Global minimization of an off-lattice potential energy function using a chaperone-based refolding method

Abstract

A global energy minimization method based on what is known about the mechanisms of the GroEL/GroES chaperonin system is applied to two 22‐mers of an off‐lattice protein model whose native states are β‐hairpins and which have structural similarity to short peptides known to interact strongly with the GroEL substrate binding domain. These model substrates have been used by other workers to test the effectiveness of a number of global minimization techniques, and are regarded as providing a significant challenge. The minimization method developed here is progressively elaborated from an initial simple form that targets exposed hydrophobic regions for unfolding to include a refolding phase that encourages the later recompactification of partly unfolded substrate; this refolding phase is seen to be crucial in the successful application of the method. The optimal handling of hydrophilic monomers within the model is also systematically explored, and it is seen that the best interpretation of their role is one that allows the chaperonin model to operate in “proofreading” mode whereby misfolded substrates are recognized by their surface exposure of a large proportion of hydrophobic monomers. The final version of the model allows native‐like structures to be found quickly, on average for the two 22‐mer substrates after 6 or 7 chaperone contacts. These results compare very favorably with those that have been obtained elsewhere using generic global minimization methods such as those based on thermal annealing. The paper concludes with a discussion of the place of the technique within the general category of hypersurface deformation methods for global minimization, and with suggestions as to how the chaperone‐based method developed here could be elaborated so as to be effective on longer substrate chains that give rise to more complex tertiary structures in their native states. © 2001 John Wiley & Sons, Inc. Biopolymers 59: 411–426, 2001

GroEL-Mediated Protein Folding: Making the Impossible, Possible

“…The experimental observation of accelerated RuBisCO folding inside the GroELGroES cavity suggests that the folding landscape of a protein can be fundamentally altered by encapsulation (Brinker et al, 2001). Several computational studies, using both simple lattice and more detailed off-lattice models, have also provided support for this conclusion (Betancourt and Thirumalai, 1999;Gorse, 2001;Zhou and Dill, 2001;Klimov et al, 2002;Baumketner et al, 2003;Takagi et al, 2003;Jewett et al, 2004;Xu et al, 2005).…”

Reconciling theories of chaperonin accelerated folding with experimental evidence

“…Active models IAM via ATP The traditional iterative annealing model (IAM) says that the ATP-driven cycles of binding and unbinding to GroEL accelerate folding by periodically disrupting or destabilizing off-pathway misfolded states [9,10,22,72,73,77,80,[102][103][104][105][106][107][108][109][110][111][112][113][114]. We suggest that GroEL may be able to accomplish this without releasing substrates into the cytosol (the stationary IAM).…”

“…The more frequently this occurs, the more opportunities a protein has to escape, leading to faster folding, for this class of frustrated, trapped proteins. Accelerated folding due to iterative denaturation has been predicted mathematically [104,109,114,148], and has been observed in minimalist polymer simulations (on a lattice [103,104,110] and off-lattice [111,125]). …”

Assessment of Escherichia coli B with enhanced permeability to fluorochromes for flow cytometric assays of bacterial cell function

“…An off‐lattice chaperone model38 has recently been presented by the author that includes both unfolding and refolding phases, and where the latter phase allows nontrivial interactions between the substrate monomers and the surrounding chaperone enclosure, providing active guidance toward a nativelike structure during the refolding phase. This chaperone‐derived energy minimization procedure was shown to be able to greatly enhance folding rates for two 22‐mer chains of the well‐known BLN (hydrophobic, hydrophilic, neutral) three‐dimensional off‐lattice heteropolymer model of Honeycutt and Thirumalai39; these same 22‐mers had previously been used by other workers as a testbed for a number of other (nonbiologically inspired) global minimization procedures 40, 41.…”