3-Dimensional Domain Swapping - Wodak Lab

Swapped dimer structure of the GB1 quadruple mutant, highlighting the non native intermolecular interactions formed between Phe34 side chains, and the volume that these side chains occupy in the core of the dimer.
Main global degrees of freedom in conformations of intermediates along the swapping reaction. Intermediates are composed on two GB1 chains (red and green), that exchange chain segments of variable lengths between them. The non contiguous structural domains are related by two fold symmetry (axis indicted), and are flexibly connected through the 2 exchanged chain segments, such that one domain is relatively free to adopt different orientations relative to the other domain.
Representative native­like and non­native swapped dimer conformations sampled during the simulations of GB1 quadruple mutant dimer. (a) Ribbon diagram of a representative native­like conformation sampled during the unconstrained sampling runs performed using the MRR sampling procedure, starting from the experimental structure of the swapped dimer formed by the GB1 quadruple mutant. In this conformation the relative orientation of the NCSD's is close to, and within the 17.5°cone around, that in the native dimer (see main text and Supplementary Material for details). The intermolecular Hbonds between β2/β2' are somewhat loosened but not severed. (b) Ribbon diagram of one of the representative non­native conformations sampled in the unconstrained simulations of the GB1 swapped dimer structure (quadruple mutant sequence) In this conformation the intermolecular H­bonds between β2/β2' have been severed, thereby splitting the β­sheet into 2 halves, whereas the non­native intermolecular contacts involving the C­termini of the helices and the following loop remain essentially intact. The fact that the latter contacts tend to be maintained more consistently in sampled conformations than the sheet structure suggests that they contribute more to the GB1 swapped dimer stability.

Three dimensional domain swapping is a process whereby two or more identical protein molecules associate to form dimers or higher order oligomers by exchanging identical structural elements, such that native intra-molecular interactions are replaced by their inter-molecular counterparts. This process emerges as a ubiquitous mechanism for homo-oligomer formation in many completely unrelated protein systems. But neither the physical factors that promote swapping nor the detailed mechanism and energetic aspects of this process are presently understood. It is believed that swapped oligomers may be key intermediates in the formation of larger protein assemblies including amyloid-like fibers associated with degenerative diseases, such as Alzheimer, type II diabetes, and many others.

We are currently investigating a new class of mechanisms for the swapping reaction that involve a progressive (and reversible) transformation between the monomeric and oligomeric states of the protein. In this mechanism swapping starts from either the N- or C- terminus of the protein chain and progresses by exchanging an increasing portion of the chains between subunits until a sufficiently stable conformational state is reached. During this process, native intra-molecular contacts are exchanged for their inter-molecular counterparts such that the total number of the native contacts in the system remains essentially constant and solvent exposure is minimized at all times. Employing detailed atomic models and classical force-fields, we recently computed the complete free energy profiles of the swapping process in the B1 domain of protein G (GB1) by combining an efficient sampling procedure related to the Methadynamics method with the use of multiple copies (replicas) of the system. Relating the computed free energy profiles to the stability of the monomeric and swapped dimer end states, has enabled us to rationalize the role of the amino acid sequence and to assess contributions from native and non-native interactions in fostering the swapping process.

As part of this project we are currently characterizing all the swapped oligomer structure and the PDB, and extending our simulation method to other systems.

For further details see:

  • Malevanets A, Sirota FL, Wodak SJ.
    Mechanism and energy landscape of domain swapping in the B1 domain of protein G.
    J Mol Biol. 2008 Sep 26;382(1):223-35.

Group members:   Anatoly Malevanets (PhD)
  Steve MacKinnon (Graduate Student)
Funding sources:
  PrioNet Canada, CIHR and Sickkids

Wodak Lab:
3-Dimensional Domain Swapping