• Interdisciplinary Bio Central
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• v.1 no.2
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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.

• BMB Reports
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• v.49 no.6
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• pp.349-354
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• 2016

The archaeon Sulfolobus solfataricus P1 carboxylesterase is a thermostable enzyme with a molecular mass of 33.5 kDa belonging to the mammalian hormone-sensitive lipase (HSL) family. In our previous study, we purified the enzyme and suggested the expected amino acids related to its catalysis by chemical modification and a sequence homology search. For further validating these amino acids in this study, we modified them using site-directed mutagenesis and examined the activity of the mutant enzymes using spectrophotometric analysis and then estimated by homology modeling and fluorescence analysis. As a result, it was identified that Ser151, Asp244, and His274 consist of a catalytic triad, and Gly80, Gly81, and Ala152 compose an oxyanion hole of the enzyme. In addition, it was also determined that the cysteine residues are located near the active site or at the positions inducing any conformational changes of the enzyme by their replacement with serine residues.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.655-659
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• 2000

A 11.5-kb DNA fragment containing an endo-inulinase gene was cloned from Xanthomonas oryzae #5. It contained a single open reading frame of 3,999bp, encoding a polypeptide composed of signal peptide of 32 amino acids and mature protein of 1,301 amino acids. From the comparison of amino acids sequences with fructan hydrolases, inulinase, levanase and CFTase, the sequence of the endo-inulinase had highly homology of 72% with CFTase of B. circulans, and six highly conserved regions including the ${\beta}-fructosidase$ motif were found.

• Journal of Life Science
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• v.8 no.3
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• pp.285-293
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• 1998

We have cloned an internal fragment of the putative transoisase gene of MLE in the silkworm, Bombyx mori, using PCR method with degenerative oligonucleotide primers designed to represent regions of amino acids encoding transposase. The resulting PCR clone, designed as BmoMAR, cords a partial ORF(152 a.a.) of MLE in which interrupted by five stop codons, and the sequence of its deduced amino acids showed 37% homology with Mos1, an active mariner, from Drosophila mauritiana. Furthermore, the BmoMAR exhibits nucleotide and amino acid homology with 59% and 37% from Apis mellifera and D. mauritiana 7.9 clone, respectively. This result strongly that a MLE is present in the genome of B. mori.

• The Journal of Korean Society of Virology
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• v.30 no.1
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• pp.1-10
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• 2000

The nonstructural protein NSP4, encoded by gene 10 of rotavirus, has been shown to playa role in viral assembly and known to be an enterotoxin, causing diarrhea in mouse pups. NSP4 gene was cloned from CBNU-2 (virulent bovine rotavirus/diarrheic fecal sample) and CBNU-1 (cell-culture adapted bovine rotavirus/isolated from CBNU-2 and 75 times passaged on MA104 cells), respectively, by reverse transcriptase-polymerase chain reaction (RT-PCR) and sequenced and compared. The sequence data indicated that the NSP4 genes of bovine rotavirus (BRV) were 751 bases in length and encoded one open reading frame of 175 amino acids beginning at base 42 and terminating at base 569. Differences in nucleotide sequence between CBNU-2 and CBNU-1 were observed at 6 positions (base 274, 296, 391, 394, 396 and 579). NSP4 gene of BRV exhibited a high degree of nucleotide (90% and 94%) and amino acid sequence (91% and 97%) homology with those of SA11 and UK but a low degree of nucleotide (77% and 79%) and amino acids sequence (81% and 85%) homology with those of Wa and OSU.

• Applied Microscopy
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• v.51
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• pp.17.1-17.10
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• 2021

Our previous study on the binding activity between Cel5H and clay minerals showed highest binding efficiency among other cellulase enzymes cloned. Here, based on previous studies, we hypothesized that the positive amino acids on the surface of Cel5H protein may play an important role in binding to clay surfaces. To examine this, protein sequences of Bacillus licheniformis Cel5H (BlCel5H) and Paenibacillus polymyxa Cel5A (PpCel5A) were analyzed and then selected amino acids were mutated. These mutated proteins were investigated for binding activity and force measurement via atomic force microscopy (AFM). A total of seven amino acids which are only present in BlCel5H but not in PpCel5A were selected for mutational studies and the positive residues which are present in both were omitted. Of the seven selected surface lysine residues, only three mutants K196A(M2), K54A(M3) and K157T(M4) showed 12%, 7% and 8% less clay mineral binding ability, respectively compared with wild-type. The probable reason why other mutants did not show altered binding efficiency might be due to relative location of amino acids on the protein surface. Meanwhile, measurement of adhesion forces on mica sheets showed a well-defined maximum at 69±19 pN for wild-type, 58±19 pN for M2, 53±19 pN for M3, and 49±19 pN for M4 proteins. Hence, our results demonstrated that relative location of surface amino acids of Cel5H protein especially positive charged amino acids are important in the process of clay mineral-protein binding interaction through electrostatic exchange of charges.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.48-54
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• 2008

