SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

Srinivasulu Yerukala Sathipati; Ming-Ju Tsai; Tonia Carter; Sanjay K Shukla; Shinn-Ying Ho

doi:10.1016/j.xpro.2022.101460

SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

STAR Protoc. 2022 May 24;3(3):101460. doi: 10.1016/j.xpro.2022.101460. eCollection 2022 Sep 16.

Authors

Srinivasulu Yerukala Sathipati¹, Ming-Ju Tsai², Tonia Carter³, Sanjay K Shukla³, Shinn-Ying Ho⁴

Affiliations

¹ Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA. Electronic address: sathipathi.srinivasulu@marshfieldclinic.org.
² Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
³ Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
⁴ Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Center for intelligent Drug Systems and Smart Bio-Devices (IDS(2)B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan; College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.

Abstract

We describe a protocol to identify physicochemical properties using amino acid sequences of spike (S) proteins of SARS-CoV-2. We present an S protein prediction technique named SPIKES, incorporating an inheritable bi-objective combinatorial genetic algorithm to determine the host species specificity. This protocol addresses the S protein amino acid sequence data collection, preprocessing, methodology, and analysis. For complete details on the use and execution of this protocol, please refer to Yerukala Sathipati et al. (2022).

Keywords: Bioinformatics; Microbiology; Proteomics; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Host Specificity
SARS-CoV-2* / genetics
Spike Glycoprotein, Coronavirus* / genetics

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2