A Mathematical Framework for Protein Structure Comparison

Comparison of protein structures is important for revealing the evolutionary relationship among proteins, predicting protein functions and predicting protein structures. Many methods have been developed in the past to align two or multiple protein structures. Despite the importance of this problem, rigorous mathematical or statistical frameworks have seldom been pursued for general protein structure comparison. One notable issue in this field is that with many different distances used to measure the similarity between protein structures, none of them are proper distances when protein structures of different sequences are compared. Statistical approaches based on those non-proper distances or similarity scores as random variables are thus not mathematically rigorous. In this work, we develop a mathematical framework for protein structure comparison by treating protein structures as three-dimensional curves. Using an elastic Riemannian metric on spaces of curves, geodesic distance, a proper distance on spaces of curves, can be computed for any two protein structures. In this framework, protein structures can be treated as random variables on the shape manifold, and means and covariance can be computed for populations of protein structures. Furthermore, these moments can be used to build Gaussian-type probability distributions of protein structures for use in hypothesis testing. The covariance of a population of protein structures can reveal the population-specific variations and be helpful in improving structure classification. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions. We show that our method performs comparably with commonly used methods in protein structure classification on a large manually annotated data set. Author Summary: Protein structure comparison is important for understanding the evolutionary relationships among proteins, predicting protein functions, and predicting protein structures. Despite its importance, there have been no rigorous mathematical or statistical frameworks for protein structure comparison. One notable issue in this field is that with many different similarity measures used in comparing protein structures, none of them are proper distances when protein structures of different sequences are compared. In this study, we develop a mathematical framework for protein structure comparison by treating protein structures as three dimensional curves. A formal distance, geodesic distance, can be computed for any two protein structures. In this framework, population-specific variations within protein families can be characterized through building probability distributions for structures of protein families. The mean and covariance computed from groups of protein structures can also help to improve the classifications of protein structures. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions.