Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and...

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• Short linear motifs (SLiMs) are disordered protein segments crucial for various biological processes.
• SLiMs function as recognition sites, targeting signals, and binding sites, despite lacking regular secondary structures.
• Understanding SLiM conformation is key to deciphering their regulatory roles.

Purpose of the Study:

• To investigate the conformational landscape of two specific SLiM motifs (GRRDSG and GRRTSG) representative of the RxxS class.
• To elucidate the impact of residue-residue interactions on SLiM structure and dynamics.
• To compare experimental findings with molecular dynamics simulations.

Main Methods:

• Utilized a combination of spectroscopic techniques: Nuclear Magnetic Resonance (NMR), Infrared (IR) spectroscopy, vibrational spectroscopy, and UV circular dichroism.
• Determined Ramachandran plots for the selected SLiM motifs.
• Performed molecular dynamics simulations using Amber ff14SB and CHARMM 36m force fields.

Main Results:

• Residue interactions significantly redistribute conformational populations between polyproline II and β-strand basins.
• Extended structures are stabilized over turn-forming and helical conformations due to these interactions.
• Increasing temperature favors β-strand populations over polyproline II.
• Molecular dynamics simulations, while indicating residue-residue interactions, did not fully replicate the experimentally observed structural changes.

Conclusions:

• SLiMs possess distinct conformational propensities influenced by local and non-local residue interactions.
• These interactions stabilize specific structural states (extended, β-strand) and influence their temperature-dependent behavior.
• Experimental spectroscopic data reveals nuances in SLiM conformational dynamics not fully captured by current molecular dynamics force fields.