Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• Aptamers are synthetic nucleic acids with high affinity and specificity for diverse targets.
• Their protein-binding capabilities make them valuable tools in science, comparable to antibodies.
• Understanding protein-aptamer interactions is crucial for developing novel applications.

Purpose of the Study:

• To review the structural aspects of protein-aptamer recognition.
• To analyze the architectures and binding mechanisms of protein-aptamer complexes.
• To highlight the impact of cryo-electron microscopy (cryo-EM) on structural studies.

Main Methods:

• Exhaustive survey of the Protein Data Bank (PDB) for protein-aptamer complex structures.
• Analysis of 144 PDB entries with atomic-level information.
• Examination of structural transitions from unbound to bound states.

Main Results:

• Identified 144 PDB entries detailing protein-aptamer complexes.
• Observed a significant increase in determined structures due to cryo-EM.
• Characterized diverse complex architectures and aptamer conformational changes upon binding.

Conclusions:

• Structural data reveals intricate protein-aptamer recognition mechanisms.
• Cryo-EM has accelerated the determination of these complex structures.
• Computational approaches contribute to understanding these molecular interactions.