Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins

Area of Science:

• Molecular biology
• Evolutionary biology
• Biochemistry

Background:

• Molecular sites can perform general or specific functions, exhibiting different evolutionary variabilities.
• Functional density quantifies sites with specific roles, while weighted functional density considers variability at these sites to infer interaction specificity.

Purpose of the Study:

• To analyze the distinction between general and specific molecular functional sites.
• To explore the relationship between functional site types, evolutionary variability, and protein evolution.
• To evaluate weighted functional density as a measure of interaction specificity.

Main Methods:

• Analysis of evolutionary variability in molecular sites.
• Definition and application of functional density and weighted functional density.
• Discussion of the relationship between site functions, covarions, and amino acid degeneracy.

Main Results:

• Proteins lacking general-function sites alongside specific ones may exhibit "frozen" primary structures due to decreased site variability.
• Functional "degeneracy" of amino acids increases interdependence among general functions.

Conclusions:

• Weighted functional density is a partial indicator of interaction specificity, limited when values approach unity.
• The interplay between general and specific functional sites significantly influences protein evolution and structural stability.