Electron paramagnetic resonance analysis of the vimentin tail domain reveals points of order in a largely disordered region and conformational adaptation upon filament assembly.

Very little data have been reported that describe the structure of the tail domain of any cytoplasmic intermediate filament (IF) protein. We report here the results of studies using site directed spin labeling and electron paramagnetic resonance (SDSL-EPR) to explore the structure and dynamics of the tail domain of human vimentin in tetramers (protofilaments) and filaments. The data demonstrate that in contrast to the vimentin head and rod domains, the tail domains are not closely apposed in protofilaments. However, upon assembly into intact IFs, several sites, including positions 445, 446, 451, and 452, the conserved "beta-site," become closely apposed, indicating dynamic changes in tail domain structure that accompany filament elongation. No evidence is seen for coiled-coil structure within the region studied, in either protofilaments or assembled filaments. EPR analysis also establishes that more than half of the tail domain is very flexible in both the assembly intermediate and the intact IF. However, by positioning the spin label at distinct sites, EPR is able to identify both the rod proximal region and sites flanking the beta-site motif as rigid locations within the tail. The rod proximal region is well assembled at the tetramer stage with only slight changes occurring during filament elongation. In contrast, at the beta site, the polypeptide backbone transitions from flexible in the assembly intermediate to much more rigid in the intact IF. These data support a model in which the distal tail domain structure undergoes significant conformational change during filament elongation and final assembly.

The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography.

Despite the passage of ∼30 years since the complete primary sequence of the intermediate filament (IF) protein vimentin was reported, the structure remains unknown for both an individual protomer and the assembled filament. In this report, we present data describing the structure of vimentin linker 1 (L1) and rod 1B. Electron paramagnetic resonance spectra collected from samples bearing site-directed spin labels demonstrate that L1 is not a flexible segment between coiled-coils (CCs) but instead forms a rigid, tightly packed structure. An x-ray crystal structure of a construct containing L1 and rod 1B shows that it forms a tetramer comprising two equivalent parallel CC dimers that interact with one another in the form of a symmetrical anti-parallel dimer. Remarkably, the parallel CC dimers are themselves asymmetrical, which enables them to tetramerize rather than undergoing higher order oligomerization. This functionally vital asymmetry in the CC structure, encoded in the primary sequence of rod 1B, provides a striking example of evolutionary exploitation of the structural plasticity of proteins. EPR and crystallographic data consistently suggest that a very short region within L1 represents a minor local distortion in what is likely to be a continuous CC from the end of rod 1A through the entirety of rod 1B. The concordance of this structural model with previously published cross-linking and spectral data supports the conclusion that the crystallographic oligomer represents a native biological structure.

Site-directed spin labeling and electron paramagnetic resonance determination of vimentin head domain structure.

Intermediate filament (IF) proteins have been predicted to have a conserved tripartite domain structure consisting of a largely alpha-helical central rod domain, flanked by head and tail domains. However, crystal structures have not been reported for any IF or IF protein. Although progress has been made in determining central rod domain structure, no structural data have been reported for either the head or tail domains. We used site-directed spin labeling and electron paramagnetic resonance to analyze 45 different spin labeled mutants spanning the head domain of vimentin. The data, combined with results from a previous study, provide strong evidence that the polypeptide backbones of the head domains form a symmetric dimer of closely apposed backbones that fold back onto the rod domain, imparting an asymmetry to the dimer. By following the behavior of spin labels during the process of in vitro assembly, we show that head domain structure is dynamic, changing as a result of filament assembly. Finally, because the vimentin head domain is the major site of the phosphorylation that induces disassembly at mitosis, we studied the effects of phosphorylation on head domain structure and demonstrate that phosphorylation drives specific head domain regions apart. These data provide the first evidence-based model of IF head domain structure.

Head and rod 1 interactions in vimentin: identification of contact sites, structure, and changes with phosphorylation using site-directed spin labeling and electron paramagnetic resonance.

We have used site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) to identify residues 17 and 137 as sites of interaction between the head domain and rod domain 1A of the intermediate filament protein vimentin. This interaction was maximal when compared with the spin labels placed at up- and downstream positions in both head and rod regions, indicating that residues 17 and 137 were the closest point of interaction in this region. SDSL EPR characterization of residues 120-145, which includes the site of head contact with rod 1A, reveals that this region exhibits the heptad repeat pattern indicative of alpha-helical coiled-coil structure, but that this heptad repeat pattern begins to decay near residue 139, suggesting a transition out of coiled-coil structure. By monitoring the spectra of spin labels placed at the 17 and 137 residues during in vitro assembly, we show that 17-137 interaction occurs early in the assembly process. We also explored the effect of phosphorylation on the 17-137 interaction and found that phosphorylation-induced changes affected the head-head interaction (17-17) in the dimer, without significantly influencing the rod-rod (137-137) and head-rod (17-137) interactions in the dimer. These data provide the first direct evidence for, and location of, head-rod interactions in assembled intermediate filaments, as well as direct evidence of coiled-coil structure in rod 1A. Finally, the data identify changes in the structure in this region following in vitro phosphorylation.

Role of the specifically targeted lysine residues in the glycation dependent loss of chaperone activity of alpha A- and alpha B-crystallins.

