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5. Discovery and identification of medium‐chain fatty acid responsive promoters in Saccharomyces cerevisiae

Author

He Peixin, Li Han, Lei Li, Danya Han, Qinhong Wang, and Huang Shen

Subjects
0106 biological sciences, chemistry.chemical_classification, 0303 health sciences, Candidate gene, Environmental Engineering, biology, Saccharomyces cerevisiae, Fatty acid, Bioengineering, Promoter, biology.organism_classification, 01 natural sciences, Transcriptome, 03 medical and health sciences, Synthetic biology, chemistry, Biochemistry, 010608 biotechnology, Gene expression, Medium chain fatty acid, 030304 developmental biology, Biotechnology
Abstract

Medium-chain fatty acids (MCFAs) and their derivatives are important chemicals that can be used in lubricants, detergents, and cosmetics. MCFAs can be produced in several microbes, although production is not high. Dynamic regulation by synthetic biology is a good method of improving production of chemicals that avoids toxic intermediates, but chemical-responsive promoters are required. Several MCFA sensors or promoters have been reported in Saccharomyces cerevisiae. In this study, by using transcriptomic analysis of S. cerevisiae exposed to fatty acids with 6-, 12-, and 16-carbon chains, we identified 58 candidate genes that may be responsive to MCFAs. Using a fluorescence-based screening method, we identified MCFA-responsive promoters, four that upregulated gene expression, and three that downregulated gene expression. Dose-response analysis revealed that some of the promoters were sensitive to fatty acid concentrations as low as 0.02-0.06 mM. The MCFA-responsive promoters reported in this study could be used in dynamic regulation of fatty acids and fatty acid-derived products in S. cerevisiae.

Published
2020

7. The Urological Association of Asia clinical guideline for urinary stone disease

Author

Abbas Basiri, Shrawan Kumar Singh, Yao Liang Deng, Lei Shi, Cheng Huang Shen, Gyawali Pr, Sopheap Bou, Sung Yong Cho, Husain Alenezi, Kemal Sarica, Takahiro Yasui, Praveen Singam, Yung Khan Tan, Manint Usawachintachit, Tarmono Djojodemedjo, Kazumi Taguchi, and Anthony C. F. Ng

Subjects
medicine.medical_specialty, Asia, Urology, 030232 urology & nephrology, Ethnic group, Nephrolithotomy, Percutaneous, 03 medical and health sciences, 0302 clinical medicine, Recurrence, Secondary Prevention, Asian country, medicine, Humans, Societies, Medical, business.industry, Foundation (evidence), Endoscopy, Guideline, Evidence-based medicine, Systematic review, 030220 oncology & carcinogenesis, Family medicine, Etiology, Urinary Calculi, business, Systematic Reviews as Topic, Urinary stone disease
Abstract

The Urological Association of Asia, consisting of 25 member associations and one affiliated member since its foundation in 1990, has planned to develop Asian guidelines for all urological fields. The field of stone diseases is the third of its guideline projects. Because of the different climates, and social, economic and ethnic environments, the clinical practice for urinary stone diseases widely varies among the Asian countries. The committee members of the Urological Association of Asia on the clinical guidelines for urinary stone disease carried out a surveillance study to better understand the diversity of the treatment strategy among different regions and subsequent systematic literature review through PubMed and MEDLINE database between 1966 and 2017. Levels of evidence and grades of recommendation for each management were decided according to the relevant strategy. Each clinical question and answer were thoroughly reviewed and discussed by all committee members and their colleagues, with suggestions from expert representatives of the American Urological Association and European Association of Urology. However, we focused on the pragmatic care of patients and our own evidence throughout Asia, which included recent surgical trends, such as miniaturized percutaneous nephrolithotomy and endoscopic combined intrarenal surgery. This guideline covers all fields of stone diseases, from etiology to recurrence prevention. Here, we present a short summary of the first version of the guideline - consisting 43 clinical questions - and overview its key practical issues.

