Investigations on C-H...pi interactions in RNA binding proteins

Area of Science:

• Structural Biology
• Biochemistry
• Computational Biology

Background:

• RNA binding proteins play vital roles in cellular processes.
• Non-covalent interactions significantly influence protein structure and function.
• C-H···π interactions are increasingly recognized for their role in molecular recognition.

Purpose of the Study:

• To investigate the prevalence and characteristics of C-H···π interactions in RNA binding proteins.
• To identify the specific amino acid residues involved in these interactions.
• To understand the contribution of C-H···π interactions to protein stability and conservation.

Main Methods:

• Analysis of crystal structures of 59 RNA binding proteins.
• Identification and quantification of C-H···π interactions using computational tools.
• Secondary structure preference analysis and conservation score assessment of interacting residues.

Main Results:

• An average of 55 C-H···π interactions per protein were observed, with one significant interaction per nine residues.
• Main-chain to side-chain C-H···π interactions were predominant, with Phe, Tyr, and Trp residues frequently involved as donors and acceptors.
• Long-range interactions were common, and over 50% of interacting residues showed high conservation and stabilization centers.

Conclusions:

• C-H···π interactions are a significant stabilizing force in RNA binding proteins.
• Specific aromatic and other residues play key roles in mediating these interactions.
• These interactions contribute to the evolutionary conservation and stability of RNA binding proteins.