Increase in the molecular weight and radius of gyration of apocalmodulin induced by binding of target peptide: evidence for complex formation

Measurements of accurate x-ray scattering data of protein solutions using small stationary sample cells

In this paper, we report a method of precise in situ x-ray scattering measurements on protein solutions using small stationary sample cells. Although reduction in the radiation damage induced by intense synchrotron radiation sources is indispensable for the correct interpretation of scattering data, there is still a lack of effective methods to overcome radiation-induced aggregation and extract scattering profiles free from chemical or structural damage. It is found that radiation-induced aggregation mainly begins on the surface of the sample cell and grows along the beam path; the diameter of the damaged region is comparable to the x-ray beam size. Radiation-induced aggregation can be effectively avoided by using a two-dimensional scan (2D mode), with an interval as small as 1.5 times the beam size, at low temperature (e.g., 4 degrees C). A radiation sensitive protein, bovine hemoglobin, was used to test the method. A standard deviation of less than 5% in the small angle region was observed from a series of nine spectra recorded in 2D mode, in contrast to the intensity variation seen using the conventional stationary technique, which can exceed 100%. Wide-angle x-ray scattering data were collected at a standard macromolecular diffraction station using the same data collection protocol and showed a good signal/noise ratio (better than the reported data on the same protein using a flow cell). The results indicate that this method is an effective approach for obtaining precise measurements of protein solution scattering.

Annular arrangement and collaborative actions of four domains of protein-disulfide isomerase: a small angle X-ray scattering study in solution

We presented for the first time a small angle x-ray scattering study of intact protein-disulfide isomerase (PDI) in solution. The restored model revealed that PDI is a short and roughly elliptical cylinder with a molecular mass of 69 kDa and dimensions of 105 x 65 x 40 A, and the four thioredoxin-fold domains in the order a-b-b'-a' are arranged in an annular fashion. Atomic force microscope imaging also supported the finding that PDI appears as an approximately flat elliptical cylinder. A PDI species with apparent molecular mass of 116 kDa measured by using size-exclusion chromatography, previously assumed to be a dimer, was determined to exist mainly as a monomer by using analytical ultracentrifugation. The C-terminal fragment 441-491 contributed to the anomalous molecular mass determination of PDI by size-exclusion chromatography. The annular model of PDI accounted for the cooperative properties of the four domains in both the isomerase and chaperone functions of PDI.

The C-terminal (331–376) Sequence of Escherichia coli DnaJ Is Essential for Dimerization and Chaperone Activity

DnaJ, an Escherichia coli Hsp40 protein composed of 376 amino acid residues, is a chaperone with thioldisulfide oxidoreductase activity. We present here for the first time a small angle x-ray scattering study of intact DnaJ and a truncated version, DnaJ (1-330), in solution. The molecular weight of DnaJ and DnaJ (1-330) determined by both small angle x-ray scattering and size-exclusion chromatography provide direct evidence that DnaJ is a homodimer and DnaJ (1-330) is a monomer. The restored models show that DnaJ is a distorted omega-shaped dimeric molecule with the C terminus of each subunit forming the central part of the omega, whereas DnaJ (1-330) exists as a monomer. This indicates that the deletion of the C-terminal 46 residues of DnaJ impairs the association sites, although it does not cause significant conformational changes. Biochemical studies reveal that DnaJ (1-330), while fully retaining its thiol-disulfide oxidoreductase activity, is structurally less stable, and its peptide binding capacity is severely impaired relative to that of the intact molecule. Together, our results reveal that the C-terminal (331-376) residues are directly involved in dimerization, and the dimeric structure of DnaJ is necessary for its chaperone activity but not required for the thiol-disulfide oxidoreductase activity.

