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

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

Srinivasulu Yerukala Sathipati  1 , Ming-Ju Tsai  2 , Tonia Carter  3 , Sanjay K Shukla  3 , Shinn-Ying Ho  4
Affiliations

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

Srinivasulu Yerukala Sathipati et al. STAR Protoc. .

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.

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Conflict of interest statement

The authors declare competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Screenshots showing spike protein data acquisition from databases (A and B) (A) Displaying SARS-CoV-2 data from GISAID and (B) NCBI databases. An example of amino acid sequence in FASTA format.
Figure 2
Figure 2
The steps involved in feature selection algorithm
Figure 3
Figure 3
The comparison of physicochemical property (AAindex ID: RACS820104) between spike proteins of human and animal host coronaviruses The ID RACS820104 represents the average relative fractional occurrence in EL(i).
Figure 4
Figure 4
The comparison of amino acid compositions between spike proteins of human and animal host coronaviruses
Figure 5
Figure 5
Spike glycoprotein complex Spike glycoprotein (PDB: 6ACJ, EM 4.2 Angstrom) in complex with ACE2 (green ribbon) showing the amino acid changes that occurred between Rousettus bat coronavirus (GenBank: AOG30822.1) and hCoV/Wuhan/WIV05/2019. The mutations in different strains are shown as colored balls.
Figure 6
Figure 6
Secondary structure and surface hydrophobicity of spike protein 6VXX
See this image and copyright information in PMC

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