NGOME-Lite

NGOME-Lite predicts spontaneous asparagine deamidation rates and estimates protein half-lives from amino acid sequences to analyze protein stability, deamidation dynamics, and turnover across taxa.

Key Features:

• Sequence-Based Prediction: Uses sequence-based methods to predict spontaneous asparagine deamidation by accounting for intrinsic sequence propensities and local structural influences on deamidation rate.
• Speed and Efficiency: Operates over two orders of magnitude faster than existing algorithms while maintaining comparable accuracy for large-scale analyses.
• Proteomic Analysis Mode: Provides half-life estimates for intact proteins using either sequence propensities alone or combined sequence propensities and structural protection factors.
• Cross-Taxa Application: Applied to over 257,000 sequences across 38 proteomes, revealing more rapid spontaneous deamidation in Eukarya than in Bacteria attributable to differing structural protection.
• Correlation with Protein Turnover: Predictions correlate with protein turnover rates in humans, mice, rats, C. elegans, and budding yeast, but not consistently in certain plants and bacteria.

Scientific Applications:

• Large-scale proteomic analyses: Enables proteome-wide assessment of deamidation dynamics and half-life estimation without requiring structural data in sequence-only mode.
• Protein stability and function studies: Supports investigation of protein stability, function, and degradation by providing deamidation rates and half-life estimates.
• Comparative evolutionary analyses: Facilitates comparison of deamidation dynamics and structural protection across taxa to study evolutionary differences in protein maintenance.

Methodology:

Employs a sequence-based approach that accounts for intrinsic sequence propensities and local structural influences on deamidation rates and predicts protein half-lives by considering sequence-driven factors and structural protection mechanisms.