Ribonuclease T1 has different dimensions in the thermally and chemically denatured states: a dynamic light scattering study

Gast, Klaus; Zirwer, Dietrich; Damaschun, Hilde; Hahn, Ulrich; Müller-Frohne, Marlies; Wirth, Matthias; Damaschun, G.

doi:10.1016/s0014-5793(97)00058-6

Cited by 19 publications

(13 citation statements)

References 39 publications

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“…The presence of an equilibrium between an extended and a compact conformer in the unfolded state of cytochrome c has been shown before by fluorescence spectroscopy and small angle x-ray scattering experiments (14,23,24). The formation of the collapsed unfolded states for multiple other proteins has also been demonstrated (25-29).…”

Section: Resultsmentioning

confidence: 80%

Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

Haldar

Chattopadhyay

2012

Journal of Biological Chemistry

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Background: Early events of protein folding are difficult to follow. Results: The unfolded state may have extended and compact conformers, which interconvert at early microsecond. Conclusion: Hydrophobic compaction and secondary structure formation do not occur simultaneously in aqueous solution. They occur simultaneously in the presence of urea. Significance: Hydrophobic collapse has been monitored at single molecular resolution.

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Section: Resultsmentioning

confidence: 80%

Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

Haldar

Chattopadhyay

2012

Journal of Biological Chemistry

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“…[40][41][42][43] The SAXS data recorded on ACTR and hNHE1cdt show that an overall contraction of the ensemble of structures occurs with increasing temperature. The contraction could be caused by a change in either the transient secondary structure or the tertiary structure.…”

Section: Discussionmentioning

confidence: 98%

Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?

Kjærgaard¹,

Nørholm²,

et al. 2010

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Structural characterization of intrinsically disordered proteins (IDPs) is mandatory for deciphering their potential unique physical and biological properties. A large number of circular dichroism (CD) studies have demonstrated that a structural change takes place in IDPs with increasing temperature, which most likely reflects formation of transient a-helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble. This phenomenon was explored at residue resolution by multidimensional NMR spectroscopy. Intrinsic chemical shift referencing allowed us to identify regions of transiently formed helices and their temperature-dependent changes in helicity. All helical regions were found to lose rather than gain helical structures with increasing temperature, and accordingly these were not responsible for the change in the CD spectra. In contrast, the nonhelical regions exhibited a general temperature-dependent structural change that was independent of long-range interactions. The temperature-dependent CD spectroscopic signature of IDPs that has been amply documented can be rationalized to represent redistribution of the statistical coil involving a general loss of PPII conformations.Keywords: intrinsically disordered protein (IDP); transient secondary structure; temperature dependence; polyproline II; circular dichroism (CD); nuclear magnetic resonance spectroscopy (NMR); sodium-proton (Na1/H1) exchanger 1 (NHE1); S-phase delayed 1 (Spd1); activator for thyroid hormone and retinoid receptors (ACTR) Abbreviations: ACTR, activator for thyroid hormone and retinoid receptors; CBP, CREB-binding protein; CD, circular dichroism; IDP, intrinsically disordered protein; NCBD, nuclear coactivator binding domain; NHE1cdt, sodium-proton (Na þ /H þ ) exchanger 1 C-terminal distal tail; NMR, nuclear magnetic resonance; PPII, polyproline II; RDC, residual dipolar coupling; SAXS, small-angle X-ray scattering; Spd1, S-phase delayed 1.

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“…For example, although DLS measurements on RNase A unfolded by reduction of its disulfides showed a slight compaction with temperature (37), recent SAXS measurements reported no significant change of R g (35). A significant collapse of RNase T1 in 5.3 M GdmCl was observed by DLS (38). No change in R g was reported for ␤-lactoglobulin in 8 M urea between 0 and 25°C (36).…”

Section: Discussionmentioning

confidence: 99%

“…For simple polymers and polymer models that do not involve a temperature-dependent interaction energy, conformational entropy favors open conformations, leading to chain expansion with increasing temperature (34), an effect that is assumed frequently to be dominant also for unfolded proteins. Although none of the sparse experimental results on this topic show such an expansion, they exhibit substantial variation, ranging from the absence of any detectable temperature dependence (35,36) to slight (37,38) and stronger (39) collapse, with some inconsistencies between measurements even on the same protein (35,37,40), calling for a systematic investigation of this issue. Ensemble investigations are limited largely to highly unfolding conditions to exclude interference from the signal of folded molecules and to minimize aggregation.…”

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confidence: 99%

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

Nettels

Müller-Späth²,

Küster³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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216

252

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We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With singlemolecule FRET, this question can be addressed even under nearnative conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperaturedependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin ␣ suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.FRET ͉ polymer ͉ protein folding ͉ secondary structure ͉ chain dimensions T here is an increasing interest in the properties of unfolded proteins and their roles in the folding and cellular functions of proteins. A key motivation is that many proteins are marginally stable and only fold in the presence of their ligands or binding partners, opening new regulatory possibilities (1, 2). An important reason for recent progress is the growing availability of methods that provide structural information on these conformationally heterogeneous systems, such as NMR (3), scattering methods (4, 5), and single-molecule . Although NMR provides mostly local details, small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and single-molecule FRET provide overall hydrodynamic or long-range distance information. An important advantage of single-molecule FRET is the separation of folded and unfolded subpopulations (9). As a result, unfolded state properties can be investigated even in the presence of folded molecules (i.e., under near-native conditions, which are physiologically most relevant). This advance has led to the observation of a continuous collapse of the unfolded state with decreasing denaturant concentrations (10), a behavior that now has been demonstrated for a large number of proteins (11-18) and peptides (19). Recent advances in the application of theoretical models have led to a quantitative description of this unfolded state collapse in terms of polymerphysical concepts (15,(20)(21)(22)(23). Such chain compaction also has been demonstrated to result in increased internal friction and a slowdown of intramolecular dynamics of the polypeptide (19, 26), which can affect...

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Ribonuclease T1 has different dimensions in the thermally and chemically denatured states: a dynamic light scattering study

Cited by 19 publications

References 39 publications

Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

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