Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module

Michał Wojciechowski,Pham Dinh Quoc Huy,Mai Suan Li,Bartosz Różycki,Marek Cieplak,Edward A Bayer

doi:10.1038/s41598-018-23380-9

Abstract

The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.

Highlights

The fibrous plant cell walls are the major source of carbon and energy on Earth
These structural methods combined with molecular dynamics simulations or other modeling methods can lead to insights into dynamic properties and conformational heterogeneity of the protein complexes under study[14,22,23]
Neither PDB:1OHZ nor PDB:2CCL, encompasses the corresponding residues at the N- and C-terminus of the C. thermocellum Doc. Both of these Coh-Doc structures lack the the N- and C-terminal tails in Doc. We modeled these terminal segments and, interestingly, discovered that they have a substantial influence on the energy landscapes of the Coh-Doc complex

Summary

Introduction

The fibrous plant cell walls are the major source of carbon and energy on Earth They are made primarily of cellulose and hemicellulose, which are difficult to degrade into simple sugars. A number of atomic structures of cellulosome-constituing domains and subunits have been solved by X-ray crystallography and NMR. There is no single method that could be used to solve structures of the cellulosomes: they are not directly accessible to X-ray crystallography due to the presence of the disordered linkers ( their constituent domains can be crystallized separately); they are not accessible to protein NMR because of their large sizes; and their inherent flexibility makes them still practically inaccessible to cryoEM. Commonly denoted by CipA24, consists of nine type-I Cohs that show large sequence similarity. The scaffoldins in many mesophilic bacteria commonly bear five or six Cohs[25]

Methods

Results

Conclusion