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Accounting for Protein Flexibility Upon Macromolecular Association:
Difficulties and Challenges for the Docking Methods

by Karine Bastard and Chantal Prévost

Protein flexibility upon association

Protein motions are involved in numerous basic functions such as catalysis, regulation of cellular activity, transport of metabolites and cellular locomotion.
Different levels of flexibility have been observed in proteins: side-chain, loop and domain (shear and hinge bending) movements.
These motions are largely covered on the World Wide Web.  Protein flexibility is also implied in the binding process resulting the formation of macromolecular assemblies. This process was first described by the lock and key model: the structure of the partner and that of the receptor complement each other. Studies have proved that the induced fit model is often more accurate: the structure of the partner and the structure of the receptor adapt to each other during association. This may occur because each partner modifies the chemical and steric properties of the other.

The induced fit model is supported by multiple observations in different proteins such as streptavidin, zymogen, the met repressor and many others. In the cited examples, the proteins undergo large conformational changes that result in surface loop movements:
    - a disordered loop situated near the active site of streptavidin refolds over the biotin molecule once it is docked to the protein, thus protecting it from the environment
    - shifts of inhibitor loop of zymogen alter the pattern of hydrogen bonding and allow binding to chymotrypsinogen
    - when the met repressor binds to DNA, an eight residue loop of met repressor changes its hairpin conformation into a conformation that wraps around the DNA phosphate backbone.

At macromolecular interfaces, changes occur for a variety of reasons: to form specific interactions, to avoid steric clashes, or to enhance shape complementarity and allow hydrogen bonding. In the case of proteins, this often involves flexible loops which can be defined as disordered or mobile protein segments consisting of roughly six to twenty amino-acids. They often display no regular secondary structure, but they can include structured segments, typically beta-hairpin.

Importance of considering loop movements during the docking process

A challenge for docking methods is to predict the structure of a macromolecular complex starting from the coordinates of unbound components. In order to systematically explore the conformational space and to predict surface regions where the interactions are most likely to occur, numerous methods treat the proteins as rigid bodies and use a scoring function based on surface complementarity. These procedures perfom poorly in cases where the unbound molecules display conformational differences relative to the bound ones in the main-chain, or, more commonly in loop arrangements. Indeed, surface loop movements during association can modify the steric and electrostatic properties of the protein face presented to the partner (see picture below).

The mobile loop is in red and orange, the protein is in green. The accessible surface differs widely of when going from one conformation to the other.

It seems necessary to account for induced surface remodeling during the search for the interacting surfaces by allowing the receptor to adapt to its partner in an induced fit process.To address this problem, we have recently developped a new docking method, termed MC2, which allows loop and side-chain movements at the protein surface during macromolecular association. In a test-case study, the method was able to predict the structure of the complex at the atomic level and to unambiguously predict the conformation of an interfacial loop.

    Although reliable docking can now be achieved for systems that do not undergo important induced conformational change on association, the results of the CAPRI contest, held in September 2002, point to the need for handling protein conformational flexibility. This task is a complicating factor in computational macromolecular docking. Such methods should locate flexible regions and allow this flexibility to be taken account during the association process while conserving the search rapidity necessary for post-genomic applications.
    In order to tackle this problem with scientists from the docking field, we proposed a CECAM workshop on Flexible Macromolecular Docking. Groups which have experience in aspects of flexible docking and representants from small molecule docking and protein folding communities will bring their experience together to tackle the problem of protein flexibility.

Author: Karine Bastard. Last update: January 15, 2004.
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