Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil

Determination of a high precision structure of a novel protein, Linum usitatissimum trypsin inhibitor (LUTI), using computer-aided assignment of NOESY cross-peaks

The solution structure of a novel 69 residue proteinase inhibitor, Linum usitatissimum trypsin inhibitor (LUTI), was determined using a method based on computer aided assignment of nuclear Overhauser enhancement spectroscopy (NOESY) data. The approach applied uses the program NOAH/DYANA for automatic assignment of NOESY cross-peaks. Calculations were carried out using two unassigned NOESY peak lists and a set of determined dihedral angle restraints. In addition, hydrogen bonds involving amide protons were identified during calculations using geometrical criteria and values of HN temperature coefficients. Stereospecific assignment of beta-methylene protons was carried out using a standard procedure based on nuclear Overhauser enhancement intensities and 3J(alpha)(beta) coupling constants. Further stereospecific assignment of methylene protons and diastereotopic methyl groups were established upon structure-based method available in the program GLOMSA and chemical shift calculations. The applied algorithm allowed us to assign 1968 out of 2164 peaks (91%) derived from NOESY spectra recorded in H2O and 2H2O. The final experimental data input consisted of 1609 interproton distance restraints, 88 restraints for 44 hydrogen bonds, 63 torsion angle restraints and 32 stereospecifically assigned methylene proton pairs and methyl groups. The algorithm allowed the calculation of a high precision protein structure without the laborious manual assignment of NOESY cross-peaks. For the 20 best conformers selected out of 40 refined ones in the program CNS, the calculated average pairwise rmsd values for residues 3 to 69 were 0.38 A (backbone atoms) and 1.02 A (all heavy atoms). The three-dimensional LUTI structure consists of a mixed parallel and antiparallel beta-sheet, a single alpha-helix and shows the fold of the potato 1 family of proteinase inhibitors. Compared to known structures of the family, LUTI contains Arg and Trp residues at positions P6' and P8', respectively, instead of two Arg residues, involved in the proteinase binding loop stabilization. A consequence of the ArgTrp substitution at P8' is a slightly more compact conformation of the loop relative to the protein core.

States and transitions during forced unfolding of a single spectrin repeat

Spectrin is a vital and abundant protein of the cytoskeleton. It has an elongated structure that is made by a chain of so-called spectrin repeats. Each repeat contains three antiparallel alpha-helices that form a coiled-coil structure. Spectrin forms an oligomeric structure that is able to cross-link actin filaments. In red cells, the spectrin/actin meshwork underlying cell membrane is thought to be responsible for special elastic properties of the cell. In order to determine mechanical unfolding properties of the spectrin repeat, we have used single molecule force spectroscopy to study the states of unfolding of an engineered polymeric protein consisting of identical spectrin domains. We demonstrate that the unfolding of spectrin domains can occur in a stepwise fashion during stretching. The force-extension patterns exhibit features that are compatible with the existence of at least one intermediate between the folded and the completely unfolded conformation. Only those polypeptides that still contain multiple intact repeats display intermediates, indicating a stabilisation effect. Precise force spectroscopy measurements on single molecules using engineered protein constructs reveal states and transitions during the mechanical unfolding of spectrin. Single molecule force spectroscopy appears to open a new window for the analysis of transition probabilities between different conformational states.

Flexibility of the alpha-spectrin N-terminus by EPR and fluorescence polarization

The structure and flexibility of the biologically important alpha-spectrin amino terminal region was examined by the use of fluorescence and EPR spectroscopy. The region studied has been previously demonstrated to be essential for the alpha-spectrin:beta-spectrin association of the tetramerization site. Appropriate spectroscopic probe moieties were coupled to this region in a recombinant fragment of human erythroid alpha-spectrin. There was good agreement between the EPR and fluorescence techniques in most of this region. Mobility determinations indicated that a portion of the region was relatively immobilized. This is significant, since although predictive methods have indicated that this region should be alpha-helical, previous experimental evidence obtained on smaller synthetic peptides had indicated that this region was disordered. Observed rigidity appears to be incompatible with such a disordered state, and has important ramifications for the flexibility of this molecule that is so integral to its role in stabilizing erythrocyte membranes.