Published
2019

12. Mitotic arrest induced in human DU145 prostate cancer cells in response to KHC-4 treatment

Author

Cheng Huang Shen, Sheng-Chu Kuo, Chun-Hsu Yao, Wei Jen Ting, Su Ying Wen, You Liang Hsieh, Chia Yao Shen, Dennis Jine Yuan Hsieh, Chih Yang Huang, Tien Huang Lin, Wen Shin Chien, and Hsi Chin Wu

Subjects
0301 basic medicine, Cyclin-dependent kinase 1, education.field_of_study, Cell cycle checkpoint, Chemistry, Cell growth, Health, Toxicology and Mutagenesis, Population, Cell migration, General Medicine, Management, Monitoring, Policy and Law, Toxicology, Bioinformatics, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, DU145, Cell culture, 030220 oncology & carcinogenesis, Cancer research, Cyclin B1, education
Abstract

In this study, the antitumor activity of KHC-4 was analyzed using human prostate cancer (CaP) cells and the underlining anticancer mechanisms of KHC-4 were identified. KHC-4 inhibited cell proliferation and induced cytotoxicity in the castration-resistant CaP DU145 cell line. The most effective concentration of KHC-4 was 0.1 μM. Cell cycle analysis demonstrated that KHC-4 treatment caused G2/M arrest and a subsequent increase in the sub-G1 population. Furthermore, KHC-4 is up-regulated p21, p27, and p53 in a time- and concentration-dependent manner. The exposure of cells to KHC-4 induced Cdk1/cyclin B1 complex activity, which led to cell cycle arrest. Moreover, KHC-4 inhibited the activities of MMP-2 and MMP-9 to inhibit tumor cell metastasis. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1879-1887, 2016.

Published
2015

15. Combretastatin A-4 inhibits cell growth and metastasis in bladder cancer cells and retards tumour growth in a murine orthotopic bladder tumour model

Author

Jin-Yi Wu, Yi-Wen Liu, Jiann-Der Wu, Jia-Jen Shee, Yi-Wen Lin, and Cheng-Huang Shen

Subjects
Pharmacology, Combretastatin A-4, Combretastatin, Pathology, medicine.medical_specialty, Chemotherapy, Bladder cancer, medicine.medical_treatment, Cancer, Cell cycle, Biology, urologic and male genital diseases, medicine.disease, female genital diseases and pregnancy complications, Metastasis, chemistry.chemical_compound, chemistry, Cancer cell, medicine, Cancer research
Abstract

BACKGROUND AND PURPOSE Bladder cancer is a highly recurrent cancer after intravesical therapy, so new drugs are needed to treat this cancer. Hence, we investigated the anti-cancer activity of combretastatin A-4 (CA-4), an anti-tubulin agent, in human bladder cancer cells and in a murine orthotopic bladder tumour model.

Published
2010

16. The aggressiveness of urinary tract urothelial carcinoma increases with the severity of chronic kidney disease

Author

Cheng-Huang Shen, Kuan-Yu Hung, Ing-Ching Jong, Pei-Chun Chiang, Peir-Haur Hung, Yen-Ling Chiu, Tun-Jun Tsai, and Chang-Te Lin

Subjects
Male, Nephrology, Urologic Neoplasms, medicine.medical_specialty, Urology, Urinary system, Renal function, urologic and male genital diseases, Gastroenterology, End stage renal disease, chemistry.chemical_compound, Internal medicine, medicine, Humans, Aged, Creatinine, business.industry, Incidence (epidemiology), Retrospective cohort study, Middle Aged, medicine.disease, female genital diseases and pregnancy complications, Surgery, chemistry, Chronic Disease, Female, Kidney Diseases, Urothelium, Epidemiologic Methods, business, Glomerular Filtration Rate, Kidney disease
Abstract

OBJECTIVE To assess, in a retrospective cohort, urinary tract urothelial carcinoma (UT-UC) in patients with various stages of chronic kidney disease (CKD) and their clinicopathological features, as patients with end-stage renal disease (ESRD) have a higher incidence of UT-UC, but the relationship between early stages of CKD and characteristics of UT-UC are less well known. PATIENTS AND METHODS The study included 267 patients with pathologically confirmed UT-UC from January 1994 to December 2006; all had a physical examination (blood pressure), and measurements of laboratory data (serum creatinine, serum haemoglobin) and pathological data. The glomerular filtration rate (GFR) was calculated using the Modification of Diet in Renal Disease equation. Patients were divided into three groups by individual GFR (mL/min), i.e. >60 (no/mild CKD), 30–60 (CKD stage 3) and

Published
2009

17. Genetic polymorphism of sulfotransferase 1A1, cigarette smoking, hazardous chemical exposure and urothelial cancer risk in a Taiwanese population

Author

Guang-Dar Juang, Cheng-Huang Shen, Thomas I-Sheng Hwang, Hung Yi Chiou, Yuan-Hung Wang, and Ke-yun Shao

Subjects
medicine.medical_specialty, education.field_of_study, business.industry, Urology, Population, Odds ratio, Gastroenterology, Confidence interval, Toxicology, Chemical exposure, Age and gender, Cigarette smoking, Internal medicine, Genotype, Urothelial cancer, Medicine, business, education
Abstract