Earlier studies have shown significant loss of chaperone activity in alpha-crystallin from diabetic lenses. In vitro glycation studies have suggested that glycation of alpha-crystallin could be the major cause of chaperone activity loss. The following lysine (K) residues in alpha-crystallin have been identified as the major glycation sites: K11, K78, and K166 in alpha A-crystallin and K90, K92, and K166 in alpha B-crystallin. The present study was aimed to assess the contribution of each of the above glycation site in the overall glycation and loss of chaperone activity by mutating them to threonine followed by in vitro glycation with fructose. Level of glycated protein (GP) was determined by phenylboronate affinity chromatography, advanced glycation end products (AGEs) by direct ELISA using anti-AGE polyclonal antibody, and chaperone activity by using alcohol dehydrogenase as the target protein. K11T, K78, and K166T mutants of alpha A showed 33, 17, and 27% decrease in GP and 32, 18, and 21% decrease in AGEs, respectively, as compared to alpha A-wt. Likewise, K90T, K92T, K90T/K92T, and K166T mutants of alpha B showed 18, 21, 29, and 12% decrease in GP and 22, 24, 32, and 16% decrease in AGEs, respectively. Chaperone activity also showed concomitant increase with decreasing glycation and AGEs formation. alpha A-K11T and alpha B-K90T/K92T mutants showed the largest decrease in glycation and increase in chaperone activity.

C-Terminal truncation affects subunit exchange of human alphaA-crystallin with alphaB-crystallin.

In human lenses, C-terminal cleavage of alphaA-crystallin at residues 172,168, and 162 have been reported. The effect of C-terminal truncation of alphaA-crystallin on subunit exchange and heterooligomer formation with alphaB-crystallin and homooligomer formation with native alphaA-crystallin is not known. We have conducted fluorescence resonance energy transfer studies which have shown that the rates of subunit exchange of alphaA(1-172 )and alphaA(1-168 )with alphaB-wt were two-fold lower than for alphaA-wt interacting with alphaB-wt. The subunit exchange rate between alphaA(1-162) and alphaB-wt was six-fold lower. These data suggest that cleavage of the C-terminal residues could significantly affect heterooligomerization. On the other hand, the subunit exchange rates between alphaA-wt and the truncated alphaA-crystallins were either unchanged or only slightly decreased, which suggest that homooligomerization may not be significantly influenced by C-terminal truncation. The main conclusion from this study is that cleavage of C-terminal residues of alphaA-crystallin including the nine residues of the flexible tail is expected to significantly affect the formation of heteroaggregates. Reconstitution experiments showed that the presence of an intact C-terminus is essential for the formation of fully integrated heteroaggregates with equal proportion of alphaA and alphaB subunits.

Cleavage of the C-terminal serine of human alphaA-crystallin produces alphaA1-172 with increased chaperone activity and oligomeric size.

This study aimed to study the oligomeric size, structure, hydrodynamic properties, and chaperone function of the C-terminally truncated human alphaA-crystallin mutants with special emphasis on alphaA1-172 which is the cleavage product of the Ser172-Ser173 bond, unique to human lenses and constituting a major part of alphaA-crystallin. Various truncated forms of human alphaA-crystallins were prepared by site-directed mutagenesis. The proteins were expressed in Escherichia coli BL21(DE3) pLysS cells and purified by size exclusion column chromatography. Molecular masses and the other hydrodynamic properties were determined by dynamic light scattering measurements. The secondary and tertiary structural changes were assessed by far- and near-UV CD spectra measurements, respectively. Chaperone activity was determined by using ADH, insulin, and betaL-crystallin as the target proteins. alphaAlpha1-172 exhibited a significant increase in oligomeric size, i.e., 866 kDa by light scattering measurements as compared to 702 kDa in alphaA-wt. alphaAlpha1-172 and alphaA-wt had similar secondary structure, but the former exhibited slightly altered tertiary structure. The most interesting observation was that alphaAlpha1-172 behaved as a 28-46% better chaperone than alphaA-wt. The oligomeric size and structure of alphaAlpha1-168 were similar to those of alphaA-wt, while the chaperone activity was decreased by 12-23%. alphaAlpha1-162, on the other hand, had an oligomeric size of 400 kDa, a decrease in chaperone activity of 80-100%, and significantly altered secondary and tertiary structures. The data show that the overall chaperone function of alphaA-crystallin will be significantly improved by the presence of the major truncated product alphaAlpha1-172. This will be beneficial to the lens undergoing oxidative stress. Since alphaAlpha1-168 and alphaAlpha1-162 are present only in small amounts, their effect would be minimal.

Role of arginine-163 and the 163REEK166 motif in the oligomerization of truncated alpha A-crystallins.

To gain insight into the mechanism by which Arg-163 influences oligomerization of alphaA-crystallin, we prepared a series of truncated alphaA-crystallins with or without mutation of the Arg-163 residue. Expression of the proteins was achieved in Escherichia coli BL21 (DE3) pLysS cells, and alphaA-crystallin was purified by size-exclusion chromatography. Molecular mass was determined by molecular sieve HPLC, chaperone activity was assayed with alcohol dehydrogenase as the target protein, and structural changes were ascertained by circular dichroism (CD) measurements. With an increasing number of residues deleted, there was about a 3% decrease in oligomeric size per residue, until 10 residues were deleted. When 11 residues, including Arg-163, were deleted, the oligomeric size decreased 85%. Mutation of Arg-163 to Gly (R163G) did not affect the molecular mass in the full-length alphaA-crystallin. However, R163G mutants of all the truncated alphaA-crystallins showed a decrease in oligomeric size, those lacking 8, 9, and 10 residues showing 60-80% decrease and those lacking 5, 6, and 7 residues showing only a 7-14% decrease as compared to the corresponding truncated alphaA-crystallin. These data suggest that R163, E164, E165, and K166 in the REEK motif are also relevant to alphaA-crystallin oligomerization. The molecular masses of alphaA1-163 and alphaA1-163 (R163K) were nearly the same, which suggests that the role of Arg-163 is to provide a positive charge for intersubunit electrostatic interactions in the C-terminal domain. In alphaA1-162 (S162R), recovery of the molecular mass to the level in alphaA1-163 has not occurred; this shows that the actual position of R163 is important.