A putative ${\omega}$-aminotransferase gene, cc3143 (aptA), from Caulobacter crescentus was screened by bioinformatical tools and overexpressed in E. coli, and the substrate specificity of the ${\omega}$-aminotransferase was investigated. AptA showed high activity for short-chain ${\beta}$-amino acids. It showed the highest activity for 3-amino-n-butyric acid. It showed higher activity toward aromatic amines than aliphatic amines. The 3D model of the ${\omega}$-aminotransferase was constructed by homology modeling using a dialkylglycine decarboxylase (PDB ID: 1DGE) as a template. Then, the ${\omega}$-aminotransferase was rationally redesigned to increase the activity for 3-amino-3-phenylpropionic acid. The mutants N285A and V227G increased the relative activity for 3-amino-3-phenylpropionic acid to 3-amino-n-butyric acid by 11-fold and 3-fold, respectively, over that of wild type.

• The Plant Pathology Journal
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• v.15 no.1
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• pp.68-71
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• 1999

To illustrate the action mechanism of pencycuron on Rhizoctonia solani, two experiments were conducted including the comparison of amino acids of $\beta$-tubulin between R-C (sensitive isolate) and Rh-131 (non-sensitive isolate), and the inhibitory effect of pencycuron on tubulin assembly in vitro. Both $\beta$-tubulin genes of R-C and Rh-131 proved to have 1,582 nucleotides encoding a protein of 445 amino acids, showing 98% homology in amino acid sequences between them. It was found that codons at 103, 236, and 267 for lysine (AGG), valine (GTC) and isoleucine (ATT) in R-C were replaced by codons for methionine (ATG), isoleucine (ATT) and methionine (ATG) in Rh-131, respectively. No inhibitory effect of pencycuron on the tubulin assembly was observed. It suggests that pencycuron may have no direct inhibitory effects on the assembly of tubulin at least in vitro.

• Food Science of Animal Resources
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• v.33 no.3
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• pp.331-334
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• 2013

Osteopontin (OPN) is a secreted phosphorylated glycoprotein. It has an important role in multiple biological processes including cell survival, bone remodeling, inhibition of ectopic calcification, as well as, is thought to have potential immune modulation activities. In this work, we isolated and characterized a full-length open reading frame (ORF) of Korean native cow's OPN from Korean native cow's (Hanwoo) kidney, and successfully cloned firstly on Hanwoo's OPN. The sequencing results indicated that the isolated cDNA was 1190 bp in length containing a complete ORF of 837 bp. It encoded a precursor protein Hanwoo's OPN consisting of 278 amino acids with a signal peptide of 16 amino acids. Amino acid homology was found to be 99.3% as compared to the corresponding sequences of Holstein bone marrow OPN. Hanwoo's kidney OPN and Holstein bone marrow OPN are different only in two amino acid residues 42 and 56, amino acid residue 42 is Thr (T) ${\leftrightarrow}$ Ile (I), and amino acid residue 56 is Ala (A) ${\leftrightarrow}$ Thr (T) respectively. These results from the present work would be helpful to elucidate the biological function of Hanwoo's OPN and provided a foundation for further insight into role of Hanwoo's OPN.

• Journal of Microbiology and Biotechnology
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• v.11 no.4
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• pp.668-676
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• 2001

Pseudomonas sp. strain SY5 is a PCB-degrading bacterium [24] that includes two different enzymes (BphC1 and BphC2) encoding 2,3-dihdroxybiphenyl 1,2-dioxygenase and BphD encoding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase. The bphC1 and bphC2 genes were found to consist of 897 based encoding 299 amino acids and 882 bases encoding 294 amino acids, respectively, whereas the bphD gene consisted of 861 bases encoding 287 amino acids. According to a homology search, a 50% and 39% similarity between the bphC1 and bphC2 genes at the nucleotide and amino acid level was shown, respectively. The bphC1 gene showed a 38% and 45% similarity at the amino acid level to Alcaligenes eutrophus A5 and Rhodococcus rhodochrous, respectively, whereas, bphC2 showed a 95% and 43% similarity, respectively. A comparison of the deduced amino acid sequence of the bphD product of Pseudomonas sp. SY5 with that of A. eutrophus A5, Pseudomons sp. KKS102, and LB400 showed a sequence identity of 92, 92, and 79%, respectively. Strain SY5 was originally isolated from municipal sewage containing recalcitrant organic compounds an found to have a high degradability of various aromatic compounds [23]. The current study found that strain SY5 had two extradiol-type dioxygenases, which did not hybridize with each other as they had a low similarity, yet a similar structure of evolutionarily conserved amino acids residues for catalytic activity between BphC1 and BphC2 was observed.