Unfolding proteins by external forces and temperature: the importance of topology and energetics

Unfolding of proteins by forced stretching with atomic force microscopy or laser tweezer experiments complements more classical techniques using chemical denaturants or temperature. Forced unfolding is of particular interest for proteins that are under mechanical stress in their biological function. For beta-sandwich proteins (a fibronectin type III and an immunoglobulin domain), both of which appear in the muscle protein titin, the results of stretching simulations show important differences from temperature-induced unfolding, but there are common features that point to the existence of folding cores. Intermediates detected by comparing unfolding with a biasing perturbation and a constant pulling force are not evident in temperature-induced unfolding. For an alpha-helical domain (alpha-spectrin), which forms part of the cytoskeleton, there is little commonality in the pathways from unfolding induced by stretching and temperature. Comparison of the forced unfolding of the two beta-sandwich proteins and two alpha-helical proteins (the alpha-spectrin domain and an acyl-coenzyme A-binding protein) highlights important differences within and between protein classes that are related to the folding topologies and the relative stability of the various structural elements.

Spin label EPR structural studies of the N-terminus of alpha-spectrin

Spectrin, a vital component in human erythrocyte, is composed of alpha- and beta-subunits, which associate to form (alphabeta)2 tetramers. The tetramerization site is believed to involve the alpha-spectrin N-terminus and the beta-spectrin C-terminus. Abnormal interactions in this region may lead to blood disorders. It has been proposed that both termini consist of partial structural domains and that tetramerization involves the association of these partial domains. We have studied the N-terminal region of a model peptide for alpha-spectrin by making a series of double spin-labeled peptides and studying their dipolar interaction by electron paramagnetic resonance methods. Our results indicate that residues 21-42 of the N-terminus region exhibit an alpha-helical conformation, even in the absence of B-spectrin.

FTIR-Spectroscopy of multistranded coiled coil proteins

Coiled coils of different order were investigated using infrared (IR) spectroscopy. Recently, we demonstrated that dimeric coiled coils display unique vibrational spectra with at least three separable bands instead of only one band of a classical alpha-helix in the amide I region. This was attributed to a distortion of the helical structure by the supercoil bending, giving rise to bands that are not observed in the undistorted helix. Here, we investigated coiled coils forming trimers, tetramers, and pentamers. These higher order coiled coils, in general, possess larger superhelical pitches, resulting in a smaller helical distortion. We found that all coiled coils studied, including the native dimeric GCN4 leucine zipper and its variants leading to parallel trimers and tetramers as well as the rod portions of fibritin (parallel trimer), alpha-actinin (antiparallel spectrin type trimer), and COMP (parallel pentamer), displayed the typical three band pattern of the coiled coil amide I spectra. However, the separation of these three bands and their positional deviation from the classical alpha-helical band position was correlated to the extent of the helical distortion as reflected by the pitch values of the supercoils. The most pronounced spectral anomaly was found for the tropomyosin dimer with a reported helical pitch of 137 A, whereas the smallest spectral distortion was found for the pentameric COMP complex and the tetrameric leucine zipper mutant, both with a pitch of about 205 A.

Structure of the alpha-actinin rod: molecular basis for cross-linking of actin filaments

We have determined the crystal structure of the two central repeats in the alpha-actinin rod at 2.5 A resolution. The repeats are connected by a helical linker and form a symmetric, antiparallel dimer in which the repeats are aligned rather than staggered. Using this structure, which reveals the structural principle that governs the architecture of alpha-actinin, we have devised a plausible model of the entire alpha-actinin rod. The electrostatic properties explain how the two alpha-actinin subunits assemble in an antiparallel fashion, placing the actin-binding sites at both ends of the rod. This molecular architecture results in a protein that is able to form cross-links between actin filaments.

