Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding

Abstract

We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function, and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal), and Sph (spherical compact). With an adjustment for viscosity, crowded wild-type PGK and fluorescent PGK are about 15 times or more active in 200 mg∕ml Ficoll than in aqueous solution. Our results suggest a previously undescribed solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: Rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates. We also examine T-jump unfolding of PGK as a function of crowding experimentally. We uncover a nonmonotonic folding relaxation time vs. Ficoll concentration. Theory and modeling explain why an optimum concentration exists for fastest folding. Below the optimum, folding slows down because the unfolded state is stabilized relative to the transition state. Above the optimum, folding slows down because of increased viscosity.enzymatic activity | FRET | folding kinetics | thermal denaturation | protein conformational changes P hosphoglycerate kinase (PGK) is a 415-residue metabolic enzyme that produces ATP and is composed of two roughly equally sized subunits connected by a flexible hinge (1). In the crystal structure, the ADP and diphosphoglycerate binding sites, each located at an N and C subunit, are separated. It has been suggested that a large-scale conformational change (2) is necessary to bring the two subunits together when the phosphoryl group is catalytically transferred, and a hinge-bending mechanism has been postulated (3), bringing together both substrates at the inner surfaces of the C and N subdomains (4, 5).It is still unclear how the conformational and folding dynamics of PGK is affected by the interior of a cell, which is heavily crowded by macromolecules (6, 7). Various computational and theoretical studies have been developed to address the effect of volume exclusion exerted by surrounding macromolecules on protein activity inside cells, called the "macromolecular crowding effect" (8). This effect, in addition to weak chemical interactions between proteins and crowders (9), can stabilize the folded states of a protein relative to the unfolded state (10), perturb folding barriers (11,12), and alter folding rates (13) and folding routes (14).Macromolecular crowding could selectively stabilize one folded protein structure over another (8,(15)(16)(17), particularly for proteins that are structurally malleable so their domains aligned in different orientations would have similar free energies (18). Thus, what we regard as the native structur...

Crowding and function reunite

“…However, almost everything we know about biological macromolecules in solution comes from data acquired under conditions in which the concentration of macromolecules rarely exceeds 10 g/L. In PNAS, Dhar et al (2) report the broadest study to date about the effects of macromolecular crowding on the properties of a globular protein.…”

“…Dhar et al (2) bring function to the forefront again with their study of the enzyme phosphoglycerate kinase, which catalyzes the initial ATP-generating step of glycolysis. Most importantly, the enzyme is stunningly bilobal (Fig.…”

“…Not simply resting at this result, Dhar et al (2) performed an important control to determine whether the macromolecular nature of Ficoll causes the stability increase. The fundamental component of Ficoll, sucrose, was used as a comparable small molecule crowder.…”

Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension

“…We performed Brownian dynamics simulation by numerically integrating the discretized equation of motion: r α;i ðt þ ΔtÞ ¼~r α;i ðtÞ þ Δt ζ − ∂H SOP ∂r α;i þ f δ i;22êz þ~ξ α;i ðtÞ ~r i¼1 ðtÞ ¼ 0; [3] where α ¼ x; y; z and the random force~ξ α;i ðtÞ satisfies h~ξ α;i ðtÞi ¼ 0 and it is assumed that the probability distribution of the noise in the random force is Gaussian, i.e., P½~ξ α;i ðtÞ ∝ exp −∫ dτ ½ξ α;i ðτÞ 2 4ζkB T and h~ξ α;i ðtÞ ·~ξ β;j ðt þ nΔtÞi ¼ 2ζkB T Δt δ 0;n δ i;j δ α;β with n ¼ 0; 1; 2; …. We probed the folding-unfolding dynamics of RNA hairpin by applying tension f to the 3′-end of the hairpin while fixing the position of 5′-end at temperature T ¼ 300 K. Also, we chose the friction coefficient ζ ¼ 100 m∕τ L with τ L ¼ ðma 2 ∕ϵ h Þ 1∕2 ≈ 3-5 ps corresponding to the value that a nucleotide whose size a ≈ 0.5 nm feels in water environment whose viscosity is approximately 1 cP (18).…”

“…Only recently the notion that the self-assembly and function of biomolecules in vivo could be very different from those in isolation has been highlighted in terms of macromolecular crowding and confinement (2)(3)(4). However, the implication from dynamics in vivo should not necessarily be limited to the confinement or crowding effect.…”