Protein interactions and membrane geometry - PubMed (original) (raw)

Protein interactions and membrane geometry

Michael Grabe et al. Biophys J. 2003 Feb.

Abstract

The difficulty in growing crystals for x-ray diffraction analysis has hindered the determination of membrane protein structures. However, this is changing with the advent of a new method for growing high quality membrane protein crystals from the lipidic cubic phase. Although successful, the mechanism underlying this method has remained unclear. Here, we present a theoretical analysis of the process. We show that it is energetically favorable for proteins embedded in the highly curved cubic phase to cluster together in flattened regions of the membrane. This stabilizes the lamellar phase, permitting its outgrowth from the cubic phase. A kinetic barrier-crossing model is developed to determine the free energy barrier to crystallization from the time-dependent growth of protein clusters. Determining the values of key parameters provides both a rational basis for optimizing the experimental procedure for membrane proteins that have not yet been crystallized and insight into the analogous cubic to lamellar transitions in cells. We also discuss the implications of this mechanism for protein sorting at the exit sites of the Golgi and endoplasmic reticulum and the general stabilization of membrane structures.

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Figures

FIGURE 1

Surface plot and curvature of the DMS. (A) Stereo pair showing a unit cell of the DMS, which underlies the geometry of the Pn3m lipidic cubic phase (Brakke, 1992). The extended phase iterates these “tubular units”. Stars mark the centers of monkey saddles where the curvature is a minimum (see D). (B) View of two adjacent monkey saddles. The arrow indicates the path that proteins traverse in passing between monkey saddles. (C) Cartoon of a rigid cylindrical protein embedded in a curved lipid bilayer (left side). If the membrane does not deform from its minimal surface state, undulations arise along the protein-bilayer contact curve. This creates mismatches between the hydrophobic midsections of the protein and the membrane (right side). This is energetically unfavorable, and consequently the membrane distorts to cover up the exposed hydrophobic patches, introducing mean curvature into the membrane surface. (D) The monkey saddle around one of the four sites of minimum Gaussian curvature. See Appendix A for how this is drawn. Level curves of constant Gaussian curvature are represented on the surface for a lattice constant of a = 93.3 Å (−36 (blue), −16 (yellow), 0 (center) × 10−4 Å−2). When proteins move away from these minima, the elastic energy increases several k_B_T. This effectively limits the configuration space of the proteins in the bulk cubic phase, and permits the use of a lattice model for nucleation. Axes are in Ångströms.

FIGURE 2

Membrane distortion zone around protein crystals. (A) Protein crystals embedded in the cubic phase viewed with cross-polarized light. The crystals are a deep blue and are surrounded by a hazy blue birefringent halo. Blue birefringence is indicative of a nonisotropic, possibly lamellar, lipid phase. Away from this zone the lack of birefringence is characteristic of a bulk cubic phase. (B) Cartoon representing the disturbance layer in A. The Pn3m cubic phase is thermodynamically stable for MO under the experimental conditions, whereas a lamellar phase is favored by the proteins (see Fig. 3) and the membrane lipids that form the lamellar stacks of the crystal (Landau and Rosenbusch, 1996). The connectedness between the bulk cubic phase and the growing lamellar phase allows proteins to diffuse into the crystal. However, this connection region composed of MO lipids is necessarily a higher energy configuration than the D cubic phase. The energy cost of creating this zone gives rise to an energy barrier to protein aggregation that is treated as an effective surface tension (see Eq. 3).

