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Prediction of Hot Spots in Dimer Interface of Green Fluorescent Protein

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Advances in Applied Biotechnology (ICAB 2016)

Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 444))

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Abstract

Wild-type green fluorescent protein (GFP) has a weak dimerization tendency at higher concentrations. Currently there are still a limited number of known mutated residues for the dimer interface breaking. The crystal structure of the dimer provides vital background on neighbouring residue interactions. Here well-established hot spot prediction methods, such as HotPoint, KFC2, PredHS and Robetta, were adopted to predict residues critical for dimer stabilization, i.e. hot spots. Among 17 residues appeared on the dimer interface of GFP, 10 residues were predicted as hot spots by at least one method. Some of these computational hot spots were verified with existing site-directed mutagenesis results, and the remains of the predicted residues can be candidates for further validation. Furthermore, the structural feature such as relative accessibility was found significantly different between computational hot spots and non-hot spots.

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Acknowledgements

This work was sponsored by the Natural Science Foundation of China (31370075 and 61603273), Tianjin Research Program of Application Foundation and Advanced Technology (14JCQNJC00300 and 16JCYBJC18500), Tianjin University of Science and Technology (2014CXLG28), and Tianjin Foreign Studies University (13QN15).

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Authors and Affiliations

  1. Faculty of Fundamental Courses, Tianjin Foreign Studies University, Tianjin, 300204, People’s Republic of China

    Wenjuan Zhang

  2. School of Computer Science and Information Engineering, Tianjin University of Science and Technology, Tianjin, 300457, People’s Republic of China

    Lin Wang & Zhiwei Sun

  3. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People’s Republic of China

    Bianqiang Zhang, Qiaoqiao Tang & Qiang Gao

Authors
  1. Wenjuan Zhang
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  2. Lin Wang
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  3. Zhiwei Sun
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  4. Bianqiang Zhang
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  5. Qiaoqiao Tang
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  6. Qiang Gao
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Corresponding author

Correspondence to Lin Wang .

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Editors and Affiliations

  1. College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China

    Hao Liu

  2. College of Life Sciences, Nankai University, Tianjin, China

    Cunjiang Song

  3. Institute of Biology Leiden, Leiden University, Leiden, The Netherlands

    Arthur Ram

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© 2018 Springer Nature Singapore Pte Ltd.

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Zhang, W., Wang, L., Sun, Z., Zhang, B., Tang, Q., Gao, Q. (2018). Prediction of Hot Spots in Dimer Interface of Green Fluorescent Protein. In: Liu, H., Song, C., Ram, A. (eds) Advances in Applied Biotechnology. ICAB 2016. Lecture Notes in Electrical Engineering, vol 444. Springer, Singapore. https://doi.org/10.1007/978-981-10-4801-2_35

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