Download MendeleyDesign principles of the common Gly-X6-Gly membrane protein building block.
Golden, K., Avarvarei, C., Anderson, C.T., Holcomb, M., Tang, W., Dai, X., Zhang, M., Mailie, C.A., Sanchez, B.B., Chen, J.S., Forli, S., Mravic, M.(2025) Proc Natl Acad Sci U S A 122: e2503134122-e2503134122
- PubMed: 41055983 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1073/pnas.2503134122
- Primary Citation Related Structures:
8SRN - PubMed Abstract:
Protein behavior in lipids is poorly understood and inadequately represented in current computational models. Design and prediction abilities for bilayer-embedded molecular structures may be improved by characterizing membrane proteins' most frequent, favored structural features to glean both context-specific and general principles. We used protein design to proactively interrogate the sequence-structure relationship and stabilizing atomic details of two highly prevalent antiparallel transmembrane (TM) motifs with Small-X 6 -Small consensus sequences. A fragment-based data-mining and sequence statistical inference method including cross-evolutionary structure-aligned covariance enabled engineering of de novo TM protein assemblies by successfully encoding Gly-X6-Gly and Ala-X6-Ala building blocks. A highly stable glycine-based design's X-ray structure hosts Cα-H∙∙∙O = C H-bonding alongside extensive backbone-directed van der Waals packing, idealizing features of this motif in Nature. Data-driven design navigates sequence space to directly inquire upon how to encode and stabilize vital membrane protein structural elements, facilitating efficacious construction of lipid-embedded architectures of increasing complexity.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.
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