Biology subjects

Zavrtanik, U.

Publications and source records attributed to Zavrtanik, U..

2 recordsLinked to original sources

bioRxiv2023

Analysis of the peptide helicity using ensemble spectroscopic model with re-calibrated parameters

The -helix is the fundamental building block of protein structure. Understanding the physical principles that determine how a specific amino acid sequence defines helicity is a key step towards elucidating the sequence-structure relationship. An established method for quantitation of helix content using circular dichroism (CD) relies on the linear spectroscopic model. In this model, the helix length-correction is not applied to each ensemble conformer individually, rather an average value is assumed for all conformers. Here we assess the validity of this approximation and introduce a more physically realistic ensemble-based analysis of the CD signal. We find that the linear model tends to underestimate peptide helicity, with the difference depending on the ensemble composition. Using a CD dataset covering a broad range of helicities, we re-calibrate spectroscopic parameters (helix and coil baselines) and determine helix-coil parameters for a set of alanine-rich peptides. Our results show that the ensemble model can leverage the small spectroscopic differences between peptide conformers, enabling it to extract more information from the experimental data. We show that some previously poorly-defined quantities, such as helix nucleation constant and heat capacity change associated with helix folding, can be reliably determined using ensemble model. Overall, the presented ensemble-based treatment of the CD signal, together with the re-calibrated values of the spectroscopic baseline parameters, provides a coherent framework for the analysis of the peptide helix content. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/563921v1_ufig1.gif" ALT="Figure 1"> View larger version (7K): org.highwire.dtl.DTLVardef@e10dc8org.highwire.dtl.DTLVardef@14fe8ccorg.highwire.dtl.DTLVardef@13cb2fborg.highwire.dtl.DTLVardef@aafa3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

What stabilizes pre-folded structures in the intrinsically disordered α-helical binding motifs?

Many examples are known of regions of intrinsically disordered proteins (IDPs) that fold into -helices upon binding their globular protein targets. In their unbound state these regions possess a small amount of residual helicity, referred to as pre-folded structure, which has been studied on case by case basis. In order to investigate what determines these pre-folded structures we compiled a database of peptides that fold-upon-binding, and experimentally characterized their helicity in the unbound and target-bound state. These regions are more hydrophobic and lack proline residues compared to IDPs in general. On average they possess about 17% helicity in the pre-folded state and gain 40% of helicity upon target binding. We observe that the locations of pre-folded helical regions strongly overlap with those in the targetbound IDPs. To understand this correlation, we analyzed per-residue energetic contributions stabilizing helical structure and found that target-interacting IDP have higher helix propensity. Notably, leucine is the most common residue involved in IDP-target interactions and, due to its high helix propensity, it strongly stabilizes pre-folded helical structures. For many IDP binding motifs, particularly those enriched in leucine, we observe that they not only mediate target-interactions but also confer stability to the pre-folded structure. Collectively, this shows that the formation of pre-folded helical elements is coupled to the IDP-target interactions, explaining why such elements are a common feature of -helical binding motifs. Moreover, it probably explains the preference for leucine among IDP-target hotspots, even though this residue is underrepresented among hotspots in the interfaces between globular proteins.

bioinformatics↗