Biomolecular Crystals Research Articles

Shock value: advancing sustainable sensing materials

Shock value: advancing sustainable sensing materials Biomolecular crystals have emerged as exciting new sustainable piezoelectrics. Currently, little research is focused on developing these crystals as reliable, solid-state sensors to integrate into conventional electronic devices due to their water solubility, uncontrolled growth, variable response and electroding difficulties. Pb-FREE is taking on the challenge of accelerating the design, growth, and engineering of these novel piezoelectric materials through high-throughput computational screenings, novel crystal growth procedures, and standardised electromechanical characterisation and packaging.

Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals.

Biomolecular crystals can serve as materials for a plethora of applications including precise guest entrapment. However, as grown, biomolecular crystals are fragile in solutions other than their growth conditions. For crystals to achieve their full potential as hosts for other molecules, crystals can be made stronger with bioconjugation. Building on our previous work using carbodiimide 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) for chemical ligation, here, we investigate DNA junction architecture through sticky base overhang lengths and the role of scaffold proteins in cross-linking within two classes of biomolecular crystals: cocrystals of DNA-binding proteins and pure DNA crystals. Both crystal classes contain DNA junctions where DNA strands stack up end-to-end. Ligation yields were studied as a function of sticky base overhang length and terminal phosphorylation status. The best ligation performance for both crystal classes was achieved with longer sticky overhangs and terminal 3'phosphates. Notably, EDC chemical ligation was achieved in crystals with pore sizes too small for intracrystal transport of ligase enzyme. Postassembly cross-linking produced dramatic stability improvements for both DNA crystals and cocrystals in water and blood serum. The results presented may help crystals containing DNA achieve broader application utility, including as structural biology scaffolds.

Melting entropy of crystals determined by electron-beam-induced configurational disordering.

Upon melting, the molecules in a crystal explore numerous configurations, reflecting an increase in disorder. The molar entropy of disorder can be defined by Boltzmann's formula ΔSd = Rln(Wd), where Wd is the increase in the number of microscopic states, so far inaccessible experimentally. We found that the Arrhenius frequency factor A of the electron diffraction signal decay provides Wd through an experimental equation A = AINTWd, where AINT is an inelastic scattering cross section. The method connects Clausius and Boltzmann experimentally and supplements the Clausius approach, being applicable to a femtogram quantity of thermally unstable and biomolecular crystals. The data also showed that crystal disordering and crystallization of melt are reciprocal, both governed by the entropy change but manifesting in opposite directions.

State-of-the Art Research in Biomolecular Crystals

This special issue, State-of-the Art Investigations on Biomolecular Crystals, is focused on strategies to procure suitable crystals for high-resolution X-ray crystallographic investigations [...]

Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity.

During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (R g) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize R g) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger R g). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower R g values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.

Getting the Lead Out: Biomolecular Crystals as Low-Cost, High-Performance Piezoelectric Components.

Getting the Lead Out: Biomolecular Crystals as Low-Cost, High-Performance Piezoelectric Components.

Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide crosslinking agent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) under various optimization conditions: 5′ vs. 3′ terminal phosphate, EDC concentration, EDC incubation time, and repeated EDC dose. This crosslinking and DNA ligation route did not destroy crystal diffraction. In fact, the ligation of DNA across the DNA–DNA junctions was clearly revealed via X-ray diffraction structure determination. Furthermore, crystal macrostructure was fortified. Neither the loss of counterions in pure water, nor incubation in blood serum, nor incubation at low pH (2.0 or 4.5) led to apparent crystal degradation. These findings motivate the use of crosslinked biomolecular co-crystals for purposes beyond structural biology, including biomedical applications.

Local Piezoelectric Properties of Doped Biomolecular Crystals.

Piezoelectricity is the ability of certain crystals to generate mechanical strain proportional to an external electric field. Though many biomolecular crystals contain polar molecules, they are frequently centrosymmetric, signifying that the dipole moments of constituent molecules cancel each other. However, piezoelectricity can be induced by stereospecific doping leading to symmetry reduction. Here, we applied piezoresponse force microscopy (PFM), highly sensitive to local piezoelectricity, to characterize faces of a popular biomolecular material, α-glycine, doped with other amino acids such as L-alanine and L-threonine as well as co-doped with both. We show that, while apparent vertical piezoresponse is prone to parasitic electrostatic effects, shear piezoelectric activity is strongly affected by doping. Undoped α-glycine shows no shear piezoelectric response at all. The shear response of the L-alanine doped crystals is much larger than those of the L-threonine doped crystals and co-doped crystals. These observations are rationalized in terms of host–guest molecule interactions.

