PDBsum entry 2pe9

Signaling protein

PDB id: 2pe9

Contents

Protein chains

72 a.a.

References listed in PDB file

Key reference

Title

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

Authors

Y.Ryabov, D.Fushman.

Ref.

J Am Chem Soc, 2007, 129, 7894-7902.

PubMed id

17550252

Abstract

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

Secondary reference #1

Title

An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.

Authors

Y.E.Ryabov, C.Geraghty, A.Varshney, D.Fushman.

Ref.

J Am Chem Soc, 2006, 128, 15432-15444.

PubMed id

17132010

Secondary reference #2

Title

A model of interdomain mobility in a multidomain protein.

Authors

Y.E.Ryabov, D.Fushman.

Ref.

J Am Chem Soc, 2007, 129, 3315-3327.

PubMed id

17319663

Secondary reference #3

Title

Structural properties of polyubiquitin chains in solution.

Authors

R.Varadan, O.Walker, C.Pickart, D.Fushman.

Ref.

J Mol Biol, 2002, 324, 637-647. [DOI no: 10.1016/S0022-2836(02)01198-1]

PubMed id

12460567

Figure 2.
Figure 2. pH-dependence of the amide chemical shift difference between Ub[1] and Ub[2] for the proximal domain. As can be seen from this plot, the chemical shift perturbations (Ub[2] versus Ub[1]) saturate at higher pH, so that in most amide groups there is practically no (or very small) difference between the chemical shift perturbations observed at pH 6.8 and 7.5. These data suggest that the closed conformation of Ub[2] is almost fully populated at pH 7.5. In the case of fast exchange, the relative population of the closed or open conformations at the intermediate pH values can then be estimated assuming that the observed perturbation in the peak position is a weighted average of the corresponding values for the closed (at pH 7.5) and open (pH 4.5) conformations. The estimates of the population of the open conformation obtained for the individual amide groups at pH 6.8 ranged from less than 1% to 25%, with the mean value of 15%.

Figure 3.
Figure 3. Comparison of the three-dimensional conformations of Ub[2] in solution derived here at (a) acidic pH and ((b) and (c)) at neutral conditions. For comparison, (d) shows the crystal structure of Ub[2].[13.] Structures shown in (a) and (b) were derived using 15N relaxation data (rotational diffusion tensor) while that in (c) is on the basis of RDCs (alignment tensor). The orientation of the principal axes of the rotational diffusion or alignment tensors of the Ub[2] molecule, seen by each individual Ub domain, is indicated by rods positioned at the center of mass of the corresponding domain. The z-axes (turquoise) are oriented in the horizontal direction, the y-axes (pink) are vertical, and the x-axes are oriented toward the reader. Structures for the individual domains are from 1aar.pdb;[13.] a similar orientation was obtained using other protein coordinates (see the text). The domains are colored green (proximal) and blue (distal). Cylindrical arrows (red) indicate the orientation of a-helices. The location of L8, I44, and V70 in both domains, as well as that of K48 in the proximal domain are indicated in (b). Because this approach provides the orientation (not the distance) between the domains, their relative positions in (a)-(c) are somewhat arbitrary. Also, the C terminus of the distal domain is unstructured/flexible and should easily adopt a conformation accommodating closer contact between the units. Its conformation shown here is from the crystal structure and should be considered as an illustration only. The picture was prepared using Molmol. [44.]

The above figures are reproduced from the cited reference with permission from Elsevier