Structures of two repeats of spectrin suggest models of flexibility

Spectrin is a vital component of the cytoskeleton, conferring flexibility on cells and providing a scaffold for a variety of proteins. It is composed of tandem, antiparallel coiled-coil repeats. We report four related crystal structures at 1.45 A, 2.0 A, 3.1 A, and 4.0 A resolution of two connected repeats of chicken brain alpha-spectrin. In all of the structures, the linker region between adjacent units is alpha-helical without breaks, kinks, or obvious boundaries. Two features observed in the structures are (1) conformational rearrangement in one repeat, resulting in movement of the position of a loop, and (2) varying degrees of bending at the linker region. These features form the basis of two different models of flexibility: a conformational rearrangement and a bending model. These models provide novel atomic details of spectrin flexibility.

Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles

Spectrin repeats fold into triple helical coiled-coils comprising approximately 106 amino acid residues. Using an AFM-related technique we measured the force required to mechanically unfold these repeats to be 25 to 35 pN. Under tension, individual spectrin repeats unfold independently and in an all-or-none process. The dependence of the unfolding forces on the pulling speed reveals that the corresponding unfolding potential is shallow with an estimated width of 1.5 nm. When the unfolded polypeptide strand is relaxed, several domains refold within less than a second. The unfolding forces of the alpha-helical spectrin domains are five to ten times lower than those found in domains with beta-fold, like immunoglobulin or fibronectin Ill domains, where the tertiary structure is stabilized by hydrogen bonds between adjacent strands. This shows that the forces stabilizing the coiled-coil lead to a mechanically much weaker structure than multiple hydrogen-bonded beta-sheets.

Calpain-induced proteolysis of beta-spectrins

The calcium-activated neutral protease calpain is activated in several pathological conditions. Calpain usually hydrolyses one or only a few peptide bonds in its substrate. One prominent substrate for calpain is spectrin and it has been shown that alpha-spectrin is the preferred substrate. We now show that the beta-chain of spectrin is also a substrate for calpain proteolysis, and that the cleavage site in each beta-subunit is located at the very C-terminal part of the molecule. Surprisingly, beta1sigma-spectrin is cleaved at a different site than betaIsigma2- and betaIIsigma1-spectrins despite their high degree of sequence identity.

Interactions of the alpha-spectrin N-terminal region with beta-spectrin. Implications for the spectrin tetramerization reaction

Spectrin of the erythrocyte membrane skeleton is composed of alpha- and beta-spectrin, which associate to form heterodimers and tetramers. It has been suggested that a fractional domain (helix C) in the amino-terminal region of alpha-spectrin (Nalpha region) bundles with another fractional domain in the carboxyl-terminal region of beta-spectrin (Cbeta region) to yield a triple alpha-helical bundle and that this helical bundling is largely responsible for tetramer formation. However, there are certain objections to assigning a preeminent role to this helical bundling in the tetramerization reactions. We prepared several recombinant peptides of alpha-spectrin fragments spanning only the Nalpha region (lacking the dimer nucleation site) and quantitatively studied their interaction with beta-spectrin. We found that a majority of the interactions were localized, as expected, in the Nalpha-helix C region but that there was also some contribution from the nonhomologous region. More importantly, the temperature and ionic strength dependence of this interaction in our model peptides was different from that in intact spectrin. We suggest that, although the regions involving the putative helical bundling in alpha- and beta-spectrin undoubtedly play a significant role in tetramerization, regions distal to the Nalpha-helix C region in spectrin are also involved in tetramer formation. Structural flexibility and lateral interactions may play a role in spectrin tetramerization.

Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs

The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 A for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list.

