The capping box, a recurrent hydrogen bonded motif at the N-termini of a-helices, caps 2 of the initial 4 backbone amide hydrogen donors of the helix (Harper ET, Rose GD, 1993, Biochemistry 32:7605-7609). In detail, the side chain of the first helical residue forms a hydrogen bond with the backbone of the fourth helical residue and, reciprocally, the side chain of the fourth residue forms a hydrogen bond with the backbone of the first residue. We now enlarge the earlier definition of this motif to include an accompanying hydrophobic interaction between residues that bracket the capping box sequence on either side. The expanded box motif-in which 2 hydrogen bonds and a hydrophobic interaction are localized within 6 consecutive residues -resembles a glycine-based capping motif found at helix C-termini (Aurora R, Srinivasan R, Rose OD, 1994, Science 264: 1126-1 130). Keywords: cy-helices; capping box; hydrophobic interactionsThe a-helix is characterized by main-chain hydrogen bonds between successive amide hydrogen donors and carbonyl oxygen acceptors situated 4 residues previously in sequence (Pauling et al., 1951). For the helix of average length (i.e., -12 residues), this pattern results in 8 intrasegment hydrogen bonds. Additional "capping" hydrogen bonds that satisfy the initial 4 amide hydrogens and final 4 carbonyl oxygens (Presta & Rose, 1988;Richardson & Richardson, 1988) may also be present and inhibit fraying of helix ends. Helices and their flanking residues are labeled:where N1 through C1 have backbone dihedral angles with helical values (4 = -64 k 7"; $ = -41 * 7"), Ncap and Ccap belong both to the helix and adjacent turn, and the primed residues are in the turns that bracket the helix.The determinants of helices are insufficiently understood to reliably predict protein helices from sequence alone. Following seminal early studies (Schellman, 1958;Zimm & Bragg, 1959 Sueki et al., 1984), much recent attention has been directed toward understanding the physical basis of helix formation (Presta
For almost half a century, the structure of the full-length Bacillus thuringiensis (Bt) insecticidal protein Cry1Ac has eluded researchers, since Bt-derived crystals were first characterized in 1965. Having finally solved this structure we report intriguing details of the lattice-based interactions between the toxic core of the protein and the protoxin domains. The structure provides concrete evidence for the function of the protoxin as an enhancer of native crystal packing and stability.
The chaperonin GroEL can assist protein folding and normally acts with the co-chaperonin GroES. These Escherichia coli proteins are encoded on the same operon, with GroES positioned first. In this report, we have investigated the reversible folding of GroES. Using fluorescence anisotropy of dansyl-labeled GroES, intrinsic fluorescence, bis-ANS binding, sedimentation velocity, and limited proteolysis, we show that GroES unfolds in a single, two-state transition. Importantly, intrinsic fluorescence and sedimentation velocity analyses show that GroES is capable of refolding and reassembling from a urea denatured state. The refolded GroES is fully active as shown by its ability to assist GroEL in the refolding of rhodanese. These results indicate that chaperonins may not require other chaperonins for successful folding/assembly. We also show that GroES is capable of assisting in the refolding/reassembly of fully denatured GroEL. The reversible folding of GroES coupled with the ability of GroES to assist the refolding/reassembly of GroEL suggest that the groE operon may be organized in a manner that provides a structural role in GroES/GroEL assembly as well as a functional role.
The use of noncovalent hydrophobic probes such as bis-ANS has become increasingly popular in gaining structural information about protein structure and conformation. While these probes have provided rich information about protein conformation, specific information has been limited. In this report, we extend the usefulness of the probe bis-ANS by showing that it can be covalently photoincorporated into various proteins. Using the chaperonin GroEL, we have shown that it is possible to locate important hydrophobic surfaces through photoincorporation and peptide sequencing. It has been proposed that hydrophobic surfaces on the chaperonin may be responsible for the binding of unfolded polypeptides. We show here that photoincorporation of bis-ANS is able to locate a distinct hydrophobic surface on GroEL. Incorporation of the bis-ANS occurs within a 45 residue fragment of the monomer near the middle of the primary sequence. Interestingly, photoincorporation occurs within this fragment in both tetradecamers and assembly-competent monomers. From the three-dimensional structure of GroEL, this region maps to the apical domain (residues 191-376), which has been implicated in polypeptide binding [Fenton, W. A., Kashi, Y., Furtak, K., & Horwich, A. L. (1994) Nature 371, 614-619]. In addition, the fluorescent properties of the probe are retained including the excitation and emission maxima and the sensitivity to the polarity of its environment. These results suggest that photoincorporated bis-ANS may be a useful probe for protein structure and dynamics.
The urea denaturation of the chaperonin GroEL has been studied by circular dichroism, intrinsic tyrosine fluorescence and fluorescence of the hydrophobic probe, 1,1'-bis(4-anilino)naphthalene-5,5'-disulfonic acid (bisANS). It is shown that GroEL denaturation, monitored by CD and intrinsic fluorescence measurements, can be well described by a two-state transition that is complete by 3-3.1 M urea. The beginning of this transition overlaps the urea concentrations where the oligomeric protein starts to dissociate into individual monomers. Subsequent addition of the denaturant leads to complete unfolding of the monomers. Monomers unfolded at urea concentrations higher than 3.1 M are not competent to form their native conformations under the conditions employed here, and they are not able to reassemble to oligomers upon dilution of urea. In contrast to the CD and intrinsic fluorescence measurements, bisANS bound to GroEL exhibits considerable fluorescence intensity under conditions where the CD and intrinsic fluorescence signals have already reached their minimum values (> 3.1 M urea). This binding of bisANS, under conditions where the majority of the secondary structure of GroEL has already unfolded, indicates the existence of hydrophobic residual structure. This structure cannot be detected by CD measurements, but it can be unfolded by raising further the urea concentration. The existence of this structure does not depend on the source or method of the protein preparation. Intrinsic fluorescence and trypsin digestion demonstrate no difference between the bisANS-bound form of GroEL and the free form of the protein, showing that the GroEL structure is not greatly affected by the interaction with bisANS.(ABSTRACT TRUNCATED AT 250 WORDS)
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