Biomedical subjects

Seung Yup Lee

Publications and source records attributed to Seung Yup Lee.

4 recordsLinked to original sources

PubMed2006

TASSER-based refinement of NMR structures.

The TASSER structure prediction algorithm is employed to investigate whether NMR structures can be moved closer to their corresponding X-ray counterparts by automatic refinement procedures. The benchmark protein dataset includes 61 nonhomologous proteins whose structures have been determined by both NMR and X-ray experiments. Interestingly, by starting from NMR structures, the majority (79%) of TASSER refined models show a structural shift toward their X-ray structures. On average, the TASSER refined models have a root-mean-square-deviation (RMSD) from the X-ray structure of 1.785 A (1.556 A) over the entire chain (aligned region), while the average RMSD between NMR and X-ray structures (RMSD(NMR_X-ray)) is 2.080 A (1.731 A). For all proteins having a RMSD(NMR_X-ray) >2 A, the TASSER refined structures show consistent improvement. However, for the 34 proteins with a RMSD(NMR_X-ray) <2 A, there are only 21 cases (60%) where the TASSER model is closer to the X-ray structure than NMR, which may be due to the inherent resolution of TASSER. We also compare the TASSER models with 12 NMR models in the RECOORD database that have been recalculated recently by Nederveen et al. from original NMR restraints using the newest molecular dynamics tools. In 8 of 12 cases, TASSER models show a smaller RMSD to X-ray structures; in 3 of 12 cases, where RMSD(NMR_X-ray) <1 A, RECOORD does better than TASSER. These results suggest that TASSER can be a useful tool to improve the quality of NMR structures.

Algorithms↗

PubMed2004

Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3.

Protein-folding mechanisms of two small globular proteins, IgG binding domain of protein G and alpha spectrin SH3 domain are investigated via Brownian dynamics simulations with a model made of coarse-grained physical energy functions responsible for sequence-specific interactions and weak Gō-like energies. The folding pathways of alpha spectrin SH3 are known to be mainly controlled by the native topology, while protein G folding is anticipated to be more sensitive to the sequence-specific effects than native topology. We found in the folding of protein G that the C terminal beta hairpin is formed earlier and is rigid, once ordered, in the presence of an intact C terminal turn. The alpha helix is found to exhibit repeated partial formations/deformations during folding and to be stabilized via the tertiary contact with preformed beta sheets. This predicted scenario is fully consistent with experimental phi value data. Moreover, we found that the folding route is critically affected when the hydrophobic interaction is excluded from physical energy terms, suggesting that the hydrophobicity critically contributes to the folding propensity of protein G. For the folding of alpha spectrin SH3, we found that the distal beta hairpin and diverging turn are parts formed early, fully in harmony with previous results of simple Gō-like and experimental analysis, supporting that the folding route of SH3 domain is robust and coded by the native topology. The hybrid method provides useful tools for analyzing roles of physical interactions in determining folding mechanisms.

Bacterial Proteins↗

PubMed2003

[Diagnosis of Helicobacter pylori infection with urine and stool].

BACKGROUND/AIMS: The urine antibody and stool antigen test are newly developed non-invasive tests for Helicobacter pylori (H. pylori) infection. The aim of this study was to assess the diagnostic value of these tests. METHODS: Urine and stool specimens from 50 consecutive patients who had undergone gastroscopy (28 men, mean age 54 years) were obtained. A kit for antibody against H. pylori (RAPIRUN test) was used for urine specimens and a kit for H. pylori antigen using ELISA (HpSA test) was used for stool specimens. None of patients had ever received any treatment to eradicate H. pylori. The H. pylori status was evaluated based on three different tests (histology, 13C-urea breath test, rapid urease test) and defined as positive when two of three tests were positive. RESULTS: Of 50 patients, 31 patients were diagnosed as H. pylori positive and 15 patients were negative. The RAPIRUN test was positive in 24 of 31 patients (sensitivity 77.4%) and negative in 13 of 15 patients (specificity 86.7%). The HpSA test was positive in 25 of 31 patients (sensitivity 80.1%) and negative in 14 of 15 patients (specificity 93.3%). CONCLUSIONS: The accuracies of H. pylori urine antibody and stool antigen test are similar to those of Western studies. These two tests are found to be useful methods for diagnosis of H. pylori infection in Korea.

Adolescent↗

PubMed2002

[The usefullness of percutaneous transluminal balloon angioplasty in the management of budd-Chiari syndrome].

BACKGROUND/AIMS: Membranous obstruction is the most common cause of Budd-Chiari syndrome in Orientals. Recently, percutaneous transluminal balloon angioplasty (PTBA) has been successfully applied as a treatment of membranous obstruction. We evaluated etiologies and clinical manifestations in our cases and the usefulness of PTBA. METHODS: Twelve cases of Budd-Chiari syndrome were analyzed. RESULTS: 50.3 years was the average age of the cases (ranging from 37 to 67 years). Major symptoms or signs were superficial collateral vessels on the chest or the abdomen in 6 cases, ascites in 3, abdominal pain in 4, hepatomegaly in 4, splenomegaly in 3, melena or hematemesis in 2, and leg edema in 2. Upper gastrointestinal endoscopy showed esophageal varices in 6 cases and two of these 6 cases had gastric varices. Of 8 cases with liver cirrhosis, 4 were classified as Child-Pugh class A and 4 as B. Four patients with cirrhosis had concurrent hepatocellular carcinoma including 1 patient who was HBs Ag positive. Etiologies were membranous obstruction in 11 cases and protein C deficiency in 1 case. The main site of obstruction was IVC in 8 and hepatic vein in 4. PTBA was successfully performed in 8 cases of membranous obstruction. During the mean follow-up period of 27.6 months (12-40 months), there were no reobstructions except in 2 cases. CONCLUSIONS: The most common cause of Budd-Chiari syndrome in our cases was membranous obstruction of IVC. Percutaneous transluminal balloon angioplasty is a very useful treatment method.

Adult↗