Phasing methods for protein crystallography

Unveiling success determinants for AMB-assisted phase expansion of fusion proteins in ARP/wARP

Fusion proteins (FPs) are frequently utilized as a biotechnological tool in the determination of macromolecular structures using X-ray methods. Here, we explore the use of different protein tags in various FP, to obtain initial phases by using them in a partial molecular replacement (MR) and constructing the remaining FP structure with ARP/wARP. Usually, the tag is removed prior to crystallization, however leaving the tag on may facilitate crystal formation, and structural determination by expanding phases from known to unknown segments of the complex. In this study, the Protein Data Bank was mined for an up-to-date list of FPs with the most used protein tags, Maltose Binding Protein (MBP), Green Fluorescent Protein (GFP), Thioredoxin (TRX), Glutathione transferase (GST) and the Small Ubiquitin-like Modifier Protein (SUMO). Partial MR using the protein tag, followed by automatic model building, was tested on a subset of 116 FP. The efficiency of this method was analyzed and factors that influence the coordinate construction of a substantial portions of the fused protein were identified. Using MBP, GFP, and SUMO as phase generators it was possible to build at least 75 % of the protein of interest in 36 of the 116 cases tested. Our results reveal that tag selection has a significant impact; tags with greater structural stability, such as GFP, increase the success rate. Further statistical analysis identifies that resolution, Wilson B factor, solvent percentage, completeness, multiplicity, protein tag percentage in the FP (considering amino acids), and the linker length play pivotal roles using our approach. In cases where a structural homologous is absent, this method merits inclusion in the toolkit of protein crystallographers.

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Protein Crystallization in a Microfluidic Contactor with Nafion®117 Membranes

Protein crystallization still remains mostly an empirical science, as the production of crystals with the required quality for X-ray analysis is dependent on the intensive screening of the best protein crystallization and crystal’s derivatization conditions. Herein, this demanding step was addressed by the development of a high-throughput and low-budget microfluidic platform consisting of an ion exchange membrane (117 Nafion^® membrane) sandwiched between a channel layer (stripping phase compartment) and a wells layer (feed phase compartment) forming 75 independent micro-contactors. This microfluidic device allows for a simultaneous and independent screening of multiple protein crystallization and crystal derivatization conditions, using Hen Egg White Lysozyme (HEWL) as the model protein and Hg²⁺ as the derivatizing agent. This microdevice offers well-regulated crystallization and subsequent crystal derivatization processes based on the controlled transport of water and ions provided by the 117 Nafion^® membrane. Diffusion coefficients of water and the derivatizing agent (Hg²⁺) were evaluated, showing the positive influence of the protein drop volume on the number of crystals and crystal size. This microfluidic system allowed for crystals with good structural stability and high X-ray diffraction quality and, thus, it is regarded as an efficient tool that may contribute to the enhancement of the proteins’ crystals structural resolution.

Enhanced yield-mobility products in hybrid halide Ruddlesden-Popper compounds with aromatic ammonium spacers

Hybrid halide Ruddlesden-Popper compounds are related to three-dimensional hybrid AMX₃ perovskites (e.g. where A is a monovalent cation, M is a divalent metal cation, and X is a halogen) with the general formula L₂A_n-1M_nX_3n+1 where L is a monovalent spacer cation. The crystal structure comprises perovskite-like layers separated by organic cation spacers. Here two Ruddlesden-Popper compounds with a conjugated cation, 2-(4-biphenyl)ethylammonium (BPEA) prepared by solvothermal and solvent evaporation techniques are reported. The structures of the two compounds: (BPEA)₂PbI₄ and (BPEA)₂(CH₃NH₃)Pb₂I₇, were solved by X-ray crystallography. The aromatic rings of the BPEA groups are well-separated in the organic layers leading to optical properties comparable to n = 1 and 2 hybrid halide Ruddlesden-Popper compounds with simpler alkyl ammonium cations. The ambient stability of both compounds over time was also confirmed by powder X-ray diffraction. Finally, the transient photoconductance, measured by time-resolved microwave conductivity, show that the compounds have maximum yield-mobility products respectively of 0.07 cm² V^-1 s^-1 and 1.11 cm² V^-1 s^-1 for (BPEA)₂PbI₄ and (BPEA)₂(CH₃NH₃)Pb₂I₇, both slightly enhanced over what has been measured for compounds with n-butylammonium spacer cations.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.

Inversion of Dynamical Scattering from Large-Angle Rocking-Beam Electron Diffraction Patterns

A method for ab initio structure factor retrieval from large-angle rocking-beam electron diffraction data of thin crystals is described and tested with experimental and simulated data. No additional information, such as atomicity or information about chemical composition, has been made use of. Our numerical experiments show that the inversion of dynamical scattering works best, if the beam tilt range is large and the specimen not too thick, because for moderate multiple scattering, the large tilt amplitude effectively removes local minima in this global optimization problem.

