Biomedical subjects

Sung-Joon Park

Publications and source records attributed to Sung-Joon Park.

3 recordsLinked to original sources

PubMed2005

Applying a grid technology to protein structure predictor "ROKKY".

This paper describes a sub-project of BioGrid project called "HTC (High Throughput Computing) group." Generally, a protein structure prediction which requires large amount of computational resources is done by trial-and-error method. HTC group have been developing a high throughput computing system with a flexible workflow handling mechanism for a protein structure prediction. In this paper, we show how to apply our high throughput computing system to the protein structure predictor called "ROKKY."

Computational Biology↗

PubMed2005

A study of fragment-based protein structure prediction: biased fragment replacement for searching low-energy conformation.

A novel fragment replacement strategy for the fragment-based protein structure prediction is proposed. Despite the recent advance of de novo prediction of protein tertiary structure, intricate protein topologies still exist at unsatisfactory prediction quality. Although this difficulty is in part due to the accuracy of energy functions, it also relates to the search ability of sampling methods. To enhance the global optimization method that finds low-energy conformations, this study tests a biased sampling approach. The proposed approach is inspired by the fact that local structures of a protein have geometrical rigidity and flexibility. For capturing the pivotal local structures to generate various topologies, this approach first measures the energetic fluctuation of target fragments on dihedral angles of a protein, and then the quantity is converted to probability used by probabilistic selection of fragment replacement. Due to the requirement of the dihedral angles, a Genetic Algorithm implements the proposed idea, and experimental results show that the GA is capable of providing the dihedral angles as template-like proteins. The results suggest that the proposed approach can reach low-energy conformations with comparable prediction quality to that of an existing method. Interestingly, the low-energy states were associated with the frequent replacement of fragments in natively-coil regions. However, unfavorable compactification of the predicted models was observed. All experimental data are available at http://www.proteinsilico.org/PRO/.

Algorithms↗

PubMed2002

Structural roles of cysteine 50 and cysteine 230 residues in Arabidopsis thaliana S-adenosylmethionine decarboxylase.

The Arabidopsis thaliana S-Adenosylmethionine decarboxylase (AdoMetDC) cDNA (GenBank U63633) was cloned. Site-specific mutagenesis was performed to introduce mutations at the conserved cysteine Cys(50), Cys(83), and Cys(230), and lys(81) residues. In accordance with the human AdoMetDC, the C50A and C230A mutagenesis had minimal effect on catalytic activity, which was further supported by DTNB-mediated inactivation and reactivation. However, unlike the human AdoMetDC, the Cys(50) and Cys(230) mutants were much more thermally unstable than the wild type and other mutant AdoMetDC, suggesting the structural significance of cysteines. Furthermore, according to a circular dichroism spectrum analysis, the Cys(50) and Cys(230) mutants show a higher a-helix content and lower coiled-coil content when compared to that of wild type and the other mutant AdoMetDC. Also, the three-dimensional structure of Arabidopsis thaliana AdoMetDC could further support all of the data presented here. Summarily, we suggest that the Cys(50) and Cys(230) residues are structurally important.

Adenosylmethionine Decarboxylase↗