FireProt: web server for automated design of thermostable proteins

Abstract

There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot.

Creating Flavin Reductase Variants with Thermostable and Solvent‐Tolerant Properties by Rational‐Design Engineering

“…We used two computational calculation programs—FireProt and FRESCO—to predict stable C 1 variants. The X‐ray structure of the WT C 1 (PDB ID: 5ZYR) was processed with the FireProt program to predict stable variants through a combination of energy‐ and evolution‐based computational approaches .…”

“…We used two computational calculation programs—FireProt and FRESCO—to predict stable C 1 variants. The X‐ray structure of the WT C 1 (PDB ID: 5ZYR) was processed with the FireProt program to predict stable variants through a combination of energy‐ and evolution‐based computational approaches . FireProt uses two protein engineering tools, FoldX and Rosetta, to compute the differences in folding free energy change (ΔΔ G fold ) of the WT (Δ G fold,WT ) and variant (Δ G fold,variant ) so as to evaluate the folding stability of each variant.…”

“…FireProt uses two protein engineering tools, FoldX and Rosetta, to compute the differences in folding free energy change (ΔΔ G fold ) of the WT (Δ G fold,WT ) and variant (Δ G fold,variant ) so as to evaluate the folding stability of each variant. ΔΔ G fold values of less than −1 kcal mol −1 were used to identify the stable variants . From the ΔΔ G fold values, 15 single‐point mutations were predicted as stable candidate variants.…”

“…In silico methods for design of C 1 variants : The thermostable C 1 variants were predicted by using two computational programs: FireProt and FRESCO . The dimeric structure of C 1 WT (PDB ID: 5ZYR) was processed with the aid of the FireProt program, which uses FoldX and Rosetta tools for calculation of the ΔΔ G fold values that indicate folding stability.…”

A novel peptide analogue of spike glycoprotein shows antiviral properties against SARS-CoV-2

“…Among the interacting amino acid residues of RBD, only ASN487 is found to be conserved ( Figure S3). The energy mutant model of the RBD is constructed based on thermodynamically favorable alteration between amino acids, which is based on FoldX and Rosetta (Musil et al, 2017). The combined mutant model is constructed rstly by the automated incorporation of suggested amino acid residues from energy mutant and evolutionary mutants (Table 2).…”