KERA

KERA analyzes time-series single-molecule fluorescence data to resolve kinetic events, enumerate interaction sequences, and quantify dwell times of molecular interactions.

Key Features:

• Discrete-state data processing: Processes discretized fluorescent trajectories derived from single-molecule experiments.
• Microscopy compatibility: Operates on data originating from colocalization single-molecule spectroscopy (CoSMoS) and total internal reflection fluorescence microscopy (TIRFM).
• Trajectory organization: Organizes and sorts discretized fluorescent trajectories into groups based on transition patterns.
• Transition pattern categorization: Categorizes data into groups defined by specific state-to-state transition sequences.
• Dwell-time extraction: Provides exhaustive dwell-time information for each interaction sequence.
• Multi-channel fluorescence analysis: Analyzes changes in fluorescence behavior across multiple channels to track temporal relationships between components.
• Sequence enumeration and quantification: Enumerates and quantifies sequences of molecular interactions to characterize assembly and reorganization events.
• Higher-order complex analysis: Supports inference of ternary, quaternary, and higher-order complex formation and reorganization from ordered appearance data.

Scientific Applications:

• Dynamic interaction analysis: Characterizes transient associations between labeled molecules and surface-tethered partners to study molecular interaction kinetics.
• Complex assembly studies: Determines the order of appearance and reorganization of components in the formation of ternary, quaternary, or higher-order complexes.
• Conformational dynamics: Analyzes conformational dynamics of DNA-binding proteins, exemplified by RPA and XPD helicase.
• Kinetic mechanism inference: Provides dwell-time distributions and sequence counts to support mechanistic interpretation of macromolecular assembly and disassembly.

Methodology:

Organizes and sorts discretized fluorescent trajectories, categorizes trajectories by transition patterns, computes exhaustive dwell times for each interaction sequence, analyzes multi-channel fluorescence changes to track time evolution and spatial/temporal organization, and enumerates and quantifies interaction sequences.