The concept of a random coil: Residual structure in peptides and denatured proteins

Smith, Lorna J.; Fiebig, Klaus M.; Schwalbe, Harald; Dobson, Christopher M.

doi:10.1016/s1359-0278(96)00046-6

Cited by 325 publications

(254 citation statements)

References 70 publications

Supporting

Mentioning

234

Contrasting

Unclassified

Order By: Relevance

“…Although the random coil is often perceived as a protein state lacking any stable structure and, therefore, protection, a brief sampling of this state by a protein does not necessarily expose all of the backbone amides to solvent simultaneously. Since the random coil is a macrostate representing an enormous ensemble of microstates, many of which exhibit some degree of structure and, therefore, protection (28), brief sampling of the U-state does not necessarily lead to a complete exchange of the entire backbone even if the intrinsic exchange rate is very high. This situation can be illustrated using a minimalist representation of a model energy landscape similar to that depicted in Figure 6, which utilizes a Brownian dynamic view of protein conformational kinetics (29).…”

Section: Discussionmentioning

confidence: 99%

Structural and Dynamic Characteristics of a Partially Folded State of Ubiquitin Revealed by Hydrogen Exchange Mass Spectrometry

Hoerner

Kaltashov

2005

Biochemistry

View full text Add to dashboard Cite

Structural and dynamic properties of a partially folded conformation (A-state) of ubiquitin are studied using amide hydrogen exchange in solution (HDX) and mass spectrometric detection. A clear distinction between the native state of the protein and the A-state can be made when HDX is carried out in a semicorrelated regime. Convoluted exchange patterns are interpreted with the aid of HDX simulations in a three-state system (highly structured, partially unstructured, and fully unstructured states). The data clearly indicate a highly dynamic character of the non-native state. Furthermore, combination of HDX and protein ion fragmentation in the gas phase [by means of collision-induced dissociation (CAD)] is used to evaluate the conformational stability of various protein segments specifically in the molten globular state. Chain flexibility appears to be distributed very unevenly in this non-native conformation. The highest degree of structural disorder is displayed by the C-terminal segment (Gly 53 -Gly 76 ), which was previously suggested to form a transient R-helix. The least dynamic segment of ubiquitin in the A-state is Thr 9 -Glu 18 (which was previously suggested to form a stable nativelike -strand), with the adjacent segments exhibiting somewhat diminished conformational stability. The study also demonstrates the power of mass spectrometry as a tool in providing conformer-specific information about the structure and dynamics of both native and non-native protein states coexisting in solution under equilibrium.Molten globule is a term that is used to describe a class of compact non-native protein states that are often thought to be general intermediates in protein folding, which are characterized by a substantial degree of secondary structure and a nearly complete absence of a native tertiary fold (1). Extensive studies of molten globular states of a variety of proteins were initially catalyzed by the realization that elucidating their structural and dynamic features may provide important clues for solving the protein folding problem (2,3). Since the kinetic folding intermediates are populated only transiently during the protein folding process, properties of molten globular states are often studied using the equilibrium models. In fact, it is the partially unfolded equilibrium intermediates that were initially proposed to belong to a common physical state of globular proteins, for which the term molten globular state was coined. More recently, renewed interest in the properties and behavior of molten globular states was instigated by a growing understanding that structural disorder is quite ubiquitous in vivo and often plays an important role in a variety of physiological processes (4). Such partially unstructured protein states have been implicated in a variety of processes ranging from protein translocation through membranes to ordered oligomerization, recognition, signaling, and even catalysis.The experimental tools employed in the studies of molten globular states include circular dichroism spe...

show abstract

Section: Discussionmentioning

confidence: 99%

Structural and Dynamic Characteristics of a Partially Folded State of Ubiquitin Revealed by Hydrogen Exchange Mass Spectrometry

Hoerner

Kaltashov

2005

Biochemistry

View full text Add to dashboard Cite

show abstract

“…While these previous studies provided valuable insights into the statistical properties of unfolded polypeptide chains, they mainly focused on relatively small and mostly single-domain proteins. 12,14 To verify whether the denatured states of large multi-domain proteins also exhibit similar behaviors upon chemical denaturation, here we investigate the GdnHCl induced unfolding of the F(ab′) 2 fragment of goat anti-rabbit immunoglobulin G (IgG) and also an IgG binding protein, protein A, using fluorescence correlation spectroscopy (FCS). FCS is based on correlating fluctuations in emission intensity arising from fluorescent molecules diffusing in and out of a small confocal volume, thus providing a convenient means to measure the diffusion time and hence the molecular size of the diffusing species.…”

mentioning

confidence: 99%

“…35,36 Two disulfide bridges bring the two Fab arms together to form a unique Y-shaped structure (Figure 1a). Because of its distinctive structural characteristics and the prevalence of antibodies, the folding of F(ab′) 2 as well as its constituent domains has been the subject of many studies. 35-42 Protein A (55.5 kDa), on the other hand, is a component of the cell wall of Staphylococcal aureus and is known to bind to the F C fragment of IgG.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Denaturant-induced Expansion and Compaction of a Multi-domain Protein: IgG

