Fast Collapse but Slow Formation of Secondary Structure Elements in the Refolding Transition of E.coli Adenylate Kinase

Ratner, Vladimir; Amir, Dan; Kahana, Edith; Haas, Elisha

doi:10.1016/j.jmb.2005.06.074

Cited by 48 publications

(88 citation statements)

References 64 publications

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“…Under these denaturing conditions, 25 the distance between the labeled sites is large, and hence, the FRET efficiency is null for both pairs of probes (Trp-Sal and Trp-IAEDANS). Refolding kinetics was studied in a twostep mixing mode using the stopped-flow instrument (see Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

“…Similar observations were reported earlier when other pairs of sites were labeled in the CORE domain of AK. 25,17 The mean distance between two points randomly located in a sphere of uniform density is approximately equal to the radius of the sphere. 28 The minimal radius of an approximate sphere representing the ensemble of mean intramolecular distances between residues separated by several persistence lengths was estimated to be ≥26 Å 30 for AK.…”

Section: The Dimensions Of the 5-ms Transient Collapsed Ensemblementioning

confidence: 99%

“…20,25,17,29 Is the hypothesis of very fast loop closure realistic based on what we know of protein structure and dynamics? It has been shown in several systems that, under folding conditions, encounters of residues separated by tens of residues in disordered polypeptides occur in the nanosecond and microsecond time regimes.…”

Section: The Dimensions Of the 5-ms Transient Collapsed Ensemblementioning

confidence: 99%

See 2 more Smart Citations

Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study

Ishay¹,

Rahamim²,

Orevi³

et al. 2012

Journal of Molecular Biology

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Section: Resultsmentioning

confidence: 99%

Section: The Dimensions Of the 5-ms Transient Collapsed Ensemblementioning

confidence: 99%

Section: The Dimensions Of the 5-ms Transient Collapsed Ensemblementioning

confidence: 99%

See 1 more Smart Citation

Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study

Ishay¹,

Rahamim²,

Orevi³

et al. 2012

Journal of Molecular Biology

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“…Preparation of series of labeled mutants of one protein enables the monitoring of conformational changes of each sub-domain structure. Very fast data collection enables the determination of series of sequential distance distributions along the folding pathway (Ratner et al 2000(Ratner et al , 2005Ben Ishay et al 2012b). Such experiments yield meaningful information on specific conformational changes and the order of their occurrence along the folding pathway.…”

Section: Introductionmentioning

confidence: 99%

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

et al. 2013

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The extremely fast and efficient folding transition (in seconds) of globular proteins led to the search for some unifying principles embedded in the physics of the folding polypeptides. Most of the proposed mechanisms highlight the role of local interactions that stabilize secondary structure elements or a folding nucleus as the starting point of the folding pathways, i.e., a "bottom-up" mechanism. Nonlocal interactions were assumed either to stabilize the nucleus or lead to the later steps of coalescence of the secondary structure elements. An alternative mechanism was proposed, an "up-down" mechanism in which it was assumed that folding starts with the formation of very few non-local interactions which form closed long loops at the initiation of folding. The possible biological advantage of this mechanism, the "loop hypothesis", is that the hydrophobic collapse is associated with ordered compactization which reduces the chance for degradation and misfolding. In the present review the experiments, simulations and theoretical consideration that either directly or indirectly support this mechanism are summarized. It is argued that experiments monitoring the time-dependent development of the formation of specifically targeted early-formed sub-domain structural elements, either long loops or secondary structure elements, are necessary. This can be achieved by the timeresolved FRET-based "double kinetics" method in combination with mutational studies. Yet, attempts to improve the time resolution of the folding initiation should be extended down to the sub-microsecond time regime in order to design experiments that would resolve the classes of proteins which first fold by local or non-local interactions.

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“…The occurrence of a collapse preceding protein folding was inferred from kinetic experiments (6)(7)(8)(9)(10)(11) and also reported in equilibrium experiments, using small-angle x-ray scattering (SAXS) (12) and single-molecule fluorescence (13,14). However, the thermodynamics of the CG transition have not been characterized yet.…”

mentioning

confidence: 96%

Coil–globule transition in the denatured state of a small protein

Sherman

Haran

2006

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

288

383

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Upon transfer from strongly denaturing to native conditions, proteins undergo a collapse that either precedes folding or occurs simultaneously with it. This collapse is similar to the well known coil-globule transition of polymers. Here we employ singlemolecule fluorescence methods to fully characterize the equilibrium coil-globule transition in the denatured state of the IgGbinding domain of protein L. By using FRET measurements on freely diffusing individual molecules, we determine the radius of gyration of the protein, which shows a gradual expansion as the concentration of the denaturant, guanidinium hydrochloride, is increased all the way up to 7 M. This expansion is observed also in fluorescence correlation spectroscopy measurements of the hydro- fluorescence correlation spectroscopy ͉ protein folding ͉ single-molecule fluorescence T he coil-globule (CG) transition is a hallmark of the physics of polymers in solution. When a polymer molecule is transferred from a good solvent to a bad one, it undergoes a collapse from an expanded coil-like conformation to a contracted, globule-like conformation. This collapse is typically a second-order phase transition and can be accounted well by mean-field theory (1, 2). Proteins are heteropolymers and therefore should exhibit a similar transition. Because proteins also undergo a first-order folding transition to form their native structure, it is of prime interest to deduce the relation between collapse and folding (3). If the CG transition precedes folding significantly, then the final rearrangements of the protein chain to form the native structure occur within a relatively limited configurational space, which might affect the efficiency and speed of the process. The CG transition of proteins is also important for the elucidation of the properties of their denatured states. Chain collapse can have an impact on secondary-structure formation in the denatured protein (4). Determining the energetics of the collapse, which involve changes in the solvation energy of the protein as the solution conditions are varied, might allow us to understand better the role of the denatured state in the folding transition (5).The occurrence of a collapse preceding protein folding was inferred from kinetic experiments (6-11) and also reported in equilibrium experiments, using small-angle x-ray scattering (SAXS) (12) and single-molecule fluorescence (13,14). However, the thermodynamics of the CG transition have not been characterized yet. In this work, we use two methods, singlemolecule FRET (smFRET) and fluorescence correlation spectroscopy (FCS), to measure the CG transition of a 64-amino acid protein exhibiting two-state folding, the IgG-binding domain of protein L (hereafter denoted simply as protein L) (15). The CG transition is driven by the chemical denaturant guanidinium hydrochloride (GuHCl). We then employ a version of the mean-field theory of Sanchez (16) to obtain a full thermodynamic characterization of the CG transition of a protein, identifying the transition point as well ...

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Fast Collapse but Slow Formation of Secondary Structure Elements in the Refolding Transition of E.coli Adenylate Kinase

Cited by 48 publications

References 64 publications

Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study

Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

Coil–globule transition in the denatured state of a small protein

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