Target recognition by calmodulin: the role of acid region contiguous to the calmodulin-binding domain of calcineurin A

Small-angle X-ray scattering was used to investigate the role of acid region contiguous to the calmodulin-binding domain (391-414) of calcineurin in the target recognition by calmodulin. Three synthetic peptides with the residues 385-414, 380-414 and 374-414 of calcineurin A were used for this aim. The X-ray data are consistent with the fact that calmodulin binds all three peptides with or without Ca2+. Without Ca2+, the whole peptide including acid residues interacts with dumbbell shaped calmodulin, while the acid region is extruded from globular shaped calmodulin with Ca2+. Consequently, a conformation of sequence 374-414 in calcineurin might be changed by Ca2+-signal via calmodulin, suggesting the consequence of this region with acid residues in the full activation mechanism of calcineurin by Ca2+-bound calmodulin.

Unfolding intermediate of a multidomain protein, calmodulin, in urea as revealed by small-angle X-ray scattering

The denaturation of calmodulin (CaM) induced by urea has been studied by small-angle X-ray scattering, which is a direct way to evaluate the shape changes in a protein molecule. In the absence of Ca(2+), the radii of gyration (R(g)) of CaM are 20.8+/-0.3 A in the native state and about 34+/-1.0 A in the unfolded state. The transition curve derived from Kratky plots indicates a bimodal transition via a stable unfolding intermediate around 2.5 M urea. In the presence of Ca(2+) and in the presence of both Ca(2+) and a target peptide, the R(g) values are 21.5+/-0.3 and 18.1+/-0.3 A in the native state and 26.7+/-0.4 and 24.9+/-0.4 A at 9 M urea, respectively. The results indicate that a stable unfolding intermediate still persists in 9 M urea. The present results suggest that the shape of unfolding intermediates is an asymmetric dumbbell-like structure, one in the folded and one in the unfolded state.

Relative affinity constants by electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry: calmodulin binding to peptide analogs of myosin light chain kinase

Synthetic RS20 peptide and a set of its point-mutated peptide analogs have been used to analyze the interactions between calmodulin (CaM) and the CaM-binding sequence of smooth-muscle myosin light chain kinase both in the presence and the absence of Ca(2+). Particular peptides, which were expected to have different binding strengths, were chosen to address the effects of electrostatic and bulky mutations on the binding affinity of the RS20 sequence. Relative affinity constants for protein/ligand interactions have been determined using electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. The results evidence the importance of electrostatic forces in interactions between CaM and targets, particularly in the presence of Ca(2+), and the role of hydrophobic forces in contributing additional stability to the complexes both in the presence and the absence of Ca(2+).

Solution X-ray scattering data show structural differences among chimeras of yeast and chicken calmodulin: implications for structure and function

We present here the first evidence, obtained by the use of small-angle X-ray scattering, of the solution structures of chimeras constructed from yeast (Saccharomyces cerevisiae, Sc) and chicken (Gallus gallus, Gg) calmodulin (CaM). The chimeric proteins used in this study are Sc(1-129)/Gg(130-148), Sc(1-128)/Gg(129-148), Sc(1-87)/Gg(88-148), and Sc(1-72)/Gg(73-148) CaMs, in which Sc(1-)(n)() and Gg(()(n)(+1)-148) descend from yeast and chicken CaM in the chimeric proteins, respectively. Under the Ca(2+)-saturated condition, the solution structure of Sc(1-128)/Gg(129-148) CaM has a dumbbell-like shape which is characteristic of vertebrate-type CaM, while that of Sc(1-129)/Gg(130-148) CaM takes an intermediate structure between the dumbbell-like shape and a compact globular shape. The results provide the direct evidence that the replacement of Asp(129) with Ser(129) induces an interaction between two lobes of Sc(1-129)/Gg(130-148) CaM and brings them close together. It implies that a site interacting with the N-lobe is induced in the C-lobe, although site IV that is unable to bind Ca(2+) hinders the ability of the C-lobe to undergo the conformational change to the full open state. In the presence of both Ca(2+) and a peptide synthesized to mimic the CaM binding domain on myosin light chain kinase, MLCK-22p, the solution structures of these chimeric CaMs take a similar compact globular shape but their interactions are quite different. The solution structure and interactions of Sc(1-72)/Gg(73-148) CaM are similar to those of Sc(1-87)/Gg(88-148) CaM. The structure of Sc(1-87)/Gg(88-148) CaM is similar to that of Sc(1-128)/Gg(129-148) CaM, but their interactions are different. The result indicates that the replacement of Glu(119) with Ala(119) has a critical effect on their interactions. Thus, the functional differences among these chimeric CaMs, which have been reported previously [Nakashima, K., et al. (1996) Biochemistry 35, 5602-5610], have been interpreted on the basis of the structures and interactions.