2D Layered Dipeptide Crystals for Piezoelectric Applications

Abstract2D piezoelectric materials such as transition metal dichalcogenides are attracting significant attention because they offer various benefits over bulk piezoelectrics. In this work, the fabrication of layered biomolecular crystals of diphenylalanine (FF) obtained via a co‐assembly of l,l‐ and d,d‐ enantiomers of FF monomers is reported. Their crystal structure, thermal and chemical stabilities, and piezoelectric properties are investigated. Single crystal X‐ray diffraction results show that FF enantiomers are arranged in the form of bilayers consisting of monomers with alternating chirality packed into a tape‐like monoclinic structure belonging to a polar space group P21. Each bilayer (≈1.5 nm thick) demonstrates strong out‐of‐plane piezoelectricity (d33 ≈ 20 pm V−1) that is almost an order of magnitude higher than in the archetypical piezoelectric material quartz. The grown crystals demonstrate better thermal and chemical stabilities than self‐assembled hexagonal FF nanotubes studied in the past. Piezoelectric bilayers, being held via weak aromatic interaction in the bulk crystals, can be exfoliated by mechanical or chemical methods, thus resulting in a 2D piezoelectric material, which can find various applications in biocompatible and ecologically friendly electromechanical microdevices, such as sensors, actuators, and energy harvesting elements used in implantable and wearable electronics.

Hybridization of Biomolecular Crystals and Low-Dimensional Materials.

In cellular environments, metabolites, peptides, proteins, and other biomolecules can self-assemble into planar and fibrilar molecular crystals. We use atomistic molecular dynamics simulations to show that such biomolecular crystals coupled with low-dimensional materials can form stable hybrid superstructures. We discuss enantiopure and racemic TRP and PHE amino acid crystals adsorbed on or intercalated between graphene, phosphorene, and carbon nanotubes. While racemic biomolecular crystals tend to stay straight in solutions and when adsorbed on flat and cylindrical nanosurfaces, enantiopure crystals undergo twisting. Mixed material properties of these hybrid superstructures can be attractive in many applications.

Macromolecular crystallization: basics and advanced methodologies

For the first time, about 155 years ago and as a laboratory curiosity, German biologists observed the crystals of hemoglobin from worms and fishes. Since then, the crystallization of proteins, nucleic acids and big biological structures, like viruses, has been developed into a broad research field including several applications, for example in the drug discovery. This review is divided into four major sections. The first section addresses the specific physicochemical properties of biomolecular crystals accompanied by kinetics of supersaturation, nucleation and growth which are the three main steps required to achieve macromolecular crystals. Besides, various physical, chemical and biochemical parameters influencing the process of macromolecular crystallization are reviewed. The second part deals with classical approaches, such as vapor and batch diffusion methods, available to create macromolecular crystals. The third part overviews novel approaches including microgravity, cocrystallization, membrane-assisted crystallization and microfluidic array chips involved in more complicated techniques for growing macromolecular crystals and controlling their size and orientation. In the end, considering the very significant role of automation in providing biomolecules’ crystals in recent years, we provided a brief explanation about robotics and their importance in developing high-throughput crystallization. RDC-NMR and SAXS/WAXS hybrid methods with the aim of obtaining structural information of complex macromolecular assemblies are also discussed.

Atomistic-Benchmarking towards a protocol development for rapid quantitative metrology of piezoelectric biomolecular materials

Biomolecular crystals are an emerging class of piezoelectric materials that are both biocompatible and biodegradable, which enables their use in biomedical applications and smart devices while ensuring eco-friendly production and disposal. However, accurate quantification of the piezoelectric response of soft sub-micron crystals remains a significant challenge, as conventional piezoelectric measurement techniques are suited to ceramics, thin films, and polymers. Here, we demonstrate the use of a novel piezoresponse force microscopy (PFM) methodology for robust, reliable quantification of the electromechanical response of biomolecular crystals. As a strong test of high accuracy and precision, we show that PFM, integrated with quantum mechanical (QM) density functional theory (DFT) calculations, can distinguish the piezoelectric responses of near-isopiezoelectric amino acid crystals. We show that a statistical approach, combined with experimental best practices, provides effective piezoelectric coefficients of biomolecular single crystals accurately and unambiguously. This work opens the door to high-throughput screening and characterisation of natural and engineered soft piezoelectric crystals for eco-friendly energy harvesters and biodegradable medical implants, reducing dependence on lead-based and rare-earth-containing piezoelectric materials.

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations

Summary X-ray crystallography is the primary tool for biomolecular structural determination. However, contacts formed through the crystal lattice are known to affect structures, especially for small and flexible molecules such as DNA oligomers, by introducing significant structural changes in comparison to solution. Furthermore, why molecules crystallize in certain symmetry groups, which role crystallization additives play, and whether they are just innocuous and unspecific crystallization catalysts remain unclear. By using one of the currently best-performing DNA force fields and applying significant computational effort, we described the nature of intermolecular forces that stabilize B-DNA crystals in various symmetry groups and solvent environments with an unprecedented level of detail. We showed a tight coupling between the lattice stability and the type of crystallization additives and that certain symmetry groups are stable only in the presence of a specific additive. Additives and crystal contacts induce small but non-negligible changes in the physical properties of DNA.

