• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.138-142
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• 2016

Replication Protein A (RPA) is the eukaryotic single-stranded DNA binding protein. It involves in DNA replication, repair, and damage response. Among three subunits, RPA70 has a protein-protein binding domain (RPA70N) at the N-terminal. It has known that the domain recruits several damage response proteins to the damaged site. Also, it is suggested that there are more candidates that interact with RPA70N. Even though several studies performed on the structural aspects of RPA70N and its ligand binding, the backbone assignments of RPA70N is not available in public. In this study, we present the backbone assignments of RPA70N.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.66-70
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• 2016

The replication protein A (RPA), is a heterotrimer with 70, 32 and 14 kDa subunits and plays a crucial role in DNA replication, recombination, and repair. The largest subunit, RPA70, binds to single-stranded DNA (ssDNA) and mediates interactions with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various temperatures, to understand the temperature dependency of ssDNA binding affinity of RPA70A. Essential residues for ssDNA binding were conserved while less essential parts were changed with the temperature. Our results provide valuable insights into the molecular mechanism of the ssDNA binding of human RPA.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.1
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• pp.18-25
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• 2018

Replication protein A (RPA) is an essential single-stranded DNA binding protein in DNA processing. It is known that N terminal domain of RPA70 (RPA70N) recruits various protein partners including damage-response proteins such as p53, ATRIP, Rad9, and MRE11. Although the common binding residues of RPA70N were revealed, dynamic properties of the protein are not studied yet. In this study, we measured $^{15}N$ relaxation parameters ($T_1,\;T_2$ and heteronuclear NOE) of human RPA70N and analyzed them using model-free analysis. Our data showed that the two loops near the binding site experience fast time scale motion while the binding site does not. It suggests that the protein binding surface of RPA70N is mostly rigid for minimizing entropy cost of binding and the loops can experience conformational changes.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.71-75
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• 2016

The replication protein A (RPA) plays a crucial role in DNA replication, recombination, and repair. RPA consists of 70, 32 and 14 kDa subunits and has high single-stranded DNA (ssDNA) binding affinity. The largest subunit, RPA70, mainly contributes to bind to ssDNA as well as interact with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various pH, to understand the effect of pH on the ssDNA binding of RPA70A. The chemical shift perturbations of binding residues were most significant at pH 6.5 and they reduced with pH increment. This study provides valuable insights into the molecular mechanism of the ssDNA binding of human RPA.

• BMB Reports
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• v.35 no.2
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• pp.194-198
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• 2002

Eukaryotic replication protein A (RPA) is a single-stranded(ss) DNA binding protein with multiple functions in DNA replication, repair, and genetic recombination. The 70-kDa subunit of eukaryotic RPA contains a conserved four cysteine-type zinc-finger motif that has been implicated in the regulation of DNA replication and repair. Recently, we described a novel function for the zinc-finger motif in the regulation of human RPA's ssDNA binding activity through reduction-oxidation (redox). Here, we show that yeast RPA's ssDNA binding activity is regulated by redox potential through its RPA32 and/or RPA14 subunits. Yeast RPA requires a reducing agent, such as dithiothreitol (DTT), for its ssDNA binding activity. Also, under non-reducing conditions, its DNA binding activity decreases 20 fold. In contrast, the RPA 70 subunit does not require DTT for its DNA binding activity and is not affected by the redox condition. These results suggest that all three subunits are required for the regulation of RPA's DNA binding activity through redox potential.

• Radiation Oncology Journal
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• v.27 no.3
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• pp.140-144
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• 2009

Purpose: This study was performed to retrospectively analyze patient survival by weighting according to the primary tumor oncotype in 160 patients with brain metastasis and who underwent whole brain radiotherapy. Materials and Methods: A total of 160 metastatic brain cancer patients who were treated with whole brain radiotherapy of 30 Gy between 2002 and 2008 were retrospectively analyzed. The primary tumor oncotype of 20 patients was breast cancer, and that of 103 patients was lung cancer. Except for 18 patients with leptomeningeal seeding, a total of 142 patients were analyzed according to the prognostic factors and the Recursive Partitioning Analysis (RPA) class. Weighted Partitioning Analysis (WPA), with the weighting being done according to the primary tumor oncotype, was performed and the results were correlated with survival and then compared with the RPA Class. Results: The median survival of the patients in RPA Class I (8 patients) was 20.0 months, that for Class II (76 patients) was 10.0 months and that for Class III (58 patients) was 3.0 months (p<0.003). The median survival of patients in WPA Class I (3 patients) was 36 months, that for the patients in Class II (9 patients) was 23.7 months, that for the patients in Class III (70 patients) was 10.9 months and that for the patients in Class IV (60 patients) was 8.6 months (p<0.001). The WPA Class might have more accuracy in assessing survival, and it may be superior to the RPA Class for assessing survival. Conclusion: A new prognostic index, the WPA Class, has more prognostic value than the RPA Class for the treatment of patients with metastatic brain cancer. This WPA Class may be useful to guide the appropriate treatment of metastatic brain lesions.

