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Updated: Jun 13, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
TMB Stab-pred: Predicting the stability of transmembrane β-barrel proteins using their sequence and structural
P Ramakrishna Reddy1, A Kulandaisamy1, M Michael Gromiha1
1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
None:
Understanding the folding and stability of transmembrane β-barrel proteins (TMBs) provides insights into their structural integrity, functional mechanisms, and implications for disease states. In this work, we have characterized the important features that influence the folding and stability of TMBs. Our results showed that lipid accessible surface area and transition energy are important for understanding the stability of TMBs. Further, this information was utilized to develop a linear regression-based method for predicting the stability of TMBs. Our method achieved a correlation and mean absolute error (MAE) of 0.96 and 0.94 kcal/mol on the jack-knife test. Moreover, we compared the stability of TMBs with globular all-β proteins and observed that long-range interactions and energetic properties are crucial for maintaining the stability of both β-barrel membrane and all-β globular proteins. On the other hand, side-chain - side-chain hydrogen bonds and lipid accessible surface area are specific to membrane proteins. These features are critical for membrane proteins because they influence a protein to embed within the membrane environment. Further, we have developed a web server, TMB Stab-pred for predicting the stability of TMBs, and it is accessible at https://web.iitm.ac.in/bioinfo2/TMBB/index.html.
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