Objectives: To investigate the association between genetic polymorphism of sulfotransferase1A1 (SULT1A1), cigarette smoking, hazardous chemical exposure and urothelial cancer risk in a Taiwanese population. Methods: In a hospital-based case–control study, a total of 300 urothelial cancer (UC) cases and 300 cancer-free controls frequency-matched by age and gender were recruited from September 1998 to December 2005. The SULT1A1 arginine213histidine (Arg213His) polymorphism was genotyped using a polymerase chain reaction–restriction fragment length polymorphism method. Results: We found that the significantly increased UC risks of ever smokers and heavy smokers (≥28 pack-years) were 2.1 (95% confidence interval [CI] = 1.4–3.3) and 2.2 (95% CI = 1.3–3.6), respectively. An increased UC risk of 1.8 (95% CI = 0.8–3.8) was observed among individuals with more than one item of hazardous chemical exposure, but it was not statistically significant. Compared with study subjects carrying the SULT1A1 Arg/Arg genotype, those with SULT1A1 Arg/His or His/His genotypes have a significantly decreased UC risk (Odds ratio [OR] = 0.5, 95% CI = 0.3–0.8). Heavy smokers carrying the SULT1A1 Arg/Arg genotype have a significantly increased UC risk (OR = 5.2, 95% CI = 2.3–11.6). Individuals who had been exposed to more than one item of hazardous chemicals and who carried the SULT1A1 Arg/Arg genotype have a significantly increased UC risk (OR = 3.7, 95% CI = 1.4–9.7). The highest significant increased UC risk (OR = 16.1, 95% CI = 2.9–87.2) was observed among ever smokers with hazardous chemical exposure and the SULT1A1 Arg/Arg genotype. Conclusions: SULT1A1 Arg213His polymorphism is associated with the development of UC, especially among cigarette smokers exposed to hazardous chemicals.

Published
2008

19. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Author

Barcelona Supercomputing Center, Lesink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Shruthi, Viswanath, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Lee, Gyu R., Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, Joao P.G.L.M., Zundert, Gydo van, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xianjin, Xu, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Fernández-Recio, Juan, Joung, Jong Y., Kim, Jong Y., Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J., Barcelona Supercomputing Center, Lesink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Shruthi, Viswanath, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Lee, Gyu R., Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, Joao P.G.L.M., Zundert, Gydo van, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xianjin, Xu, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Fernández-Recio, Juan, Joung, Jong Y., Kim, Jong Y., Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, and Wodak, Shoshana J.

Abstract

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy., We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”, Peer Reviewed, Postprint (published version)

Published
2016

20. Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Author

Lensink, Marc F., primary, Velankar, Sameer, additional, Kryshtafovych, Andriy, additional, Huang, Shen‐You, additional, Schneidman‐Duhovny, Dina, additional, Sali, Andrej, additional, Segura, Joan, additional, Fernandez‐Fuentes, Narcis, additional, Viswanath, Shruthi, additional, Elber, Ron, additional, Grudinin, Sergei, additional, Popov, Petr, additional, Neveu, Emilie, additional, Lee, Hasup, additional, Baek, Minkyung, additional, Park, Sangwoo, additional, Heo, Lim, additional, Rie Lee, Gyu, additional, Seok, Chaok, additional, Qin, Sanbo, additional, Zhou, Huan‐Xiang, additional, Ritchie, David W., additional, Maigret, Bernard, additional, Devignes, Marie‐Dominique, additional, Ghoorah, Anisah, additional, Torchala, Mieczyslaw, additional, Chaleil, Raphaël A.G., additional, Bates, Paul A., additional, Ben‐Zeev, Efrat, additional, Eisenstein, Miriam, additional, Negi, Surendra S., additional, Weng, Zhiping, additional, Vreven, Thom, additional, Pierce, Brian G., additional, Borrman, Tyler M., additional, Yu, Jinchao, additional, Ochsenbein, Françoise, additional, Guerois, Raphaël, additional, Vangone, Anna, additional, Rodrigues, João P.G.L.M., additional, van Zundert, Gydo, additional, Nellen, Mehdi, additional, Xue, Li, additional, Karaca, Ezgi, additional, Melquiond, Adrien S.J., additional, Visscher, Koen, additional, Kastritis, Panagiotis L., additional, Bonvin, Alexandre M.J.J., additional, Xu, Xianjin, additional, Qiu, Liming, additional, Yan, Chengfei, additional, Li, Jilong, additional, Ma, Zhiwei, additional, Cheng, Jianlin, additional, Zou, Xiaoqin, additional, Shen, Yang, additional, Peterson, Lenna X., additional, Kim, Hyung‐Rae, additional, Roy, Amit, additional, Han, Xusi, additional, Esquivel‐Rodriguez, Juan, additional, Kihara, Daisuke, additional, Yu, Xiaofeng, additional, Bruce, Neil J., additional, Fuller, Jonathan C., additional, Wade, Rebecca C., additional, Anishchenko, Ivan, additional, Kundrotas, Petras J., additional, Vakser, Ilya A., additional, Imai, Kenichiro, additional, Yamada, Kazunori, additional, Oda, Toshiyuki, additional, Nakamura, Tsukasa, additional, Tomii, Kentaro, additional, Pallara, Chiara, additional, Romero‐Durana, Miguel, additional, Jiménez‐García, Brian, additional, Moal, Iain H., additional, Férnandez‐Recio, Juan, additional, Joung, Jong Young, additional, Kim, Jong Yun, additional, Joo, Keehyoung, additional, Lee, Jooyoung, additional, Kozakov, Dima, additional, Vajda, Sandor, additional, Mottarella, Scott, additional, Hall, David R., additional, Beglov, Dmitri, additional, Mamonov, Artem, additional, Xia, Bing, additional, Bohnuud, Tanggis, additional, Del Carpio, Carlos A., additional, Ichiishi, Eichiro, additional, Marze, Nicholas, additional, Kuroda, Daisuke, additional, Roy Burman, Shourya S., additional, Gray, Jeffrey J., additional, Chermak, Edrisse, additional, Cavallo, Luigi, additional, Oliva, Romina, additional, Tovchigrechko, Andrey, additional, and Wodak, Shoshana J., additional

