Investigating Local Sequence-Structural Attributes of Amyloidogenic Light Chain Variable Domains

Puneet Rawat; R Prabakaran; Divya Sharma; Vasanth Mandala; Victor Greiff; Sandeep Kumar; M Michael Gromiha

doi:10.1002/prot.26815

Investigating Local Sequence-Structural Attributes of Amyloidogenic Light Chain Variable Domains

Proteins. 2025 Mar 4. doi: 10.1002/prot.26815. Online ahead of print.

Authors

Puneet Rawat^{1

2}, R Prabakaran^{2

3}, Divya Sharma², Vasanth Mandala⁴, Victor Greiff^{1

5}, Sandeep Kumar⁴, M Michael Gromiha^{2

6}

Affiliations

¹ University of Oslo and Oslo University Hospital, Oslo, Norway.
² Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
³ Department of Biology, Emory University, Atlanta, Georgia, USA.
⁴ Biotherapeutics Discovery, Boehringer-Ingelheim Inc, Ridgefield, Connecticut, USA.
⁵ Imprint Labs, LLC, New York, New York, USA.
⁶ International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama, Japan.

PMID: 40034034
DOI: 10.1002/prot.26815

Abstract

Light chain amyloidosis is a medical condition characterized by the aggregation of misfolded antibody light chains into insoluble amyloid fibrils in the target organs, causing organ dysfunction, organ failure, and death. Despite extensive research to understand the factors contributing to amyloidogenesis, accurately predicting whether a given protein will form amyloids under specific conditions remains a formidable challenge. In this study, we have conducted a comprehensive analysis to understand the amyloidogenic tendencies within a dataset containing 1828 (348 amyloidogenic and 1480 non-amyloidogenic) antibody light chain variable region (V_L) sequences obtained from the AL-Base database. Physicochemical and structural features often associated with protein aggregation, such as net charge, isoelectric point (pI), and solvent-exposed hydrophobic regions did not reveal a consistent association with the aggregation capability of the antibody light chains. However, the solvent-exposed aggregation-prone regions (APRs) occur with higher frequencies among the amyloidogenic light chains when compared with the non-amyloidogenic ones, with the difference ranging from 2% to 15% at various relative solvent-accessible surface area (rASA) cutoffs. We have, for the first time, identified structural gatekeeping residues around the APRs and assessed their impact on the amyloidogenicity of the antibody light chains. The non-amyloidogenic light chains contain these structural gatekeeper residues vicinal to their APRs more often than the amyloidogenic ones. We observed that the rASA cutoff of 35% is optimal for identifying the surface-exposed APRs, and a 4 Å distance cutoff from the APR motif(s) is optimal for identifying the structural gatekeeper residues. Moreover, lambda light chains were found to contain solvent-exposed APRs more often and surrounded by fewer gatekeepers, rendering them more susceptible to aggregation. The insights gained from this report have significant implications for understanding the molecular origins of light-chain amyloidosis in humans and the design of aggregation-resistant therapeutic antibodies.

Keywords: AL amyloidosis; aggregation‐prone regions; amyloid; antibody aggregation; antibody structure; light chain amyloidosis; structural gatekeepers.

Abstract

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