Unstructured polypeptide chains are subject to various degrees of swelling or compaction depending on the combination of solvent condition and amino acid sequence. Highly denatured proteins generally behave like random-coils with excluded volume repulsion, whereas in aqueous buffer more compact conformations have been observed for the lowpopulated unfolded state of globular proteins as well as for naturally disordered sequences. To quantitatively account for the different mechanisms inducing the swelling of polypeptides, we have examined three 14-residues peptides in aqueous buffer and in denaturant solutions, including the well characterized AGQ repeat as a reference and two variants, in which we have successively introduced charged side chains and removed the glycines. Quenching of the triplet state of tryptophan by close ½AQ1 contact with cysteine has been used in conjunction with Fo¨ rster resonance energy transfer to study the equilibrium and kinetic properties of the peptide chains. The experiments enable accessing end-to-end root mean-square distance, probability of end-toend contact formation and intrachain diffusion coefficient. The data can be coherently interpreted on the basis of a simple chain model with backbone angles obtained from a library of coil segments of proteins and hard sphere repulsion at each Ca position. In buffered water, we find that introducing charges in a glycine-rich sequence induces a mild chain swelling and a significant speedup of the intrachain dynamics, whereas the removal of the glycines results in almost a two-fold increase of the chain volume and a drastic slowing down. In denaturants we observe a pronounced swelling of all the chains, with significant differences between the effect of urea and guanidinium chloride.

Kinetics of contact formation and end-to-end distance distributions of swollen disordered peptides / A. Soranno, R. Longhi, T. Bellini, M. Buscaglia. - In: BIOPHYSICAL JOURNAL. - ISSN 0006-3495. - 96:4(2009 Feb 18), pp. 1515-1528.

Kinetics of contact formation and end-to-end distance distributions of swollen disordered peptides

A. Soranno
Primo
;
T. Bellini
Penultimo
;
M. Buscaglia
Ultimo
2009-02-18

Abstract

Unstructured polypeptide chains are subject to various degrees of swelling or compaction depending on the combination of solvent condition and amino acid sequence. Highly denatured proteins generally behave like random-coils with excluded volume repulsion, whereas in aqueous buffer more compact conformations have been observed for the lowpopulated unfolded state of globular proteins as well as for naturally disordered sequences. To quantitatively account for the different mechanisms inducing the swelling of polypeptides, we have examined three 14-residues peptides in aqueous buffer and in denaturant solutions, including the well characterized AGQ repeat as a reference and two variants, in which we have successively introduced charged side chains and removed the glycines. Quenching of the triplet state of tryptophan by close ½AQ1 contact with cysteine has been used in conjunction with Fo¨ rster resonance energy transfer to study the equilibrium and kinetic properties of the peptide chains. The experiments enable accessing end-to-end root mean-square distance, probability of end-toend contact formation and intrachain diffusion coefficient. The data can be coherently interpreted on the basis of a simple chain model with backbone angles obtained from a library of coil segments of proteins and hard sphere repulsion at each Ca position. In buffered water, we find that introducing charges in a glycine-rich sequence induces a mild chain swelling and a significant speedup of the intrachain dynamics, whereas the removal of the glycines results in almost a two-fold increase of the chain volume and a drastic slowing down. In denaturants we observe a pronounced swelling of all the chains, with significant differences between the effect of urea and guanidinium chloride.
single-molecule fluorescence ; unfolded polypeptide-chains ; loop formation ; energy-transfer ; spectroscopic ruler ; denatured protein ; electron-transfer ; amino-acids ; dynamics ; rates ; peptides ; proteins ; tryptophan ; contact formation ; phosphorescence ; end-to-end distance ; FRET
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/62372
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