Published
2016
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21. RAC1 regulate tumor necrosis factor-α-mediated impaired osteogenic differentiation of dental pulp stem cells

Author

Feng, Guijuan, primary, Shen, Qijie, additional, Lian, Min, additional, Gu, Zhifeng, additional, Xing, Jing, additional, Lu, Xiaohui, additional, Huang, Dan, additional, Li, Liren, additional, Huang, Shen, additional, Wang, Yi, additional, Zhang, Jinlong, additional, Shi, Jiahai, additional, Zhang, Dongmei, additional, and Feng, Xingmei, additional

Published
2015
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22. Blind prediction of interfacial water positions in CAPRI

Author

Barcelona Supercomputing Center, Lensink, Marc F., Moal, Iain H., Bates, Paul A., Kastritis, Panagiotis L., Melquiond, Adrien S.J., Karaca, Ezgi, Schmitz, Christophe, van Dijk, Marc, Bonvin, Alexandre M.J.J., Eisenstein, Miriam, Jiménez-Garcia, Brian, Grosdidier, Solène, Solernou, Albert, Pérez-Cano, Laura, Pallara, Chiara, Fernández-Recio, Juan, Xu, Jianqing, Muthu, Pravin, Kilambi, Krishna P., Gray, Jeffrey J., Grudinin, Sergei, Derevyanko, Georgy, Mitchell, Julie C., Wieting, John, Kanamori, Eiji, Tsuchiya, Yuko, Murakami, Yoichi, Sarmiento, Joy, Standley, Daron M., Shirota, Matsuyuki, Kinoshita, Kengo, Nakamura, Haruki, Chavent, Matthieu, Ritchie, David W., Park, Hahnbeom, Ko, Junsu, Lee, Hasup, Seok, Chaok, Shen, Yang, Kozakov, Dima, Vajda, Sandor, Kundrotas, Petras J., Vakser, Ilya A., Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Buch, Idit, Farkash, Efrat, Wolfson, Haim J., Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Shen-You, Zou, Xiaoqin, Wojdyla, Justyna A., Kleanthous, Colin, Wodak, Shoshana J., Barcelona Supercomputing Center, Lensink, Marc F., Moal, Iain H., Bates, Paul A., Kastritis, Panagiotis L., Melquiond, Adrien S.J., Karaca, Ezgi, Schmitz, Christophe, van Dijk, Marc, Bonvin, Alexandre M.J.J., Eisenstein, Miriam, Jiménez-Garcia, Brian, Grosdidier, Solène, Solernou, Albert, Pérez-Cano, Laura, Pallara, Chiara, Fernández-Recio, Juan, Xu, Jianqing, Muthu, Pravin, Kilambi, Krishna P., Gray, Jeffrey J., Grudinin, Sergei, Derevyanko, Georgy, Mitchell, Julie C., Wieting, John, Kanamori, Eiji, Tsuchiya, Yuko, Murakami, Yoichi, Sarmiento, Joy, Standley, Daron M., Shirota, Matsuyuki, Kinoshita, Kengo, Nakamura, Haruki, Chavent, Matthieu, Ritchie, David W., Park, Hahnbeom, Ko, Junsu, Lee, Hasup, Seok, Chaok, Shen, Yang, Kozakov, Dima, Vajda, Sandor, Kundrotas, Petras J., Vakser, Ilya A., Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Buch, Idit, Farkash, Efrat, Wolfson, Haim J., Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Shen-You, Zou, Xiaoqin, Wojdyla, Justyna A., Kleanthous, Colin, and Wodak, Shoshana J.

