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Related Experiment Video

Updated: May 8, 2026

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

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Water and side-chain embedded π-turns.

Bhaskar Dasgupta¹, Sucharita Dey, Pinak Chakrabarti

¹Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, West Bengal, 700 054, India.

|September 3, 2013

Summary

This summary is machine-generated.

Researchers analyzed embedded π-turns in protein structures, finding they can act as binding sites. The hydroxyl groups of Ser and Thr are key linkers, with conserved residues at terminal and linker positions.

Keywords:

Schellman motif hydrogen bonding turn conformation water/side-chain embedded turn π-turn

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Area of Science:

Structural biology
Protein structure analysis
Biophysics

Background:

Understanding protein function relies on deciphering sequence-structure relationships.
Local structural motifs, stabilized by hydrogen bonds, are crucial for protein stability.
π-Turns, characterized by (i) and (i+5) residue interactions, can embed water or protein moieties.

Purpose of the Study:

To analyze embedded π-turns and their role in protein structure.
To classify embedded π-turns and Schellman motifs based on structural and compositional features.
To investigate the role of embedded π-turns as potential binding sites.

Main Methods:

Analysis of a nonredundant protein structure dataset.
Identification and classification of 2965 embedded π-turns and 281 embedded Schellman motifs.
Geometric analysis of turn conformations and linker positions.

Main Results:

Embedded π-turns and Schellman motifs were identified and classified.
The hydroxyl group of Ser/Thr at position (i+3) is a common linker in side-chain mediated π-turns.
Residue conservation analysis highlighted conserved terminal and linker positions.

Conclusions:

Embedded π-turns can function as stable binding sites, particularly within 'nests'.
The study provides insights into the structural basis of protein function and stability.
Conserved residues in embedded π-turns suggest functional importance.