A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex

Fisher, Alice; Taniuchi, Hiroshi

doi:10.1016/0003-9861(92)90538-8

Cited by 24 publications

(24 citation statements)

References 43 publications

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“…In each of the binding events, the changing conditions lead to shifts in the populations. Experimentally, complementing fragments provide a system for studying protein folding (Taniuchi et al 1986; Fisher and Taniuchi 1992; Yang et al 1998; Spolaore et al 2001), consistent with the idea that intermolecular binding resembles intramolecular folding events (Tsai et al 1998, 1999a). Figure 1 gives a flow chart of the cutting procedure, and its legend outlines the major steps.…”

Section: Computational Dissection: the Building Block Folding Modelmentioning

confidence: 55%

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

Tsai¹,

Laureto²,

Fontana³

et al. 2002

Protein Science

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Here we present a comparison between protein fragments produced by limited proteolysis and those identified by computational cutting based on the building block folding model. The principles upon which the two methods are based are different. Limited proteolysis of natively folded proteins occurs at flexible sites and never at the level of chain segments of regular secondary structure such as ␣-helices. Therefore, the targets for limited proteolysis are locally unfolded regions. In contrast, the computational cutting algorithm considers the compactness of the fragments, their nonpolar buried surface area, and their isolatedness, that is, the surface area which was buried prior to the cutting and becomes exposed subsequently. Despite the different criteria, there is an overall correspondence between sites or regions of limited proteolysis with those identified by computational cutting. The computational cutting method has been applied to several model proteins for which detailed limited proteolysis data are available, namely apomyoglobin, cytochrome c, ribonuclease A, ␣-lactalbumin, and thermolysin. As expected, more cuts are obtained computationally than experimentally and the agreement is better when a number of proteolytic enzymes are used. For example, cytochrome c is cleaved by thermolysin at 56-57, 45-46, and at 80-81, and by proteinase K at 48-49 and 50-51. Incubation of the noncovalent and native-like complex of cytochrome c fragments 1-56 and 57-104 with proteinase K yielded the gapped protein species 1-48/57-104 and finally 1-40/57-104. Computational cutting of cytochrome c reproduced the major experimental observations, with cuts at 47, 64-65 or 65-66 and 80-81 and an unstable 32-47 region not assigned to any building block. The next step, not addressed in this work, is to probe the ability of the generated fragments to fold independently. Since both the computational algorithm and limited proteolysis attempt to dissect the protein folding problem, the general agreement between the two procedures is gratifying. This consistency allows us to propose the use of limited proteolysis to produce protein fragments that can adopt an independent folding and, therefore, to study folding intermediates. The results of the present study appear to validate the building block folding model and are in line with the proposal that protein folding is a hierarchical process, where parts constituting local minima of energy fold first, with their subsequent association and mutual stabilization to finally yield the global fold.Keywords: Folding intermediates; limited proteolysis; protein anatomy; protein flexibility; protein folding; protein fragments Supplemental material: See www.proteinscience.org.How the amino acid sequence in the polypeptide chain directs and specifies the three-dimensional protein fold is still an open problem (Matthews 1995). A number of experimental and computational methods have been developed to address the protein folding problem. There is a growing body of evidence indicating that while f...

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Section: Computational Dissection: the Building Block Folding Modelmentioning

confidence: 55%

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

Tsai¹,

Laureto²,

Fontana³

et al. 2002

Protein Science

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“…Peptide complexes formed by complementation of fragments are known for several multi-domain proteins (for a review, see Fisher & Taniuchi, 1992). Circular permutation studies have indicated that the cleavage of loops or turns does not generally unfold proteins (Viguera et al, 1995;Garrett et al, 1996).…”

Section: Discussion Lack Of Structure In Ci2 Fragmentsmentioning

confidence: 99%

Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2

Ladurner

Itzhaki

Prat‐Gay

et al. 1997

Journal of Molecular Biology

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“…Even proteins of rather small size are known to reassemble noncovalently from multiple fragments. For cytochrome c, a complex of three fragments has electron acceptor activity (Fisher and Taniuchi 1992). Cytochrome c might be considered a special case because the heme remains covalently attached via thioether links to one fragment, and its iron ion provides coordination with both fragments.…”

Section: Nature and Limits Of Reconstitutionmentioning

confidence: 99%

“…Thus, chain connectivity is at once both restrictive and permissive, and is commonly viewed as essential for protein folding and structure. Yet the widespread phenomenon of protein reconstitution (Hirs and Timasheff 1986; Fisher and Taniuchi 1992; Håkansson and Linse 2002) demonstrates that many native structures tolerate breaks in the polypeptide chain, and native contacts reform from separated fragments in an assembly reaction akin to intramolecular folding (Fig. 1).…”

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confidence: 99%

Protein reconstitution and three‐dimensional domain swapping: Benefits and constraints of covalency

et al. 2007

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The phenomena of protein reconstitution and three-dimensional domain swapping reveal that highly similar structures can be obtained whether a protein is comprised of one or more polypeptide chains. In this review, we use protein reconstitution as a lens through which to examine the range of protein tolerance to chain interruptions and the roles of the primary structure in related features of protein structure and folding, including circular permutation, natively unfolded proteins, allostery, and amyloid fibril formation. The results imply that noncovalent interactions in a protein are sufficient to specify its structure under the constraints imposed by the covalent backbone.

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A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex

Cited by 24 publications

References 43 publications

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2

Protein reconstitution and three‐dimensional domain swapping: Benefits and constraints of covalency

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