Binding Site Vectors Enable Mapping of Cytochrome P450 Functional Landscapes

Area of Science:

• Biochemistry
• Computational Biology
• Structural Biology

Background:

• Comparing protein binding sites is crucial for understanding function, but challenging due to inconsistent definitions and descriptor limitations.
• Existing methods often fail to capture the full complexity of binding site dynamics and interactions.

Purpose of the Study:

• To introduce a novel computational framework, binding site vectors, for high-resolution comparison of macromolecular binding sites.
• To demonstrate the utility of binding site vectors in revealing functional relationships, particularly within the cytochrome P450 enzyme family.

Main Methods:

• Developed binding site vectors integrating structural and electrostatic properties, extending spherically from the pocket center.
• Applied the framework to over 600 human and plant cytochrome P450 structures and 23 molecular dynamics simulation ensembles.
• Utilized geometric anchoring for systematic comparison across diverse macromolecular systems.

Main Results:

• Binding site vectors capture shape and electrostatic features multidimensionally.
• Comparisons revealed structural-functional relationships missed by sequence or backbone analyses.
• Incorporating conformational ensembles enhanced the detection of subtle functional distinctions in cytochrome P450 enzymes.

Conclusions:

• Binding site vectors offer a robust computational framework for comparing macromolecular binding sites.
• This method provides deeper mechanistic insights and supports functional classification of complex biological systems.
• The approach is particularly valuable for dynamic systems like cytochrome P450 enzymes.