How random is a highly denatured protein?

Calmettes, P.; Durand, Dominique; Desmadril, Michel; Minard, Philippe; Receveur, Véronique; Smith, Jeremy C.

doi:10.1016/0301-4622(94)00081-6

Cited by 91 publications

(96 citation statements)

References 43 publications

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“…For example, proteins unfolded at high concentrations of denaturant produce Kratky scattering profiles exhibiting the monotonic increase indicative of an expanded, coil-like conformation (11), and the x-ray and neutron scattering profiles of denatured yeast phosphoglycerate kinase and neocarzinostatin closely match those calculated for excluded-volume random coils (41,42). The observation of random-coil dimensional scaling is seemingly inconsistent, however, with previous spectroscopic studies, which indicate significant residual structure for even highly denatured proteins.…”

Section: Discussionmentioning

confidence: 61%

Random-coil behavior and the dimensions of chemically unfolded proteins

Kohn

Millett

Jacob

et al. 2004

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

658

758

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Spectroscopic studies have identified a number of proteins that appear to retain significant residual structure under even strongly denaturing conditions. Intrinsic viscosity, hydrodynamic radii, and small-angle x-ray scattering studies, in contrast, indicate that the dimensions of most chemically denatured proteins scale with polypeptide length by means of the power-law relationship expected for random-coil behavior. Here we further explore this discrepancy by expanding the length range of characterized denatured-state radii of gyration (RG) and by reexamining proteins that reportedly do not fit the expected dimensional scaling. We find that only 2 of 28 crosslink-free, prosthetic-group-free, chemically denatured polypeptides deviate significantly from a power-law relationship with polymer length. The RG of the remaining 26 polypeptides, which range from 16 to 549 residues, are well fitted (r2 = 0.988) by a power-law relationship with a best-fit exponent, 0.598 ± 0.028, coinciding closely with the 0.588 predicted for an excluded volume random coil. Therefore, it appears that the mean dimensions of the large majority of chemically denatured proteins are effectively indistinguishable from the mean dimensions of a random-coil ensemble

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Section: Discussionmentioning

confidence: 61%

Random-coil behavior and the dimensions of chemically unfolded proteins

Kohn

Millett

Jacob

et al. 2004

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

658

758

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“…The difference between the LE and EVB scattering profiles arises primarily from excluded volume. Using both analytical and sphere-based models, it has been demonstrated that PGK under the present conditions exhibits excluded-volume behavior~Calmettes et al., 1994;Petrescu et al, 1998!. Under the present conditions, the long-range interactions between different segments of the chain are generally repulsive-this is seen both in the present excludedvolume chain modeling and in the experimental determination of the second virial coefficient~see Petrescu et al, 1998!.…”

Section: Resultsmentioning

confidence: 92%

“…Although this is valuable information for denatured states~Eliezer et al, 1995;Kataoka et al, 1995;Chen et al, 1996;Kataoka & Goto, 1997!, there exists the additional possibility that this technique can be extended to provide a more detailed picture, involving the determination of the chain flexibility at higher resolution. With this aim, we have pursued a program to characterize the configurational statistics of a strongly-denatured protein~Calmettes et al, 1993, 1994Petrescu et al, 1997Petrescu et al, , 1998Receveur et al, 1997!. The system investigated is phosphoglycerate kinase~PGK!…”

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confidence: 99%

Change in backbone torsion angle distribution on protein folding

et al. 2000

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Understanding protein folding requires the determination of the configurational space accessible to the protein at different stages in folding. Here, computer simulation analysis of small angle neutron scattering results is used to probe the change in the distribution of configurations on strong denaturation of a globular protein, phosphoglycerate kinase, in 4 M guanidine hydrochloride solution. To do this atomic-detail ensembles of the unfolded protein chain are modeled and their scattering profiles compared with the experiment. The local conformational statistics are found to strongly influence the experimental intensity at scattering vectors between 0.05 and 0.3 Å Ϫ1 . Denaturation leads to a reduction in the protein atom-pair distance distribution function over the ;3-15 Å region that is associated with a quantifiable shift in the backbone torsional angle~w,c! distribution toward the b region of the Ramachandran plot.Keywords: atomic-detail models of unfolded protein ensemble; protein folding; small-angle neutron scattering A complete understanding of protein folding kinetics and thermodynamics requires the determination of the configurational statistics of proteins at various stages in folding. This involves the development and combination of experimental and theoretical tools for characterizing the large number of possible configurations that can coexist in any given unfolded state~see, for example, Wolynes et al

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“…However, the Kratky plot at pH 4.2 shows clear evidence of some degree of disorder. According to random polymer theory, in cases where the scattering object obeys Gaussian statistics, a Kratky plot will contain a plateau in the q range 3R g Ϫ1 Ͻ q Ͻ 1.4b Ϫ1 , where b is the statistical length of the polymer chain, which has been seen in proteins denatured by guanidinium chloride (44). Some evidence of random polymer-like behavior is visible at pH 4.2 in Fig.…”

Section: Discussionmentioning

confidence: 90%

Small Angle Neutron Scattering Reveals pH-dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I

Pingali

O’Neill

McGaughey

et al. 2011

Journal of Biological Chemistry

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Cellobiohydrolase I (Cel7A) of the fungus Trichoderma reesei (now classified as an anamorph of Hypocrea jecorina) hydrolyzes crystalline cellulose to soluble sugars, making it of key interest for producing fermentable sugars from biomass for biofuel production. The activity of the enzyme is pH-dependent, with its highest activity occurring at pH 4 -5. To probe the response of the solution structure of Cel7A to changes in pH, we measured small angle neutron scattering of it in a series of solutions having pH values of 7.0, 6.0, 5.3, and 4.2. As the pH decreases from 7.0 to 5.3, the enzyme structure remains well defined, possessing a spatial differentiation between the cellulose binding domain and the catalytic core that only changes subtly. At pH 4.2, the solution conformation of the enzyme changes to a structure that is intermediate between a properly folded enzyme and a denatured, unfolded state, yet the secondary structure of the enzyme is essentially unaltered. The results indicate that at the pH of optimal activity, the catalytic core of the enzyme adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted and suggest that the increased range of structures afforded by this disordered state plays an important role in the increased activity of Cel7A through conformational selection.

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How random is a highly denatured protein?

Cited by 91 publications

References 43 publications

Random-coil behavior and the dimensions of chemically unfolded proteins

Random-coil behavior and the dimensions of chemically unfolded proteins

Change in backbone torsion angle distribution on protein folding

Small Angle Neutron Scattering Reveals pH-dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I

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