• International Journal of Vascular Biomedical Engineering
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• v.1 no.2
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• pp.36-41
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• 2003

Both flow visualizations and computational fluid dynamics were performed to determine hemodynamics in a total cavopulmonary connection (TCPC) model for surgically correcting congenital heart defects. From magnetic resonance images, an anatomically correct glass model was fabricated to visualize steady flow. The total flow rates were 4, 6 and 8L/min and flow rates from SVC and IVC were 40:60. The flow split ratio between LPA and RPA was varied by 70:30, 60:40 and 50:50. A pressure-based finite-volume software was used to solve steady flow dynamics in TCPC models. Results showed that superior vena cava(SVC) and inferior vena cava(IVC) flow merged directly to the intra-atrial conduit, creating two large vortices. Significant swirl motions were observed in the intra-atrial conduit and pulmonary arteries. Flow collision or swirling flow resulted in energy loss in TCPC models. In addition, a large intra-atrial channel or a sharp bend in TCPC geometries could influence on energy losses. Energy conservation was efficient when flow rates in pulmonary branches were balanced. In order to increase energy efficiency in Fontan operations, it is necessary to remove a flow collision in the intra-atrial channel and a sharp bend in the pulmonary bifurcation.

• International Journal of Vascular Biomedical Engineering
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• v.2 no.1
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• pp.11-16
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• 2004

Both flow visualizations and computational fluid dynamics were performed to determine hemodynamics in a total cavopulmonary connection (TCPC) model for surgically correcting congenital heart defects. From magnetic resonance images, an anatomically correct glass model was fabricated to visualize steady flow. The total flow rates were 4, 6 and 8L/min and flow rates from SVC and IVC were 40:60. The flow split ratio between LPA and RPA was varied by 70:30, 60:40 and 50:50. A pressure-based finite-volume software was used to solve steady flow dynamics in TCPC models. Results showed that superior vena cava(SVC) and inferior vena cava(IVC) flow merged directly to the intra-atrial conduit, creating two large vortices. Significant swirl motions were observed in the intra-atrial conduit and pulmonary arteries. Flow collision or swirling flow resulted in energy loss in TCPC models. In addition, a large intra-atrial channel or a sharp bend in TCPC geometries could influence on energy losses. Energy conservation was efficient when flow rates in pulmonary branches were balanced. In order to increase energy efficiency in Fontan operations, it is necessary to remove a flow collision in the intra-atrial channel and a sharp bend in the pulmonary bifurcation.

• Proceedings of the KOSOMBE Conference
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• v.1996 no.05
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• pp.203-206
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• 1996

To understand the local fluid dynamics for different desists of Fontan operation, five models were made out of Pyrex glass to facilitate in-vitro study. Model I, II and III have same position of the center of the anastomosis of the IVC( inferior vena cava) with that of the SVC(superior vena cava), but Model IV and V have 10 mm offset between them. Also the anastomotic junction angles are different(Model I and $IV:90^{\circ}$, Model II and $V:70^{\circ}$, Model $III:45^{\circ}$). These models were then connected to a flow loop for flow visualization study. In Model I any dominant vortex was not seen in the central region of the juntion, but a large unstable vortex was created in the Model II and III. In Model IV and V a significant stagnation region was created in the middle of the offset region. It also showed that the flow direction from the IVC and SVC to the LPA(left pulmonary artery) and RPA(right pulmonary artery) highly depends on the offset of the junction rather than the anastomotic junction angle.

• Journal of Korean Neurosurgical Society
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• v.44 no.6
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• pp.358-363
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• 2008

Objective : This study was performed to assess the efficacy of GKS in patients with ten or more brain metastases. Methods : From Aug 2002 to Dec 2007, twenty-six patients (13 men and 13 women) with ten or more cerebral metastatic lesions underwent GKS. The mean age was 55 years (32-80). All patients had Karnofsky performance status (KPS) score of 70 or better. According to recursive partitioning analysis (RPA) classification, 3 patients belonged to class I and 23 to class II. The location of primary tumor was lung (21), breast (3) and unknown (2). The mean number of the lesions per patient was 16.6 (10-37). The mean cumulated volume was 10.9 cc (1.0-42.2). The median marginal dose was 15 Gy (9-23). Overall survival and the prognostic factors for the survival were retrospectively analyzed by using Kaplan Meier method and univariate analysis. Results : Overall median survival from GKS was 34 weeks (8-199). Local control was possible for 79.5% of the lesions and control of all the lesions was possible in at least 14 patients (53.8%) until 6 months after GKS. New lesions appeared in 7 (26.9%) patients during the same period. At the last follow-up, 18 patients died; 6 (33.3%) from systemic causes, 10 (55.6%) from neurological causes, and 2 (11.1 %) from unknown causes. Synchronous onset in non-small cell lung cancer (p=0.007), high KPS score (${\geq}80$, p=0.029), and controlled primary disease (p=0.020) were favorable prognostic factors in univariate analysis. Conclusion : In carefully selected patients, GKS may be a treatment option for ten or more brain metastases.