This Article Full Text Full Text (PDF) Supplement All Versions of this Article: biophysj.107.119651v1 94/5/1575    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Contreras Martínez, L. M. Articles by DeLisa, M. P. PubMed PubMed Citation Articles by Contreras Martínez, L. M. Articles by DeLisa, M. P.

In Silico Protein Fragmentation Reveals the Importance of Critical Nuclei on Domain Reassembly

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York

Correspondence: Address reprint requests to Fernando A. Escobedo, School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853. Tel.: 607-255-8243; Fax: 607-255-9166; E-mail: fe13{at}cornell.edu; or to Matthew P. DeLisa at the same address. Tel.: 607-254-8560; Fax: 607-255-9166; E-mail: md255{at}cornell.edu.

Protein complementation assays (PCAs) based on split protein fragments have become powerful tools that facilitate the study and engineering of intracellular protein-protein interactions. These assays are based on the observation that a given protein can be split into two inactive fragments and these fragments can reassemble into the original properly folded and functional structure. However, one experimentally observed limitation of PCA systems is that the folding of a protein from its fragments is dramatically slower relative to that of the unsplit parent protein. This is due in part to a poor understanding of how PCA design parameters such as split site position in the primary sequence and size of the resulting fragments contribute to the efficiency of protein reassembly. We used a minimalist on-lattice model to analyze how the dynamics of the reassembly process for two model proteins was affected by the location of the split site. Our results demonstrate that the balanced distribution of the "folding nucleus," a subset of residues that are critical to the formation of the transition state leading to productive folding, between protein fragments is key to their reassembly.