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PreprintCited by 6Machine Learning in BioinformaticsProtein Structure and DynamicsEnzyme Catalysis and Immobilization

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HaloClass: Salt-Tolerant Protein Classification with Protein Language Models

Open access
Narang, Kush, Nath, Abhigyan, Hemstrom, William, Chu, Simon K. S.·2024·The Protein Journal
DOI 10.21203/rs.3.rs-5027369/v1PMC PMC11543744

Preprint — published as 10.1007/s10930-024-10236-7 · Paper page

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Abstract

Salt-tolerant proteins, also known as halophilic proteins, have unique adaptations to function in high-salinity environments. These proteins have naturally evolved in extremophilic organisms, and more recently, are being increasingly applied as enzymes in industrial processes. Due to an abundance of salt-tolerant sequences and a simultaneous lack of experimental structures, most computational methods to predict stability are sequence-based only. These approaches, however, are hindered by a lack of structural understanding of these proteins. Here, we present HaloClass, an SVM classifier that leverages ESM-2 protein language model embeddings to accurately identify salt-tolerant proteins. On a newer and larger test dataset, HaloClass outperforms existing approaches when predicting the stability of never-before-seen proteins that are distal to its training set. Finally, on a mutation study that evaluated changes in salt tolerance based on single- and multiple-point mutants, HaloClass outperforms existing approaches, suggesting applications in the guided design of salt-tolerant enzymes.

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Fig. 1 Structural comparison of homologous salt-tolerant and non-tolerant proteins. Salt-tolerant structures are shown in green and non-tolerant structures are in orange. In panel A, all eight homologous pairs analyzed from Siglioccolo et al. [19] are superimposed. In panel B, a helix from two catalase-peroxidases is highlighted (salt-tolerant: 1ITK; non-tolerant: 2FXG)
Fig. 1 Structural comparison of homologous salt-tolerant and non-tolerant proteins. Salt-tolerant structures are shown in green and non-tolerant structures are in orange. In panel A, all eight homologous pairs analyzed from Siglioccolo et al. [19] are superimposed. In panel B, a helix from two catalase-peroxidases is highlighted (salt-tolerant: 1ITK; non-tolerant: 2FXG)CC BY · PubMed Central
Fig. 2 Models for the wild-type and a mutant of the salt-tolerant DNA ligase N. The figure shows superimposed AlphaFold 3 structures for the DNA ligase N from Haloferax volcanii. The wild-type is in light blue, and the mutant type with 8 aspartic acids mutated to glutamic acids is in dark blue; mutated side-chains are displayed. The structures have an RMSD of 0.62Å
Fig. 2 Models for the wild-type and a mutant of the salt-tolerant DNA ligase N. The figure shows superimposed AlphaFold 3 structures for the DNA ligase N from Haloferax volcanii. The wild-type is in light blue, and the mutant type with 8 aspartic acids mutated to glutamic acids is in dark blue; mutated side-chains are displayed. The structures have an RMSD of 0.62ÅCC BY · PubMed Central

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Metadata

Authors
Narang, K., Nath, A., Hemstrom, W., & Chu, S. K. S.
Affiliations
  • University of California, Davis (US)
  • Pt. Jawahar Lal Nehru Memorial Medical College (IN)
  • Purdue University West Lafayette (US)
Corresponding author
Narang, Kush
ORCID
Venue
The Protein Journal
Publisher
Springer Science and Business Media LLC
Published
2024-10-10
Volume
43
Issue
6
Pages
1035-1044
ISSN
1572-3887 (ISSN-L)
DOI
10.21203/rs.3.rs-5027369/v1
PMC
PMC11543744
OpenAlex
W4403605087
Cited by
6
References
1
Citations by year
2026: 4 · 2025: 2
FWCI
0.81
Type
journal article
Language
en
Open access
Licence
Locations
  • The Protein Journal (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
Keywords
halophilic proteins, protein stability prediction, protein language models, ESM-2 embeddings, protein classification, support vector classifier, protein mutations, enzyme design, extremophiles
MeSH terms
Models, Molecular, Proteins, Computational Biology, Databases, Protein, Salt Tolerance, Support Vector Machine

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