Protein conformational changes studied by diffusion NMR spectroscopy: application to helix-loop-helix calcium binding proteins

Pulsed-field gradient (PFG) diffusion NMR spectroscopy studies were conducted with several helix-loop-helix regulatory Ca(2+)-binding proteins to characterize the conformational changes associated with Ca(2+)-saturation and/or binding targets. The calmodulin (CaM) system was used as a basis for evaluation, with similar hydrodynamic radii (R(h)) obtained for apo- and Ca(2+)-CaM, consistent with previously reported R(h) data. In addition, conformational changes associated with CaM binding to target peptides from myosin light chain kinase (MLCK), phosphodiesterase (PDE), and simian immunodeficiency virus (SIV) were accurately determined compared with small-angle X-ray scattering results. Both sets of data demonstrate the well-established collapse of the extended Ca(2+)-CaM molecule into a globular complex upon peptide binding. The R(h) of CaM complexes with target peptides from CaM-dependent protein kinase I (CaMKI) and an N-terminal portion of the SIV peptide (SIV-N), as well as the anticancer drug cisplatin were also determined. The CaMKI complex demonstrates a collapse analogous to that observed for MLCK, PDE, and SIV, while the SIV-N shows only a partial collapse. Interestingly, the covalent CaM-cisplatin complex shows a near complete collapse, not expected from previous studies. The method was extended to related calcium binding proteins to show that the R(h) of calcium and integrin binding protein (CIB), calbrain, and the calcium-binding region from soybean calcium-dependent protein kinase (CDPK) decrease on Ca(2+)-binding to various extents. Heteronuclear NMR spectroscopy suggests that for CIB and calbrain this is likely because of shifting the equilibrium from unfolded to folded conformations, with calbrain forming a dimer structure. These results demonstrate the utility of PFG-diffusion NMR to rapidly and accurately screen for molecular size changes on protein-ligand and protein-protein interactions for this class of proteins.

Dynamic light scattering study of calmodulin-target peptide complexes

Dynamic light scattering (DLS) has been used to assess the influence of eleven different synthetic peptides, comprising the calmodulin (CaM)-binding domains of various CaM-binding proteins, on the structure of apo-CaM (calcium-free) and Ca(2+)-CaM. Peptides that bind CaM in a 1:1 and 2:1 peptide-to-protein ratio were studied, as were solutions of CaM bound simultaneously to two different peptides. DLS was also used to investigate the effect of Ca(2+) on the N- and C-terminal CaM fragments TR1C and TR2C, and to determine whether the two lobes of CaM interact in solution. The results obtained in this study were comparable to similar solution studies performed for some of these peptides using small-angle x-ray scattering. The addition of Ca(2+) to apo-CaM increased the hydrodynamic radius from 2.5 to 3.0 nm. The peptides studied induced a collapse of the elongated Ca(2+)-CaM structure to a more globular form, decreasing its hydrodynamic radius by an average of 25%. None of the peptides had an effect on the conformation of apo-CaM, indicating that either most of the peptides did not interact with apo-CaM, or if bound, they did not cause a large conformational change. The hydrodynamic radii of TR1C and TR2C CaM fragments were not significantly affected by the addition of Ca(2+). The addition of a target peptide and Ca(2+) to the two fragments of CaM, suggest that a globular complex is forming, as has been seen in nuclear magnetic resonance solution studies. This work demonstrates that dynamic light scattering is an inexpensive and efficient technique for assessing large-scale conformational changes that take place in calmodulin and related proteins upon binding of Ca(2+) ions and peptides, and provides a qualitative picture of how this occurs. This work also illustrates that DLS provides a rapid screening method for identifying new CaM targets.