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics.

IR laser-induced protein crystal transformation.

A method and the design of instrumentation, and its preliminary practical realisation, including test experiments, with the object of inducing phase changes of biomolecular crystals by controlled dehydration through heating with infrared (IR) light are described. The aim is to generate and select crystalline phases through transformation in the solid state which have improved order (higher resolution in X-ray diffraction experiments) and reduced mosaic spread (more uniformly aligned mosaic blocks) for diffraction data collection and analysis. The crystal is heated by pulsed and/or constant IR laser irradiation. Loss of crystal water following heating and its reabsorption through equilibration with the environment is measured optically by a video system. Heating proved superior to traditional controlled dehydration by humidity change for the test cases CODH (carbon monoxide dehydrogenase) and CLK2 (a protein kinase). Heating with IR light is experimentally simple and offers an exploration of a much broader parameter space than the traditional method, as it allows the option of varying the rate of phase changes through modification of the IR pulse strength, width and repeat frequency. It impacts the crystal instantaneously, isotropically and homogeneously, and is therefore expected to cause less mechanical stress.

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

Biomolecular X-ray structures typically provide a static, time- and ensemble-averaged view of molecular ensembles in crystals. In the absence of rigid-body motions and lattice defects, B-factors are thought to accurately reflect the structural heterogeneity of such ensembles. In order to study the effects of averaging on B-factors, we employ molecular dynamics simulations to controllably manipulate microscopic heterogeneity of a crystal containing 216 copies of villin headpiece. Using average structure factors derived from simulation, we analyse how well this heterogeneity is captured by high-resolution molecular-replacement-based model refinement. We find that both isotropic and anisotropic refined B-factors often significantly deviate from their actual values known from simulation: even at high 1.0 Å resolution and Rfree of 5.9%, B-factors of some well-resolved atoms underestimate their actual values even sixfold. Our results suggest that conformational averaging and inadequate treatment of correlated motion considerably influence estimation of microscopic heterogeneity via B-factors, and invite caution in their interpretation.

Peptide Crystal Simulations Reveal Hidden Dynamics

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom RMSD; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom RMSD. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(-) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data as well as to validate computational chemistry methods.

Efficient UV detection of protein crystals enabled by fluorescence excitation at wavelengths longer than 300 nm

It is well known that most proteins and many other biomolecules fluoresce when illuminated with UV radiation, but it is also commonly accepted that utilizing this property to detect protein crystals in crystallization setups is limited by the opacity of the materials used to contain and seal them. For proteins, this fluorescence property arises primarily from the presence of tryptophan residues in the sequence. Studies of protein crystallization results in a variety of setup configurations show that the opacity of the containment hardware can be overcome at longer excitation wavelengths, where typical hardware materials are more transparent in the UV, by the use of a powerful UV-light source that is effective in excitation even though not at the maximum of the excitation response. The results show that under these circumstances UV evaluation of crystallization trials and detection of biomolecular crystals in them is not limited by the hardware used. It is similarly true that a deficiency in tryptophan or another fluorescent component that limits the use of UV light for these purposes can be effectively overcome by the addition of fluorescent prostheses that bind to the biomolecule under study. The measurements for these studies were made with a device consisting of a potent UV-light source and a detection system specially adapted (i) to be tunable via a motorized and software-controlled absorption-filter system and (ii) to convey the excitation light to the droplet or capillary hosting the crystallization experiment by quartz-fibre light guides.

Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals

Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.

Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics

When polychromatic X-rays are shined onto crystalline material, they generate a Laue diffraction pattern. At third generation synchrotron radiation sources, a single X-ray pulse of approximately 100 ps duration is enough to produce interpretable Laue data from biomolecular crystals. Thus, by initiating biological turnover in a crystalline protein, structural changes along the reaction pathway may be filmed by ultra-fast Laue diffraction. Using laser-light as a trigger, transient species in photosensitive macromolecules can be captured at near atomic resolution with sub-nanosecond time-resolution. Such pump-probe Laue experiments have now reached an outstanding level of sophistication and have found a domain of excellence in the investigation of light-sensitive proteins undergoing cyclic photo-reactions and producing stiff crystals. The main theoretical concepts of Laue diffraction and the challenges associated with time-resolved experiments on biological crystals are recalled. The recent advances in the design of experiments are presented in terms of instrumental choices, data collection strategy and data processing, and some of the inherent difficulties of the method are highlighted. The discussion is based on the example of myoglobin, a protein that has traversed the whole history of pump-probe Laue diffraction, and for which a massive amount of data have provided considerable insight into the understanding of protein dynamics.