Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

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Authors
Millership, C 
Phillips, JJ 
Main, ERG 
Abstract

Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typically, homozipper Ising models have been used. These treat the repeat protein as a series of identical interacting subunits (the repeated motifs) that couple together to form the folded protein. However, they cannot describe subunits of differing stabilities. Here we show that a more sophisticated heteropolymer Ising model can be constructed and fitted to two new helix deletion series of consensus tetratricopeptide repeat proteins (CTPRs). This analysis, showing an asymmetric spread of stability between helices within CTPR ensembles, coupled with the Ising model's predictive qualities was then used to guide reprogramming of the unfolding pathway of a variant CTPR protein. The designed behaviour was engineered by introducing destabilising mutations that increased the thermodynamic asymmetry within a CTPR ensemble. The asymmetry caused the terminal α-helix to thermodynamically uncouple from the rest of the protein and preferentially unfold. This produced a specific, highly populated stable intermediate with a putative dimerisation interface. As such it is the first step in designing repeat proteins with function regulated by a conformational switch.

Description
Keywords
linear Ising model, protein design, protein folding, repeat protein, Models, Chemical, Protein Folding, Repetitive Sequences, Amino Acid, Thermodynamics
Journal Title
J Mol Biol
Conference Name
Journal ISSN
0022-2836
1089-8638
Volume Title
Publisher
Elsevier BV
Sponsorship
C.M. is supported by a BBSRC studentship. B.B.S.R.C Grant E005187/1 and QMUL supported this work and J.J.P