Ionic strength effect on the thermal unfolding of alpha-spectrin peptides

In previous work, we have shown that the ionic strength-mediated differences found for the hydrodynamic dimensions of the human erythrocyte spectrin are not caused by secondary structural changes, but are caused more probably by subtle changes in tertiary interactions (LaBrake, C. C., Wang, L., Keiderling, T. A., and Fung, L. W.-M. (1993) Biochemistry 32, 10296-10302.). The substructure of spectrin has been suggested to be composed largely of triple alpha-helical bundle structural domains in tandem. In the present study, we used fluorescence and circular dichroism methods to study ionic strength effects on intact spectrin dimers and on recombinant peptides of spectrin domains of different lengths. We observed little ionic strength effect on the thermal unfolding temperature, Tm, values in these systems. However, we found that ionic strength-induced cooperativity in the unfolding processes was similar for the spectrin dimer and for peptides with two or three domains, as measured by entropy changes (DeltaSm). Although single-domain peptides exhibited rather variable DeltaSm values, depending on the specific domain, they showed little salt effects on the DeltaSm values themselves. This suggests that spectrin undergoes subtle ionic strength-induced conformational changes, probably near the interdomain regions of the molecule. These conformational changes may be responsible for the observed hydrodynamic and unfolding properties in intact spectrin under different ionic strength conditions. We suggest that recombinant peptides of various lengths may serve as models for studying the structural flexibility in spectrin.

Structural comparisons of calponin homology domains: implications for actin binding

BACKGROUND

The actin-binding site of several cytoskeletal proteins is comprised of two calponin homology (CH) domains in a tandem arrangement. As a single copy, the CH domain is also found in regulatory proteins in muscle and in signal-transduction proteins. The three-dimensional structures of three CH domains are known, but they have not yet clarified the molecular details of the interaction between actin filaments and proteins harbouring CH domains.

RESULTS

We have compared the crystal structure of a CH domain from beta-spectrin, which has been refined to 1.1 A resolution, with the two CH domains that constitute the actin-binding region of fimbrin. This analysis has allowed the construction of a structure-based sequence alignment of CH domains that can be used in further comparisons of members of the CH domain family. The study has also improved our understanding of the factors that determine domain architecture, and has led to discussion on the functional differences that seem to exist between subfamilies of CH domains, as regards binding to F-actin.

CONCLUSIONS

Our analysis supports biochemical data that implicate a surface centered at the last helix of the N-terminal CH domain as the most probable actin-binding site in cytoskeletal proteins. It is not clear whether the C-terminal domains of the tandem arrangement or the single CH domains have this function alone. This may imply that although the CH domains are homologous and have a conserved structure, they may have evolved to perform different functions.

Validation of protein models derived from experiment

The growing number of protein structures solved at atomic resolution holds the promise of further improvements in geometry-based validation parameters. Additionally, the estimated standard uncertainties of the atomic coordinates have been computed for a number of X-ray structures, providing a measure of the coordinate precision. In NMR spectroscopy, a measure analogous to the crystallographic R-factor has been developed.

F-actin-binding proteins

The study of proteins that bind filamentous actin (F-actin) is entering an exciting stage as more and more structures are determined. After more than 50 years in which the focus was on muscle proteins, emphasis has recently shifted towards understanding the complex interplay among actin-binding molecules in non-muscle cells. To date, the binding sites for eight classes of filament-binding molecules have been determined by combining low- to intermediate-resolution maps obtained by electron microscopy with atomic structures determined by X-ray crystallography and NMR. Recent results have dramatically accentuated the importance of filament geometry and actin conformation in defining these interactions.

The modular structure of actin-regulatory proteins

Filamentous actin structures possess unique biophysical and biochemical properties and are required for cell locomotion, cell division, compartmentalization and morphological processes. The site-specific assembly and disassembly of these structures are directed by actin-regulatory proteins. This article reviews how structural studies are now defining the atomic details of small modular domains present in actin-regulatory proteins responsible for crosslinking, severing and capping of actin filaments, as well as for localization of actin filament assembly. These studies have identified three modular strategies for the design of proteins that regulate the actin cytoskeleton.