• Mass Spectrometry Letters
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• v.10 no.4
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• pp.117-122
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• 2019

This study demonstrated the sensitivity of electron capture dissociation mass spectrometry (ECD-MS) to probe subtle conformational changes in gaseous melittin ions induced by the substitution of an amino acid. ECD-MS was performed for triply and quadruply-protonated melittin and its variants obtained by a single amino acid substitution, namely, D-Pro14, Pro14Ala, and Leu13Ala. Although native triply-protonted melittin showed only a few peptide backbone cleavage products, the D-Pro14 and Pro14Ala variants exhibited extensive backbone fragments, suggesting the occurrence of a significant structural or conformational change induced by a single amino acid substitution at Pro14. On the contrary, the substitution at Leu13, namely Leu13Ala (+3), did not cause significant changes in the ECD backbone fragmentation pattern. Thus, the sensitivity of ECD-MS is demonstrated to be good enough to probe the aforementioned conformational change in melittin.

• Interdisciplinary Bio Central
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• v.6 no.4
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• pp.3.1-3.10
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• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• Bulletin of the Korean Chemical Society
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• v.26 no.6
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• pp.989-992
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• 2005

Dynamic kinetic resolution of $\alpha$-bromo carboxylic acid derivatives in nucleophilic substitution with chiral $\alpha$-amino ester nucleophiles in the presence of TBAI and DIEA has been investigated for stereoselective syntheses of 1,1'-iminodicarboxylic acid derivatives. Nucleophilic substitutions with various chiral $\alpha$-amino esters gave iminodiacetates 2-8 with stereoselectivities up to 87 : 13 dr. Also, the reactions of N-($\alpha$-bromo-$\alpha$-phenylacetyl)-L-alanine methyl ester with L-alanine, D-alanine and glycine methyl ester nucleophiles afforded N-carboxyalkyl dipeptide analogues 10-12 up to 90 : 10 dr.

• Journal of Microbiology
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• v.45 no.1
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• pp.75-78
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• 2007

Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent evolution in the Korean clade. At amino acid level, there were 17 substitutions and $G{\rightarrow}E$ substitution at position 37 may be responsible for change in predicted secondary structure.

• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.129-131
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• 2006

Through molecular phylogenetic analysis using the nef gene sequences of HIV-l isolated from Korean registered in the NCBI GenBank together with 41 reference strains and 94 foreign isolates, we verified that most (${\sim}80%$) of Korean isolates belonged to subtype B and 78% of subtype B were clustered together exclusively of foreign isolates, and this cluster was named Korean clade subtype B ($K_cB$). Similarity study suggested that the $K_cB$ cluster was more homogeneous than and clearly distinctive from the non-Korean subtype B ($NK_cB$). Comparison of the consensus amino acid sequences of the $K_cB\;or\;NK_cB$ revealed characteristic $K_cB$ signature amino acid pattern comprised of 13 amino acid residues. The $K_cB$ signature amino acid residues were critical in separating the $K_cB$ ftom the $NK_cB$, since substitution of the $NK_cB$ sequences with $K_cB$ signature amino acids relocated them to the Koran clade, and vice versa. Synonymous and nonsynonymous substitution rate study suggested positive selection event for the $K_cB$.

• Journal of KIISE:Software and Applications
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• v.34 no.7
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• pp.595-602
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• 2007

This paper proposes a method that discriminates signal peptide and predicts the cleavage site of the secretory proteins cleaved by the signal peptidase I. The preprocessing stage uses hydrophobicity scales of amino acids in order to predict the presence of signal sequence and the cleavage site. The preprocessing enhances the performance of the prediction method by eliminating the non-secretory proteins in the early stage of prediction. for the effective use of support vector machine for the signal sequence prediction, the biologically relevant distance between the amino acid sequences is defined by using the hydrophobicity and substitution matrix; the hydrophobicity can be used to Predict the location of amino acid in a cell and the substitution matrix represents the evolutionary relationships of amino acids. The proposed method showed 98.9% discrimination rates from signal sequences and 88% correct rate of the cleavage site prediction on Swiss-Prot release 50 protein database using the 5-fold-cross-validation. In the comparison tests, the proposed method has performed significantly better than other prediction methods.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.42 no.4
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• pp.433-440
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• 2016

In this study, a poly (amino acid)s derivative grafted with retinoic acids, which could form self-assemblies in an aqueous solution, was successfully synthesized. The synthesized amphiphilic poly (amino acid)s were controlled with 5, 10, 30 mol% substitution of retinoic acid. Then, the amphiphilic poly (amino acid)s were self-assembled by inter/intra molecular stacking of retinoic acids in an aqueous solution. Also, the increasing the degree of substitution (DS) of retinoic acids decreased the size of self-assembled nanoparticles and induced structural transition to bilayer structure from spherical structure. The retinol was stably encapsulated into a core of self-assembled nanoparticle with 10 mol% of DS. This strategy to prepare the self-assemblies of amphiphilic polyaspartamide will serve to improve the efficiency of targeted delivery for a functional cosmetic with various biological modalities.

• YAKHAK HOEJI
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• v.47 no.5
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• pp.276-282
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• 2003

For the development of new synthetic method for unnatural amino acid esters, N-aryl phenylglycine Ο-alkyl esters 4a∼i were synthesized through esterification, bromination, C-N bond formation from commercially available phenylacetic acids. An efficient and practical reaction condition for esters 2a∼c was that the starting materials 1a∼c were refluxed in absolute methanol for 3 hours with catalytic concentrated hydrosulfuric acid. In addition, bromines 3a∼c were formated for 3h in dichloromethane at rt with N-bromosuccinimide. Bromines 3a∼c were also converted to 4a∼i through substitution of arylamines during refluxing for 24 hours in ethanol with triethylamine. Interestingly, ethyl esters 5a∼c were formed via transesterification reaction when the p-sulfamylanilino group was used as a nucleophile in ethanol solvent.

• Journal of the Korean Applied Science and Technology
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• v.37 no.6
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• pp.1597-1604
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• 2020

In this study, a synthesized poly(amino acid) self-assembly grafted with valine molecules was investigated on the skin activity of skin growth factors. The amphiphilic grafted poly(amino acid) derivatives were successfully synthesized by varying of degree of substitution(DS) and polymerization (DP) with valine molecules forming a β-sheet structure. Then, the pro-collagen biosynthesis of EGF(epidermal growth factor) was improved by 20%, and the inhibitory ability of tyrosinase activity was increased by 6.5 times by self-assembling of EGF with the poly(amino acid)s having β-sheet structures. This strategy of preparing protein self-assembly with poly(amino acid) derivatives will help improve the stability of protein growth factors and use it in medicals as well as cosmeceuticals through skin improvement.