Opening the high-pressure domain beyond 2 kbar to protein and virus crystallography--technical advance

Behavior of B- and Z-DNA Crystals under High Hydrostatic Pressure

Single crystals of B-DNA and Z-DNA oligomers were analyzed under high hydrostatic pressure and their behavior was compared to the A-DNA crystals already known. The amplitude of the base compression, when compared to the A-form of DNA (0.13 Å/GPa), was higher for the Z-DNA (0.32 Å/GPa) and was the highest for the B-DNA (0.42 Å/GPa). The B-DNA crystal degraded rapidly around 400–500 MPa, while the Z-structure was more resistant, up to 1.2 GPa.

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography

In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg²⁺·GppNHp and Ras(D33K)·Mg²⁺·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners.

The equilibria between structural states induced by pressure within the crystal structure of Ras are illustrated with different colors corresponding to different Ras substates.

Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation

High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.

Functional Sub-states by High-pressure Macromolecular Crystallography

At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.

High-pressure protein crystallography of hen egg-white lysozyme

Crystal structures of hen egg-white lysozyme (HEWL) determined under pressures ranging from ambient pressure to 950 MPa are presented. From 0.1 to 710 MPa, the molecular and internal cavity volumes are monotonically compressed. However, from 710 to 890 MPa the internal cavity volume remains almost constant. Moreover, as the pressure increases to 950 MPa, the tetragonal crystal of HEWL undergoes a phase transition from P43212 to P43. Under high pressure, the crystal structure of the enzyme undergoes several local and global changes accompanied by changes in hydration structure. For example, water molecules penetrate into an internal cavity neighbouring the active site and induce an alternate conformation of one of the catalytic residues, Glu35. These phenomena have not been detected by conventional X-ray crystal structure analysis and might play an important role in the catalytic activity of HEWL.

Pressure-imposed changes of benzoic acid crystals

Structural and energetic properties of benzoic acid crystals at pressure elevated from ambient condition up to 2.21 GPa were characterized. The directly observed variations of cell parameters and consequently cell volume are associated with many other changes including energetic, geometric, and electronic characteristics. First of all the non-monotonous change of lattice energy are noticed with the rise of pressure since the increase of stabilization up to 1GPa is followed by systematic decrease of lattice energies after extending the hydrostatic compression. There is also an observed increase of C₂²(8) synthon stabilization interaction with increase of pressure. The lattice response rather than interaction within synthons are source of observed pressure-related trend of lattice energy changes. The energy decomposition analysis revealed that the total steric interactions determine the overall trend of lattice energy change with the rise of pressure. Besides geometric aromaticity index was used as a measure of geometric changes. Serious discrepancies were noticed between HOMA values computed with the use of experimental and optimized geometries of the ring. Even inclusion of uncertainties of experimental geometries related to limited precision of X-ray diffraction measurements does not cancel mentioned discrepancies. Although HOMA exhibit similar trends at modest pressures the diversity became surprisingly high at more extreme conditions. This might suggest limitations of periodic DFT computations at elevated pressures and the experimentally observed breaking of molecules at very high pressures will probably not be accounted properly in this approach. Also limitation of direct use of experimental geometries were highlighted.

Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility?

After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

Advances in High-Pressure Biophysics: Status and Prospects of Macromolecular Crystallography

A survey of the main interests of high pressure for molecular biophysics highlights the possibility of exploring the whole conformational space using pressure perturbation. A better understanding of fundamental mechanisms responsible for the effects of high pressure on biomolecules requires high-resolution molecular information. Thanks to recent instrumental and methodological progress taking advantage of the remarkable adaptation of the crystalline state to hydrostatic compression, pressure-perturbed macromolecular crystallography is now a full-fledged technique applicable to a variety of systems, including large assemblies. This versatility is illustrated by selected applications, including DNA fragments, a tetrameric protein, and a viral capsid. Binding of compressed noble gases to proteins is commonly used to solve the phase problem, but standard macromolecular crystallography would also benefit from the transfer of experimental procedures developed for high-pressure studies. Dedicated short-wavelength synchrotron radiation beamlines are unarguably required to fully exploit the various facets of high-pressure macromolecular crystallography.

High-pressure acceleration of the growth kinetics of glucose isomerase crystals

The growth and dissolution rates of glucose isomerase crystals ({1 0 1} face) were measured in situ at 0.1 and 100 MPa. From these data, we determined that the solubilities at 25 degrees C were C(e) = 3.1 +/- 0.9 and 2.6 +/- 0.5 mg mL(-1) at 0.1 and 100 MPa, respectively. At the same supersaturation of sigma = 2.5 (sigma identical with ln(C/C(e)), C = the concentration of glucose isomerase, C(e) = the solubility) and temperature (T = 25 degrees C), the growth rate under 100 MPa was 7.6 times larger than that under 0.1 MPa. This result shows, for the first time, a kinetic acceleration of the growth rates of protein crystals with increasing pressure. The growth rates vs sigma data fitted well with a two-dimensional nucleation growth model of a polynucleation type. The fitting results indicate that the acceleration is mainly due to the decrease in the molecular surface energy of the glucose isomerase crystal with pressure.

Protein under pressure: Molecular dynamics simulation of the arc repressor

Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen-bonding pattern of the intermolecular beta-sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side-chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the beta-sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed.

High-pressure macromolecular crystallography (HPMX): status and prospects

Recent technical developments, achievements and prospects of high-pressure (HP) macromolecular crystallography (MX) are reviewed. Technical difficulties associated with this technique have been essentially solved by combining synchrotron radiation of ultra-short wavelength, large-aperture diamond anvil cells and new sample-mounting techniques. The quality of diffraction data collected at HP can now meet standards of conventional MX. The exploitation of the potential of the combination of X-ray diffraction and high-pressure perturbation is progressing well. The ability of pressure to shift the population distribution of conformers in solution, which is exploited in particular by NMR, can also be used in the crystalline state with specific advantages. HPMX has indeed bright prospects, in particular to elucidate the structure of higher-energy conformers that are often of high biological significance. Furthermore, HPMX may be of interest for conventional crystallographic studies, as pressure is a fairly general tool to improve order in pre-existing crystals with minimal perturbation of the native structure.

The first crystal structure of a macromolecular assembly under high pressure: CpMV at 330 MPa

The structure of cubic Cowpea mosaic virus crystals, compressed at 330 MPa in a diamond anvil cell, was refined at 2.8 A from data collected using ultrashort-wavelength (0.331 A) synchrotron radiation. With respect to the structure at atmospheric pressure, order is increased with lower Debye Waller factors and a larger number of ordered water molecules. Hydrogen-bond lengths are on average shorter and the cavity volume is strongly reduced. A tentative mechanistic explanation is given for the coexistence of disordered and ordered cubic crystals in crystallization drops and for the disorder-order transition observed in disordered crystals submitted to high pressure. Based on such explanation, it can be concluded that pressure would in general improve, albeit to a variable extent, the order in macromolecular crystals.