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The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Granata D, Baftizadeh F, Habchi J, Galvagnion C, De Simone A, Camilloni C, Laio A, Vendruscolo M - Sci Rep (2015)

Bottom Line: The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion.While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers.From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

View Article: PubMed Central - PubMed

Affiliation: International School for Advanced Studies (SISSA), 34136 Trieste, Italy.

ABSTRACT
The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

No MeSH data available.


Related in: MedlinePlus

Temperature-induced compaction of the Aβ40 peptide in 20 mM phosphate buffer at pH 8.(A) Values of the compaction index (CI) relative to that at 5 °C, as calculated from the hydrodynamic radii determined by NMR diffusion experiments at a concentration of 200 μM. (B) Far UV-CD spectra recorded at a concentration of 20 μM. (C) CD spectra-based values showing the increase (MRE) and the red-shift (wavelength) of the minimum mean residue ellipticities with increasing temperature. (D) CD-derived secondary structure population showing the relative change of the α-helical, β-strand, unfolded and turn populations of Aβ40 between relative to those at 5 °C. (E) Quenching of tyrosine fluorescence intensity with increasing temperature. (F) Reversibility of the quenching of tyrosine fluorescence intensity followed at 305 nm between 5 and 100 °C.
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f5: Temperature-induced compaction of the Aβ40 peptide in 20 mM phosphate buffer at pH 8.(A) Values of the compaction index (CI) relative to that at 5 °C, as calculated from the hydrodynamic radii determined by NMR diffusion experiments at a concentration of 200 μM. (B) Far UV-CD spectra recorded at a concentration of 20 μM. (C) CD spectra-based values showing the increase (MRE) and the red-shift (wavelength) of the minimum mean residue ellipticities with increasing temperature. (D) CD-derived secondary structure population showing the relative change of the α-helical, β-strand, unfolded and turn populations of Aβ40 between relative to those at 5 °C. (E) Quenching of tyrosine fluorescence intensity with increasing temperature. (F) Reversibility of the quenching of tyrosine fluorescence intensity followed at 305 nm between 5 and 100 °C.

Mentions: Given the architecture of the free energy landscape described above, these computational results suggest the possibility of a remarkable phenomenon - at increasing temperatures the Aβ40 peptide should become more structured, as it could explore regions of higher free energy. To test experimentally this prediction, we used a combination of hydrodynamic and spectroscopic approaches. As anticipated from the metadynamics simulations described above, we show that the structuring of the Aβ40 peptide increases with temperature, supporting the notion that this peptide undergoes a temperature-induced partial folding (Fig. 5). The details of the experimental procedures are presented in the Methods section.


The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Granata D, Baftizadeh F, Habchi J, Galvagnion C, De Simone A, Camilloni C, Laio A, Vendruscolo M - Sci Rep (2015)

Temperature-induced compaction of the Aβ40 peptide in 20 mM phosphate buffer at pH 8.(A) Values of the compaction index (CI) relative to that at 5 °C, as calculated from the hydrodynamic radii determined by NMR diffusion experiments at a concentration of 200 μM. (B) Far UV-CD spectra recorded at a concentration of 20 μM. (C) CD spectra-based values showing the increase (MRE) and the red-shift (wavelength) of the minimum mean residue ellipticities with increasing temperature. (D) CD-derived secondary structure population showing the relative change of the α-helical, β-strand, unfolded and turn populations of Aβ40 between relative to those at 5 °C. (E) Quenching of tyrosine fluorescence intensity with increasing temperature. (F) Reversibility of the quenching of tyrosine fluorescence intensity followed at 305 nm between 5 and 100 °C.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4620491&req=5

f5: Temperature-induced compaction of the Aβ40 peptide in 20 mM phosphate buffer at pH 8.(A) Values of the compaction index (CI) relative to that at 5 °C, as calculated from the hydrodynamic radii determined by NMR diffusion experiments at a concentration of 200 μM. (B) Far UV-CD spectra recorded at a concentration of 20 μM. (C) CD spectra-based values showing the increase (MRE) and the red-shift (wavelength) of the minimum mean residue ellipticities with increasing temperature. (D) CD-derived secondary structure population showing the relative change of the α-helical, β-strand, unfolded and turn populations of Aβ40 between relative to those at 5 °C. (E) Quenching of tyrosine fluorescence intensity with increasing temperature. (F) Reversibility of the quenching of tyrosine fluorescence intensity followed at 305 nm between 5 and 100 °C.
Mentions: Given the architecture of the free energy landscape described above, these computational results suggest the possibility of a remarkable phenomenon - at increasing temperatures the Aβ40 peptide should become more structured, as it could explore regions of higher free energy. To test experimentally this prediction, we used a combination of hydrodynamic and spectroscopic approaches. As anticipated from the metadynamics simulations described above, we show that the structuring of the Aβ40 peptide increases with temperature, supporting the notion that this peptide undergoes a temperature-induced partial folding (Fig. 5). The details of the experimental procedures are presented in the Methods section.

Bottom Line: The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion.While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers.From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

View Article: PubMed Central - PubMed

Affiliation: International School for Advanced Studies (SISSA), 34136 Trieste, Italy.

ABSTRACT
The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

No MeSH data available.


Related in: MedlinePlus