Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations

Abstract

The bacterial cytoskeletal protein FtsZ is a GTPase that is thought to provide mechanical constriction force via an unidentified mechanism. Purified FtsZ polymerizes into filaments with varying structures in vitro: while GTP-bound FtsZ assembles into straight or gently curved filaments, GDP-bound FtsZ forms highly curved filaments, prompting the hypothesis that a difference in the inherent curvature of FtsZ filaments provides mechanical force. However, no nucleotide-dependent structural transition of FtsZ monomers has been observed to support this force generation model. Here, we present a series of all-atom molecular dynamics simulations probing the effects of nucleotide binding on the structure of an FtsZ dimer. We found that the FtsZ-dimer structure is dependent on nucleotidebinding state. While a GTP-bound FtsZ dimer retained a firm monomer-monomer contact, a GDP-bound FtsZ dimer lost some of the monomer-monomer association, leading to a "hinge-opening" event that resulted in a more bent dimer, while leaving each monomer structure largely unaffected. We constructed models of FtsZ filaments and found that a GDP-FtsZ filament is much more curved than a GTP-FtsZ filament, with the degree of curvature matching prior experimental data. FtsZ dynamics were used to estimate the amount of force an FtsZ filament could exert when hydrolysis occurs (20-30 pN per monomer). This magnitude of force is sufficient to direct inward cell-wall growth during division, and to produce the observed degree of membrane pinching in liposomes. Taken together, our data provide molecular-scale insight on the origin of FtsZ-based constriction force, and the mechanism underlying prokaryotic cell division.bacterial cell division | bacterial cytoskeleton | GTP hydrolysis T he bacterial cell-division protein FtsZ, a tubulin homolog and a GTPase, polymerizes into filaments situated underneath the cytoplasmic membrane at the division site (1-3). The ftsz gene is essential and depletion of FtsZ protein leads to cells unable to divide that instead take on a filamentous morphology (4). During division, rod-shaped bacteria such as Escherichia coli synthesize new hemispherical membrane and cell wall, requiring inward forces. While an array of proteins are needed for division to occur (5, 6), FtsZ alone has been demonstrated to be sufficient for generating inward pinching forces on liposomes in vitro (7-10), and is thought to be the source of the constriction force needed for division.How FtsZ generates mechanical force is still unclear, but several models have been proposed (11), one of which is based on the intrinsic nucleotide-dependent bending of FtsZ filaments (12, 13). In the presence of GTP, purified FtsZ assembles into either straight or gently curved filaments with a radius of curvature of approximately 100 nm, while in the presence of GDP, highly curved filaments form with a radius of curvature of approximately 10 nm (12,14,15). Subsequent theoretical modeling demonstrated that the rapid transition between straight and curved FtsZ filaments...

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB

“…Interestingly, many of the conformational dynamics of the highly conserved division protein FtsZ, a tubulin homolog and GTPase, are in sharp contrast with those of MreB. For example, there is little nucleotide-dependent monomer structural variation in FtsZ, and, like tubulin, nucleotide hydrolysis induces bending in FtsZ rather than straightening for the case of MreB (22,24). In general, the actin and tubulin families serve complementary cellular roles in both prokaryotes and eukaryotes, perhaps by invoking orthogonal molecular principles.…”

“…The elastic moduli of dimer simulations were measured from the distribution of bending orientations or the distance between the centers-of-mass (Supporting Information). As a measure of the size of a monomer-monomer interface, we calculate buried solvent-accessible surface area (SASA), which is defined as half the difference between the SASA of both subunits alone and the SASA of the entire dimer (24 …”

“…Here, we examine the conformational dynamics of MreB assembly from monomer to dimer in various nucleotidebinding states using all-atom molecular dynamics (MD) simulations. MD simulations have previously elucidated the polymerization-and hydrolysis-dependent structural transitions of various prokaryotic and eukaryotic cytoskeletal proteins (20)(21)(22)(23)(24)(25). For the bacterial tubulin homolog FtsZ, MD simulations predicted a hydrolysis-dependent filament bending (24) that was later validated by X-ray crystallography (22).…”

“…MD simulations have previously elucidated the polymerization-and hydrolysis-dependent structural transitions of various prokaryotic and eukaryotic cytoskeletal proteins (20)(21)(22)(23)(24)(25). For the bacterial tubulin homolog FtsZ, MD simulations predicted a hydrolysis-dependent filament bending (24) that was later validated by X-ray crystallography (22). In the case of actin, MD simulations have shed light on the structural transition between ATP-bound "globular" actin (G-actin) and models of polymerized ADP-bound "filamentous" or "fibrous" actin (F-actin) (26).…”

Divided we stand: splitting synthetic cells for their proliferation

“…One possible solution is that the conformational change is a characteristic of the polymer rather than of separate monomers, i.e., that it occurs by changing the polymerization angle between neighboring monomers. Indeed, recently molecular dynamics simulation suggested a hingelike mechanism with an angle difference of 22:5 between the states of two monomers in the GTP-and GDP-bound forms (Hsin et al 2012).…”