Macromolecular crystal growth as revealed by atomic force microscopy

Synthesis and Characterization of MOF-Derived Structures: Recent Advances and Future Perspectives

Due to their facile tunability, metal-organic frameworks (MOFs) are employed as precursors and templates to construct advanced functional materials with unique and desired chemical, physical, mechanical, and morphological properties. By tuning MOF precursor composition and manipulating conversion processes, various MOF-derived materials commonly known as MOF derivatives can be constructed. The possibility of controlled and predictable properties makes MOF derivatives a preferred choice for numerous advanced technological applications. The innovative synthetic designs besides the plethora of interdisciplinary characterization approaches applicable to MOF derivatives provide the opportunity to perform a myriad of experiments to explore the performance and offer key insight to develop the next generation of advanced materials. Though there are many published works of literature describing various synthesis and characterization techniques of MOF derivatives, it is still not clear how the synthesis mechanism works and what are the best techniques to characterize these materials to probe their properties accurately. In this review, the recent development in synthesis techniques and mechanisms for a variety of MOF derivates such as MOF-derived metal oxides, porous carbon, composites/hybrids, and sulfides is summarized. Furthermore, the details of characterization techniques and fundamental working principles are summarized to probe the structural, mechanical, physiochemical, electrochemical, and electronic properties of MOF and MOF derivatives. The future trends and some remaining challenges in the synthesis and characterization of MOF derivatives are also discussed.

A minimal colloid model of solution crystallization nucleates crystals classically

A fundamental assumption of the classical theories of crystal nucleation is that the individual molecules from the "old" phase associate to an emerging nucleus individually and sequentially. Numerous recent studies of crystal nucleation in solution have revealed nonclassical pathways, whereby crystal nuclei are hosted and fed by amorphous clusters pre-formed in the solution. A sizable knowledge gap has persisted, however, in the definition of the molecular-level parameters that direct a solute towards classical or nonclassical nucleation. Here we construct a suspension of colloid particles of hydrodynamic diameter 1.1 μm and monitor their individual motions towards a quasi-two-dimensional crystal by scanning confocal microscopy. We combine electrostatic repulsion and polymer-induced attraction to obtain a simple isotropic pair interaction potential with a single attractive minimum of tunable depth between 1.2kBT and 2.7kBT. We find that even the smallest aggregates that form in this system structure as hexagonal two-dimensional crystals and grow and maturate by the association and exchange of single particles from the solution, signature behaviors during classical nucleation. The particles in the suspension equilibrate with those in the clusters and the volume fractions of suspensions at equilibrium correspond to straightforward thermodynamic predictions based on depth of the interparticle attraction. These results demonstrate that classical nucleation is selected by particles interacting with a minimal potential and present a benchmark for future modifications of the molecular interactions that may induce nonclassical nucleation.

A combined approach to characterize ligand-induced solid-solid phase transitions in biomacromolecular crystals

Solid-solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. The adenine riboswitch (riboA) is an RNA control element that uses ligand-induced conformational changes to regulate gene expression. Crystals of riboA, upon the addition of a ligand, undergo an SSPT from monoclinic to triclinic to orthorhombic. Here, solution atomic force microscopy (AFM) and polarized video microscopy (PVM) are used to characterize the multiple transition states throughout the SSPT in both the forward and the reverse directions. This contribution describes detailed protocols for growing crystals directly on mica or glass surfaces for AFM and PVM characterization, respectively, as well as methods for image processing and phase-transition kinetics analysis.

Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystallizability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.

Nanoscopic observation of a DNA crystal surface and its dynamic formation and degradation using atomic force microscopy

We report the direct observation of the formation and degradation of tensegrity triangle DNA crystals using atomic force microscopy (AFM). We observed the crystal surface by AFM and characterized the lattice coordination of the assembled triangle units at a molecular level. We visualized dynamic formation and degradation of the crystals and characterized them at nano-scale resolution.

Dislocations in molecular crystals

Dislocations in molecular crystals remain terra incognita. Owing to the complexity of molecular structure, dislocations in molecular crystals can be difficult to understand using only the foundational concepts devised over decades for hard materials. Herein, we review the generation, structure, and physicochemical consequences of dislocations in molecular crystals. Unlike metals, ceramics, and semiconductors, molecular crystals are often characterized by flexible building units of low symmetry, thereby limiting analysis, complicating modeling, and prompting new approaches to elucidate their role in crystallography from growth to mechanics. Such considerations affect applications ranging from plastic electronics and mechanical actuators to the tableting of pharmaceuticals.