Abstract

This is the peer reviewed version of the following article: [Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jiménez-García, B., Grosdidier, S., Solernou, A., Pérez-Cano, L., Pallara, C., Fernández-Recio, J., Xu, J., Muthu, P., Praneeth Kilambi, K., Gray, J. J., Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H.-X., Huang, S.-Y., Zou, X., Wojdyla, J. A., Kleanthous, C. and Wodak, S. J. (2014), Blind prediction of interfacial water positions in CAPRI. Proteins, 82: 620–632. doi:10.1002/prot.24439], which has been published in final form at [Link to final article using the 10.1002/prot.24439]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving., We report the first assessment of blind predictions of water positions at protein–protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions—20 groups submitted a total of 195 models—were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models—a very good docking performance per se—only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 A °, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced highquality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein–water interactions and their role in stabilizing protein complexes., The Canadian Institutes for Health Research is gratefully acknowledged for support to SJW. MFL acknowledges financial support from the French Agence Nationale de Recherche (grant ANR-12-BSV5-0009-01, Fluctuations in Structured Coulomb Fluids). (Vakser): IAV and PJK are supported by NIH grant R01GM074255. CK acknowledges support for this work from the BBSRC (grant GG/G020671/1)., Peer Reviewed, Postprint (author's final draft)

Published
2014

23. Blind prediction of interfacial water positions in CAPRI

Author

Lensink, Marc F., primary, Moal, Iain H., additional, Bates, Paul A., additional, Kastritis, Panagiotis L., additional, Melquiond, Adrien S. J., additional, Karaca, Ezgi, additional, Schmitz, Christophe, additional, van Dijk, Marc, additional, Bonvin, Alexandre M. J. J., additional, Eisenstein, Miriam, additional, Jiménez‐García, Brian, additional, Grosdidier, Solène, additional, Solernou, Albert, additional, Pérez‐Cano, Laura, additional, Pallara, Chiara, additional, Fernández‐Recio, Juan, additional, Xu, Jianqing, additional, Muthu, Pravin, additional, Praneeth Kilambi, Krishna, additional, Gray, Jeffrey J., additional, Grudinin, Sergei, additional, Derevyanko, Georgy, additional, Mitchell, Julie C., additional, Wieting, John, additional, Kanamori, Eiji, additional, Tsuchiya, Yuko, additional, Murakami, Yoichi, additional, Sarmiento, Joy, additional, Standley, Daron M., additional, Shirota, Matsuyuki, additional, Kinoshita, Kengo, additional, Nakamura, Haruki, additional, Chavent, Matthieu, additional, Ritchie, David W., additional, Park, Hahnbeom, additional, Ko, Junsu, additional, Lee, Hasup, additional, Seok, Chaok, additional, Shen, Yang, additional, Kozakov, Dima, additional, Vajda, Sandor, additional, Kundrotas, Petras J., additional, Vakser, Ilya A., additional, Pierce, Brian G., additional, Hwang, Howook, additional, Vreven, Thom, additional, Weng, Zhiping, additional, Buch, Idit, additional, Farkash, Efrat, additional, Wolfson, Haim J., additional, Zacharias, Martin, additional, Qin, Sanbo, additional, Zhou, Huan‐Xiang, additional, Huang, Shen‐You, additional, Zou, Xiaoqin, additional, Wojdyla, Justyna A., additional, Kleanthous, Colin, additional, and Wodak, Shoshana J., additional

Published
2013
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25. Clinical implications of SOCS1 methylation in myelodysplastic syndrome

Author

Wu, Shang-Ju, primary, Yao, Ming, additional, Chou, Wen-Chien, additional, Tang, Jih-Luh, additional, Chen, Chien-Yuan, additional, Ko, Bo-Sheng, additional, Huang, Shen-Yi, additional, Tsay, Woei, additional, Chen, Yao-Chang, additional, Shen, Ming-Ching, additional, Wang, Chiu-Hwa, additional, Yeh, Yo-Chia, additional, and Tien, Hwei-Fang, additional

Published
2006
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