Structural Bioinformatics Studies of Integral Transmembrane Enzymes pMMO Complex, C560, CYB, and DHSD and their AlphaFold3-Predicted Water-Soluble QTY Variants
Name
Structural_Bioinformatics_Studies_of_Integral_Transmembrane_Enzymes_pMMO_Complex,_C560,_CYB,_and_DHS.pdf
Size
3.93 MB
Format
Adobe PDF
Checksum (MD5)
0a7b54dc442e1f772c89395d1f7128bb
Author(s)
Wang, Jiayu
Pan, Emily
Zhang, Shuguang
Date Issued
January 2025
Journal
BioCosmos
Publisher
Walter de Gruyter GmbH
Citation
Wang, Jiayu, et al. "Structural Bioinformatics Studies of Integral Transmembrane Enzymes pMMO Complex, C560, CYB, and DHSD and their AlphaFold3-Predicted Water-Soluble QTY Variants." BioCosmos, vol. 4, no. 1, The Israel Biocomplexity Center, 2024, pp. 79-89.
Version
Final published version
Abstract
The QTY (glutamine, threonine, tyrosine) code is a simple protein engineering and design tool that systematically replaces the hydrophobic amino acids leucine (L), isoleucine (I), valine (V), and phenylalanine (F) into the hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y), respectively, to enable the water-solubility of membrane proteins including membrane enzymes. In this study, we present the structural bioinformatics study of six membrane protein enzymes with experimentally determined CryoEM structures including the methane monooxygenase pMMO complex (pMOA, pMOB, pMOC), CYB, C560, DHSD, and their AlphaFold3-predicted water-soluble QTY variants. We applied the QTY code only to the transmembrane alpha-helices of the proteins. We then superposed structures of CryoEM-determined native proteins with their water-soluble QTY variants. The QTY code engineered water-soluble QTY variants demonstrate remarkable structural similarity with their native structures, with RMSD (Root Mean Square Deviation) values between 0.506Å and 0.887Å despite significant (33.33-86.61%) changes to the protein sequence of the transmembrane domains. To verify the effectiveness of our study, we show the changes in hydrophobicity surfaces between the native proteins and their QTY variants, and explain the rationale behind such change. Our structural bioinformatics studies provide key insight into differences between the hydrophobic alpha-helices and alpha-hydrophilic helices. The QTY code will likely further aid the future applications of methane oxidation enzymes. The water-soluble QTY variants could aid in studying and utilization of the enzymes in aqueous environments without detergent solubilization and stabilization. These QTY variant membrane enzymes may be particularly useful for future industrial-scale production in aqueous chassis such as filamentous algae.
Subjects
Alpha-helix, amino acid structural similarities
hydrophobic to hydrophilic conversion
membrane proteins
methane monooxygenase, QTY code
MIT Department
Massachusetts Institute of Technology. Media Laboratory
Terms of Use
Creative Commons Attribution-NonCommercial-NoDerivatives
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.2478/biocosmos-2024-0006
