1.2). In addition, agglomerated WPI-fortified SMP particles exhibited the faster wetting time than the instant criterion (<20 s). As a result, the rheological and physical properties of the WPI-fortified SMP particles were effectively improved by fluidized bed agglomeration. However, the fluidized bed agglomeration process led to a slight change in the color properties. The CIE L^* decreased, and the CIE b^* increased because of the Maillard reaction. The apparent viscosity (η_a,10) and consistency index (K) values of the rehydrated solutions (60 g/180 mL water) increased with the increasing WPI ratio. These results may be useful for formulating protein-fortified milk powder with better instant properties.

• International Journal of Industrial Entomology and Biomaterials
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• v.14 no.1
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• pp.51-56
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• 2007

In a previous study, three larval cuticle protein genes were cloned from the mulberry longicorn beetle, Apriona germari (Comp. Biochem. Physiol. B 136, 803-811, 2003). In the present study, the genomic structures of these three larval cuticle protein genes (AgLCP9.2, AgLCP12.6 and AgLCP12.3) were elucidated. All three cuticle protein genes consist of one intron and two exons. Southern blot analysis of genomic DNA suggested that three cuticle protein genes are a single copy gene. In addition, a novel larval cuticle protein gene, AgLCP10.6, was cloned from A. germari in this study. The AgLCP10.6 cDNA contains an ORF of 300 nucleotides that are capable of encoding a 100-amino acid polypeptide with a predicted molecular mass of 10.6 kDa. The amino acid sequence deduced from the AgLCP10.6 cDNA contained a type-specific consensus sequence identifiable in other insect cuticle proteins and is most homologous to Drosophila melanogaster cuticle protein ACP65A (51 % protein sequence identity). Northern blot analysis revealed that AgLCP10.6 showed epidermis-specific expression.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• The KIPS Transactions:PartD
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• v.11D no.3
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• pp.519-532
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• 2004

With the explosion of bioinformatics data such proteins and genes, biologists need a integrated system to analyze and organize large datasets that interact with heterogeneous types of biological data. In this paper, we propose a integration system based on a mediated data warehouse architecture using a XML model in order to combine protein related data at biology laboratories. A fact constellation model in this system is used at a common model for integration and an integrated schema it translated to a XML schema. In addition, to track source changes and provenance of data in an integrated database employ incremental update and management of sequence version. This paper shows modeling of integration for protein structures, sequences and classification of structures using the proposed system.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Bulletin of the Korean Chemical Society
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• v.30 no.3
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• pp.623-629
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• 2009

We have performed replica-exchange molecular dynamics simulations on 41 residue peptide mainly composed of NAC (non A$\beta$ component) sequence in $\alpha$-Synuclein. To investigate conformational characteristics of intrinsically unstructured peptides, we carried out structural analysis on the ‘representative structures’ for ensemble of structures occurring at different temperatures. The secondary structure profile obtained from our simulations suggests that the NAC region of $\alpha$-synuclein can be divided into roughly three helical-like segments. It is found that the overall helix-turn-helix like topology is conserved even though the conformational fluctuations grow as the temperature increases. The coordinate-based and the distance-based representative structures exhibit noticeable differences at higher temperatures while they are similar at lower temperatures. It is found that structural variations for the coordinate-based representative structures are much larger, suggesting that distance-based representative structures provide more reliable information concerning characteristic features of intrinsically unstructured proteins. The present analysis also indicates that the conformational features of representative structures at high temperatures might be related to those in membrane or low pH environment.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• The KIPS Transactions:PartB
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• v.16B no.5
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• pp.359-366
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• BMB Reports
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• v.29 no.2
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• pp.180-182
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• 1996

One of the essential functions of virus surface proteins is the recognition of specific receptors on target cell membranes, and cellular receptors play an important role in viral pathogenesis. But the earliest steps of hepatitis B virus (HBV) infection, such as hepatocyte receptor interaction with the virus, are poorly understood. Previous work has suggested an important role of the preS1 region of HBV envelope protein in mediating viral binding to hepatocytes. Although hepatitis B virus (HBV) infection appears to be initiated by specific binding of virions to cell membrane structures via one or potentially several viral surface proteins, data showing the identification or isolation of the HBV receptor (s) are not yet available. The receptor-like proteins on the plasma membrane surface of HepG2 cells that bind to PreS1 were separated and identified using affinity chromatography, and the amino-terminal amino acid sequences of the receptor-like proteins were determined.