Guo

Chowdhury

Glasscock

et al. 2008

Journal of Molecular Biology

View full text Add to dashboard Cite

It is generally believed that unfolded or denatured proteins show random coil statistics and hence their radius of gyration simply scales with solvent quality (or denaturant concentration). Indeed, nearly all proteins studied thus far have been shown to undergo a gradual and continuous expansion with increasing denaturant concentration. Here, we use fluorescence correlation spectroscopy (FCS) to show that while protein A, a multidomain and predominantly helical protein, expands gradually and continuously with increasing concentration of guanidine hydrochloride (GdnHCl), the F(ab′) 2 fragment of goat anti-rabbit antibody IgG, a multi-subunit all β-sheet protein, however, does not show such continuous expansion behavior. Instead, it first expands and then contracts with increasing GdnHCl concentration. Even more striking is the fact that the hydrodynamic radius of the most expanded F(ab′) 2 ensemble, observed at 3-4 M GdnHCl, is ca. 3.6 times that of the native protein.Further FCS measurements involving urea and NaCl show that the unusually expanded F(ab′) 2 conformations might be due to electrostatic repulsions. Taken together, these results suggest that specific interactions need to be considered while assessing the conformational and statistical properties of unfolded proteins, particularly under conditions of low solvent quality. KeywordsFCS; Flory's random coil model; IgG; protein folding; unfolded state Despite its obvious importance in understanding how proteins fold, the unfolded or denatured state of proteins remains relatively unexplored. 1,2 Recent years have thus seen an increasing number of studies focused on the conformational properties of proteins in their unfolded state. 3-24 Of particular interest are those which assess the molecular dimensions as well as conformational dynamics of proteins under various denaturing conditions using ensemble 11-20 or single-molecule techniques. 25-32 All these studies, while involving a wide variety of peptides and proteins that span a large range of chain lengths (8-549 aa), generally support the notion that unfolded proteins behave as self-avoiding random-coils which undergo a continuous expansion with increasing denaturant concentration, following Flory's powerlaw relationship (i.e., R G = R 0 N ν ; where R G is the radius of gyration, R 0 is a constant determined *Corresponding author. Email address: gai@sas.upenn.edu. & L.G. and P.C. contributed equally to this work.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Figure 1a). Because of its distinctive structural characteristics and the prevalence of antibodies...

show abstract

“…Such structures are mostly compact and have appreciable secondary structure content. In contrast, denatured proteins are believed to be unfolded with little secondary structure (Dyson & Wright, 1993;Smith et al, 1996). In addition, there is another key difference: the denatured conformations are preselected by a Boltzmann factor (so that very high energy structures are excluded), while an unweighted energy average is used for the misfolds in Equation I .…”

Section: Relationship Of Zmisfijlds To Experimental Quantitiesmentioning

confidence: 99%

What should the Z‐score of native protein structures be?

Zhang

Skolnick

1998

Protein Science

View full text Add to dashboard Cite

The Z-score of a protein is defined as the energy separation between the native fold and the average of an ensemble of misfolds in the units of the standard deviation of the ensemble. The Z-score is often used as a way of testing the knowledge-based potentials for their ability to recognize the native fold from other alternatives. However, it is not known what range of values the Z-scores should have if one had a correct potential. Here, we offer an estimate of Z-scores extracted from calorimetric measurements of proteins. The energies obtained from these experimental data are compared with those from computer simulations of a lattice model protein. It is suggested that the Z-scores calculated from different knowledge-based potentials are generally too small in comparison with the experimental values. Keywords: knowledge-based potentials; protein folding; Z-scoresIn protein folding studies, knowledge-based potentials derived from a statistical analysis of known protein structures (Ueda et al., 1978;Maiorov & Crippen, 1992;Kolinski & Skolnick, 1994;Sippl, 1995; Mimy & Domany, 1996;Miyazawa & Jernigan, 1996;Liwo et al., 1997;Park et al., 1997) are frequently used in simplified models of proteins. The quality of such potentials is often assessed by socalled Z-scores, which test how well the potentials differentiate the native fold of a protein from an ensemble of misfolded structures. These Z-scores are calculated by (Bowie et al., 1991;Sippl, 1993): where Enotive is the energy of the native structure of a protein, is the average energy of an ensemble of misfolded structures, and arn,,f;,/ds is the standard deviation of the energy in this ensemble.However, it is not known what range of values of Z-scores should be expected for real proteins with exact potentials. Table 1 lists the Z-score ranges calculated from several typical knowledgebased potentials reported in the literature. The Z-scores vary tremendously from protein to protein. The widest spread of Z-scores was found for hydrophobic fitness potentials (Huang et al., 1996), which give a range between 1 and 24 for similar sized proteins, although on average the Z-score is quite high, around 11. In fact, because many approximations are introduced in the derivation of the knowledge-based potentials, there is a great deal of uncertainty as to the validity of these potentials (Jones & Thornton, 1996; Reprint requests to: Jeffrey Skolnick, Department of Molecular Biology. TPC-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037; e-mail: skolnick@scripps.edu.Pereira & Pochapsky, 1996;Thomas & Dill, 1996;Skolnick et al., 1997;Wang & Ben-Naim, 1997). This conflicting situation calls for examination of the physical meaning of the Z-scores.In this paper, we suggest a means of extracting Z-scores from the experimental data of proteins. Such Z-scores are defined differently than Zmr,,f,,,d.y, but it is possible to relate the two quantities. Thus, it is hoped that the results presented here can provide guidance into reaso...

show abstract

The concept of a random coil: Residual structure in peptides and denatured proteins

Cited by 325 publications

References 70 publications

Structural and Dynamic Characteristics of a Partially Folded State of Ubiquitin Revealed by Hydrogen Exchange Mass Spectrometry

Structural and Dynamic Characteristics of a Partially Folded State of Ubiquitin Revealed by Hydrogen Exchange Mass Spectrometry

Denaturant-induced Expansion and Compaction of a Multi-domain Protein: IgG

What should the Z‐score of native protein structures be?

Contact Info

Product

Resources

About