NMR-based diffusion lattice imaging

Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

Production of RXLR effector proteins for structural analysis by X-ray crystallography

Structural analysis of RXLR effector proteins from oomycete plant pathogens is an emerging area of research. These studies are aimed at understanding the molecular basis of how these proteins manipulate plant cells to promote infection and also to help define how they can lead to activation of the plant innate immune system. Here, we describe a medium-throughput procedure for cloning and expression testing oomycete RXLR proteins in Escherichia coli. We also describe methods for purification of soluble protein and crystallization, with the aim of determining three-dimensional structures by X-ray crystallography. The procedures are generally applicable to any research program where the production of soluble recombinant protein in E. coli has proven difficult, or where there is a desire to evaluate E. coli thoroughly as a host before considering alternative hosts for heterologous expression.

Emerging opportunities in structural biology with X-ray free-electron lasers

X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be 'outrun' by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of 'diffraction-before-destruction' has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical 'phase problem' by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs.

Solution- and Crystal-Phase Covalent Modification of Lysozyme by a Purpose-Designed Organoruthenium Complex. A MALDI-TOF MS Study of its Metal Binding Sites

Study of the reaction between the transition organometallic complex 4-ruthenocenyl 2,6-dimethylpyrylium tetrafluoroborate and the enzyme hen egg white lysozyme (HEWL) in solution and by diffusion in crystals was performed by use of a combination of spectroscopic and chromatographic methods. Conjugation involving the lysine residues of lysozyme appeared to occur readily, yielding very stable ruthenocenyl pyridinium adducts with average degrees of incorporation ranging from 0.2 to 1.8 metal complexes per protein molecule, depending on reaction conditions. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that the protein conjugates were in fact mixtures of unmodified, mono-, di- and sometimes tripyridinium adducts. In combination with reversed-phased HPLC, we were able to show that six different monoruthenocenyl pyridinium adducts were formed in solution. This result was confirmed by trypsin digestion of a ruthenocenyl pyridinium conjugate and MALDI-TOF MS analysis of the peptide mixture, which showed that lysines 1, 13, 33, 96, 97 and 116 were involved in the reaction with the pyrylium complex, lysines 13, 33 and 116 being the major binding sites. In the tetragonal crystal state, no binding of the ruthenium complex was shown to occur at lysine 116, owing to steric hindrance at this particular position.

Density modification for macromolecular phase improvement

Density modification provides a simple and largely automatic tool for improving phase estimates for observed structure factors. The phase information arises from a combination of the known structure factor magnitudes, the current phase estimates, and stereochemical information. The magnitudes, the current phase estimates, and stereochemical information. The addition of these phase information derived from theoretical sources renders new structures amenable to solution, and reduces the effort required to solve other structures. A diverse array of techniques which have been applied to the phase improvement problem are reviewed.

Advances in direct methods for protein crystallography

Recent advances in ab initio direct methods have enabled the solution of crystal structures of small proteins from native X-ray data alone, that is, without the use of fragments of known structure or the need to prepare heavy-atom or selenomethionine derivatives, provided that the data are available to atomic resolution. These methods are also proving to be useful for locating the selenium atoms or other anomalous scatterers in the multiple wavelength anomalous diffraction phasing of larger proteins at lower resolution.

Sigma2R, a reciprocal-space measure of the quality of macromolecular electron-density maps

It has previously been shown that the presence of distinct regions of solvent and protein in macromolecular crystals leads to a high value of the standard deviation of local r.m.s. electron density and that this can in turn be used as a reliable measure of the quality of macromolecular electron-density maps [Terwilliger & Berendzen (1999a). Acta Cryst. D55, 501-505]. Here, it is demonstrated that a similar measure, sigmaR2, the variance of the local roughness of the electron density, can be calculated in reciprocal space. The formulation is suitable for rapid evaluation of macromolecular crystallographic phases, for phase improvement and for ab initio phasing procedures.

New developments in phase refinement

A longstanding problem in X-ray crystallography is that vital information regarding the crystal phases in missing from the experimental data that are gathered in the diffraction experiment. Prior knowledge needs to be introduced in order to resolve phase ambiguities whenever the diffraction data are not sufficient to unequivocally reconstruct the crystal phases through anomalous or isomorphous differences. Very recent developments include progress in the application of direct methods to small proteins and other compounds of a similar small size (Shake 'n' Bake, SHELXD, CRUNCH and SIR96), bias-free refinement through the gamma-correction (Solomon), improvements in the determination of phase probability distributions (SHARP) and automated atomic refinement (wARP).

The Shake-and-Bake structure determination of triclinic lysozyme

The crystal structure of triclinic lysozyme, comprised of 1,001 non-H protein atoms and approximately 200 bound water molecules, has been determined ab initio (using native data alone) by the "Shake-and-Bake" method by using the computer program SnB. This is the largest structure determined so far by the SnB program. Initial experiments, using default SnB parameters derived from studies of smaller molecules, were unsuccessful. In fact, such experiments produced electron density maps dominated by a single large peak. This problem was overcome by considering the choice of protocol used during the parameter-shift phase refinement. When each phase was subjected to a single shift of +/-157.5 degrees during each SnB cycle, an unusually high percentage of random trials (approximately 22%) yielded correct solutions within 750 cycles. This success rate is higher than that typically observed, even for much smaller structures.