Domain Orientation and Dynamics in Multidomain Proteins from Residual Dipolar Couplings

Abstract

The data most commonly available for the determination of macromolecular structures in solution are NOE based distance estimates and spin-spin coupling constant based dihedral angle estimates. This information is, unfortunately, inherently short-range in nature. Thus, for many multidomain proteins, little information is available to accurately position weakly interacting domains with respect to each other. Recent studies of proteins aligned in dilute liquid crystalline solvents have shown the utility of measuring anisotropic spin interactions, such as residual dipolar couplings, to obtain unique long-range structural information. In this work, the latter approach is taken to explore the relative domain orientation in a two-domain fragment from the protein barley lectin. An approach based on singular value decomposition as opposed to simulated annealing is used to directly determine order tensors for each domain from residual (15)N-(1)H dipolar couplings, and the limitations of the two approaches are discussed. Comparison of the order tensor principal axis frames as separately determined for each domain indicates that the two domains are not oriented as in the crystal structure of wheat germ agglutinin, a highly homologous protein ( approximately 95% sequence identical). Furthermore, differences in the order tensor values suggest that the two domains are not statically positioned but are experiencing different reorientational dynamics and, to a large degree, may be considered to reorient independently. Data are also presented that suggest that a specific association occurs between one domain and the lipid bicelles comprising the liquid crystal solvent.

Three‐dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

“…For hetero-oligomeric complexes, of course, one can determine alignment tensors independently for each subunit and assemble a structure by rotating subunits to superimpose principal axis systems. 9,10,13,14,38 One of the primary limitations of the methods described is that the structure of the monomeric unit must be available. This structure could come from existing crystal structures that may not show the proper assembly for weak complexes, or it could come from NMR based structure determination.…”

A Model of Interdomain Mobility in a Multidomain Protein

“…Following the derivation by Favro 33 , we write (7) where a r , m are decomposition coefficients and E r are the corresponding rate constants which depend solely on the principal values {D x , D y , D z } of the rotational diffusion tensor D (see Supporting Information).…”

De novo determination of protein structure by NMR using orientational and long-range order restraints

“…Weak alignment of proteins, which can exist naturally due to the paramagnetic properties of the molecule (Tolman et al, 1995) or be induced by solvation in liquid crystal media (Tjandra & Bax, 1997), lipid bicelles (Sanders et al, 1994) or a suspension of ®la-mentous bacteriophage (Hansen et al, 1998), prevents complete averaging of the dipolar interaction while retaining the solution properties necessary for high resolution NMR. The measurement of dipolar couplings under these conditions provides long-range order constraints which, in combination with classical NOE data, have been shown to improve structure determination in multidomain systems and protein-ligand complexes (Tjandra, 1999;Fischer et al, 1999;Olejniczak et al, 1999;Clore & Garrett et al, 1999;Bolon et al, 1999). Nevertheless, the determination of three-dimensional protein structure using only orientational information is severely hindered by the lack of long-range distances that de®ne the topology of the molecule.…”