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Sparsely populated residue conformations in protein structures: revisiting "experimental" Ramachandran maps
Neha V Kalmankar1, C Ramakrishnan, P Balaram
1Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India.
Proteins
|August 13, 2013
Summary
Protein structures reveal rare conformations in allowed Ramachandran map regions, driven by specific amino acid interactions. These findings challenge steric rules, highlighting the importance of side-chain and backbone dynamics in protein folding.
Area of Science:
- Structural Biology
- Protein Conformation Analysis
- Computational Biochemistry
Background:
- The Ramachandran map defines accessible conformational (φ-ψ) space for amino acid residues in proteins.
- Experimental data from high-resolution protein structures show deviations from predicted allowed regions.
Purpose of the Study:
- To analyze sparsely populated and disallowed regions of the Ramachandran map observed in experimental protein structures.
- To identify amino acid propensities for these rare conformations and understand the underlying structural and energetic factors.
Main Methods:
- Categorization of protein conformational space into 14 distinct bins based on φ, ψ values.
- Analysis of residue distributions and propensities within these bins using high-resolution protein structural data.
- Detailed examination of specific residues and structural motifs in populated 'disallowed' regions.
Main Results:
- Sparsely populated zones were identified within fully allowed regions, with Asn, Asp, and His showing high propensities.
- Two distinct clusters in disallowed regions correspond to gamma turns (Bin 12) and the i + 1 position of Type II' β turns (Bin 13).
- Type II' β turns frequently occur at helix N-termini, in β hairpins, and as connectors in β strand-helix motifs.
Conclusions:
- Side-chain and backbone interactions can energetically compensate for populating seemingly disallowed regions of conformational space.
- Specific amino acid residues and secondary structure elements like Type II' β turns play crucial roles in protein architecture and stability.
- The study refines our understanding of protein conformational preferences beyond simple steric constraints.
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