PDF《ProtDataTherm: A database for》

RESEARCH ARTICLE ProtDataTherm: A database for thermostability analysis and engineering of proteins Hassan Pezeshgi Modarres1,2,3 , Mohammad R.

Mofrad2,4 , Amir Sanati-Nezhad1,5 *

1 BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta, Canada,

2 Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, 208A Stanley Hall, Berkeley, CA, United States of America,

3 School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran,

4 Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, United States of America,

5 Center for BioEngineering Research and Education, University of Calgary, Alberta, Canada * [email protected] Abstract Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications. For efficient protein thermostability engineering, different thermostability-classified data sources including sequences and 3D structures are needed for different protein families. However, no data source is available providing such data easily. It is the first release of ProtDataTherm data- base for analysis and engineering of protein thermostability which contains more than

14 million protein sequences categorized based on their thermal stability and protein family. This database contains data needed for better understanding protein thermostability and stability engineering. Providing categorized protein sequences and structures as psychro- philic, mesophilic and thermophilic makes this database useful for the development of new tools in protein stability prediction. This database is available at http://profiles.bs.ipm.ir/ softwares/protdatatherm. As a proof of concept, the thermostability that improves mutations were suggested for one sample protein belonging to one of protein families with more than

20 mesophilic and thermophilic sequences and with known experimentally measured ΔT of mutations available within ProTherm database. Introduction Thermophilic and hyper thermophilic microorganisms have become attractive to scientists specifically after reporting the microorganisms living at temperatures higher than 75?C (1). The extracted enzymes from such high temperature tolerating microorganisms have been studied to understand modulating factors of their improved thermostability and then to use it as a guidance for improving thermostability of proteins with lower thermal stability for bio- technological applications [1]. The knowledge about the preferred living temperature of PLOS ONE | https://doi.org/10.1371/journal.pone.0191222 January 29,

2018 1 /

9 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Pezeshgi Modarres H, Mofrad MR, Sanati-Nezhad A (2018) ProtDataTherm: A database for thermostability analysis and engineering of proteins. PLoS ONE 13(1): e0191222. https://doi.org/10.1371/journal. pone.0191222 Editor: Eugene A. Permyakov, Russian Academy of Medical Sciences, RUSSIAN FEDERATION Received: May 10,

2017 Accepted: December 29,

2017 Published: January 29,

2018 Copyright: ?

2018 Pezeshgi Modarres et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper. Funding: This work is supported in part by a grant from the Institute for Research in Fundamental Sciences (IPM), Tehran, Iran (grant number: BS- 1394-01-14), and The Natural Sciences and Engineering Research Council of Canada (NSERC) to Amir Sanati Nezhad. http://www.ipm.ac.ir/;