FIGURE 3

Protein energetics in the Pn3m cubic phase. (A) Computed deformation field of the monkey saddle region with a single inclusion in the bulk Pn3m cubic phase. The surface color (red and blue) represents the induced mean curvature radiating outward from the inclusion. (B) Binding energy for adding a single bR-sized protein to a growing lamellar crystal as a function of the lattice parameter. The energy is plotted using an upper and a lower bilayer bending modulus determined from experimentally measured monolayer bending moduli for the monoolein system. The monolayer values are _κ_m = 2.8 k_B_T (Vacklin et al., 2000), corresponding to the red curve, and _κ_m = 5.0 k_B_T (Chung and Caffrey, 1994), corresponding to the blue curve. These curves are plotted with bilayer bending moduli twice the recorded monolayer values. This assumes no interdigitation between the monolayer leaflets and is likely an underestimate of the true bilayer bending modulus. The elastic energy increases sharply at smaller lattice parameters, which drives the formation of crystals. (C) The energy barrier for crossing from one minimum energy site to the next is plotted as a function of the lattice parameter. The bilayer bending modulus corresponding to Vacklin et al.'s monolayer value was used (Vacklin et al., 2000). This barrier to diffusion slows the movement of proteins in the cubic phase.

FIGURE 4

Protein crystal sizes as a function of the lattice parameter. (A) Crystal edge length as a function of the lattice parameter (adapted from Nollert et al., 2001). The longest axis of bR crystals (n ≥ 10) was measured as a function of salt concentration. Separately, the lattice parameter of the cubic phase was determined as a function of the salt concentration. A linear fit was computed to the lattice parameter versus salt concentration and used to determine the crystal edge length as a function of lattice parameter as shown. (B) Natural log of the total number of proteins in a crystal as a function of the lattice parameter. bR crystals pack into hexagonal arrays at a composition of 70% protein and 30% purple membrane lipid. The volume of the crystals is V = (3√3)/8·_hl_2, where h is the height and l is the longest edge as measured in A. The height of the crystals was not accurately measured but was estimated to be linearly proportional to the length with the largest crystals having a height of ∼5 _μ_m and the smallest ∼1 _μ_m. This approximation is not critical inasmuch as the logarithm of the total number is plotted. Finally, the volume of a single bR protein was estimated from the crystal structure as _V_bR ∼ _π_152·45 Å3. The slope of the linear fit is 0.94 Å−1. From Eq. 7, the initial crystallization energy barrier ranges from 32.8 k_B_T at 86.3 Å to 43.6 k_B_T at 93.2 Å.

FIGURE 5

Upper and lower bounds for protein crystallization. The time required to nucleate a crystal has been plotted from Eq. 6 using the experimentally determined crystallization barrier height and the diffusion coefficient for bR (solid blue curve). The flat bilayer diffusion coefficient was modified in accord with the diffusion barrier between adjacent sites plotted in Fig. 3 C. The yellow zone represents the admissible range for growing crystals as shown in Fig. 4. The blue and yellow zones together represent the theoretical bounds on crystallization. Relevant times are indicated by solid red lines. The kinetic analysis predicts that the energy barrier to forming crystals is sufficiently large to prohibit nucleation in less than a year for lattice parameter values larger than 95 Å, as seen experimentally. However, the theory does not predict a lower limit cutoff for crystallization, but suggests the following scenario. At small lattice parameters, the energy barrier prevents proteins from diffusing between adjacent monkey saddle sites. This increases the nucleation time despite the low nucleation barrier. Although this effect is included in the nucleation time prediction (solid blue curve), the barrier to diffusion does not increase fast enough to drive the nucleation time up noticeably. For ∼84 Å the small axis of the protein (∼25 Å) is about equal to the diameter of the aqueous channel of the cubic phase pictured in the inset, D = a/√2 − (lipid bilayer thickness) ∼25 Å. The elastic calculations become suspect at this point and a “pinching off” effect may make the diffusion barrier increase much more quickly than predicted in Fig. 3 C. This limit is represented by the dashed blue line.

FIGURE 6

Energy barrier in k space. Crystallites smaller than the critical cluster size, K, break up on the average whereas larger clusters deterministically grow. For k ≫ K, the crystal grows with a driving force equal to ɛ.

FIGURE 7

Qualitative characteristic curves. The cut C at time t intersects characteristics giving the size of each crystal. Notice that there is a vanguard of large crystals (i.e., many characteristics) near the red curve, which is the initial characteristic. As time increases, the density of characteristics falls off.

FIGURE 8

Graph showing the dependence of _∂_t_k_0 on _k_0.

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Protein interactions and membrane geometry - PubMed (original) (raw)