Increasing the stability of the bacteriophage endolysin PlyC using rationale-based FoldX computational modeling.
Endolysins are bacteriophage-derived peptidoglycan hydrolases that represent an emerging class of proteinaceous therapeutics. While the streptococcal endolysin PlyC has been validated in vitro and in vivo for its therapeutic efficacy, the inherent thermosusceptible structure of the enzyme correlates to transient long-term stability, thereby hindering the feasibility of developing the enzyme as an antimicrobial. Here, we thermostabilized the cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain of the PlyCA catalytic subunit of PlyC using a FoldX-driven computational protein engineering approach. Using a combination of FoldX and Rosetta algorithms, as well as visual inspection, a final list of PlyC point mutant candidates with predicted stabilizing ΔΔG values was assembled and thermally characterized. Five of the eight point mutations were found experimentally to be destabilizing, a result most likely attributable to computationally modeling a complex and dynamic nine-subunit holoenzyme with a corresponding 3.3-Å X-ray crystal structure. However, one of the mutants, PlyC (PlyCA) T406R, was shown experimentally to increase the thermal denaturation temperature by ∼2.2°C and kinetic stability 16-fold over wild type. This mutation is expected to introduce a thermally advantageous hydrogen bond between the Q106 side chain of the N-terminal glycosyl hydrolase domain and the R406 side chain of the C-terminal CHAP domain.
Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
Ryan D
RD
Heselpoth
Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA.
Yizhou
Y
Yin
Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA Department of Cell Biology and Molecular Genetics, University of Maryland, 1109 Microbiology Building, College Park, MD 20742, USA.
John
J
Moult
Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA Department of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD 20742, USA nelsond@umd.edu.
Daniel C
DC
Nelson
D000465:Algorithms; D000581:Amidohydrolases / Q000737:chemistry / Q000235:genetics; D001435:Bacteriophages / Q000737:chemistry* / Q000235:genetics; D019295:Computational Biology; D018360:Crystallography, X-Ray; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics; D004795:Enzyme Stability / Q000235:genetics; D006639:Histidine / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D017354:Point Mutation; D015202:Protein Engineering; D014764:Viral Proteins / Q000737:chemistry*
D014764:Viral Proteins; D006639:Histidine; D010450:Endopeptidases; C001143:endolysin; D000581:Amidohydrolases
FoldX; antimicrobial; bacteriophage; endolysin; thermal stability