High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function

Area of Science:

• Evolutionary Biology
• Biochemistry
• Computational Biology

Background:

• Ancestral protein sequence reconstruction (APSR) offers insights into molecular function evolution.
• Current methods are limited by time-consuming lab analyses for structure and function characterization.
• Lack of unbiased data on molecular function evolution across large protein families.

Purpose of the Study:

• To develop a generalized computational protocol for analyzing historical changes in protein function across large protein families.
• To integrate ancestral sequence reconstruction with structural homology modeling and affinity prediction.
• To provide a scalable and computationally efficient approach to complement laboratory-intensive studies.

Main Methods:

• Integration of APSR with structural homology modeling.
• Application of structure-based molecular affinity prediction.
• Development of computationally efficient subroutines for scalability.

Main Results:

• The protocol enables characterization of historical protein function changes in large families.
• Identified key steps to avoid errors and optimize computational efficiency.
• Demonstrated a method to scale analysis based on available resources.

Conclusions:

• The developed protocol provides a powerful computational complement to laboratory methods.
• Generates valuable contextual information to guide experimental research.
• Facilitates a deeper understanding of molecular function evolution across diverse protein families.