Truncation Derivatives of the S-Layer Protein of Sporosarcina ureae ATCC 13881 (SslA): Towards Elucidation of the Protein Domain Responsible for Self-Assembly

The cell surface of Sporosarcina ureae ATCC 13881 is covered by an S-layer (SslA) consisting of identical protein subunits that assemble into lattices exhibiting square symmetry. In this work the self-assembly properties of the recombinant SslA were characterised with an emphasis on the identification of protein regions responsible for self-assembly. To this end, recombinant mature SslA (aa 31-1097) and three SslA truncation derivatives (one N-terminal, one C-terminal and one CN-terminal) were produced in a heterologous expression system, isolated, purified and their properties analysed by in vitro recrystallisation experiments on a functionalised silicon wafer. As a result, recombinant mature SslA self-assembled into crystalline monolayers with lattices resembling the one of the wild-type SslA. The study identifies the central protein domain consisting of amino acids 341-925 self-sufficient for self-assembly. Neither the first 341 amino acids nor the last 172 amino acids of the protein sequence are required to self-assemble into lattices.

Role of clusters in nonclassical nucleation and growth of protein crystals

The development of multistep nucleation theory has spurred on experimentalists to find intermediate metastable states that are relevant to the solidification pathway of the molecule under interest. A great deal of studies focused on characterizing the so-called "precritical clusters" that may arise in the precipitation process. However, in macromolecular systems, the role that these clusters might play in the nucleation process and in the second stage of the precipitation process, i.e., growth, remains to a great extent unknown. Therefore, using biological macromolecules as a model system, we have studied the mesoscopic intermediate, the solid end state, and the relationship that exists between them. We present experimental evidence that these clusters are liquid-like and stable with respect to the parent liquid and metastable compared with the emerging crystalline phase. The presence of these clusters in the bulk liquid is associated with a nonclassical mechanism of crystal growth and can trigger a self-purifying cascade of impurity-poisoned crystal surfaces. These observations demonstrate that there exists a nontrivial connection between the growth of the macroscopic crystalline phase and the mesoscopic intermediate which should not be ignored. On the other hand, our experimental data also show that clusters existing in protein solutions can significantly increase the nucleation rate and therefore play a relevant role in the nucleation process.

Crystal growth of MOF-5 using secondary building units studied by in situ atomic force microscopy

Crystal growth of the metal–organic framework, MOF-5, using basic zinc benzoate, [Zn₄O(O₂CC₆H₅)₆], was studied in real time using atomic force microscopy.

Crystal growth as an excitable medium

Crystal growth has been widely studied for many years, and, since the pioneering work of Burton, Cabrera and Frank, spirals and target patterns on the crystal surface have been understood as forms of tangential crystal growth mediated by defects and by two-dimensional nucleation. Similar spirals and target patterns are ubiquitous in physical systems describable as excitable media. Here, we demonstrate that this is not merely a superficial resemblance, that the physics of crystal growth can be set within the framework of an excitable medium, and that appreciating this correspondence may prove useful to both fields. Apart from solid crystals, we discuss how our model applies to the biomaterial nacre, formed by layer growth of a biological liquid crystal.

Initial crystallographic studies of a small heat-shock protein from Xylella fastidiosa

The ORF XF2234 in the Xylella fastidiosa genome was identified as encoding a small heat-shock protein of 17.9 kDa (HSP17.9). HSP17.9 was found as one of the proteins that are induced during X. fastidiosa proliferation and infection in citrus culture. Recombinant HSP17.9 was crystallized and surface atomic force microscopy experiments were conducted with the aim of better characterizing the HSP17.9 crystals. X-ray diffraction data were collected at 2.7 Å resolution. The crystal belonged to space group P4(3)22, with unit-cell parameters a = 68.90, b = 68.90, c = 72.51 Å, and is the first small heat-shock protein to crystallize in this space group.

Surface dependence of protein nanocrystal formation

The self-assembly kinetics and nanocrystal formation of the bacterial surface-layer-protein SbpA are studied with a combination of quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). Silane coupling agents, aminopropyltriethoxysilane (APTS) and octadecyltrichlorosilane (OTS), are used to vary the protein-surface interaction in order to induce new recrystallization pathways. The results show that the final S-layer crystal lattice parameters (a = b = 14 nm, gamma = 90 degrees ), the layer thickness (15 nm), and the adsorbed mass density (1700 ng cm(-2)) are independent of the surface chemistry. Nevertheless, the adsorption rate is five times faster on APTS and OTS than on SiO(2,) strongly affecting protein nucleation and growth. As a consequence, protein crystalline domains of 0.02 microm(2) for APTS and 0.05 microm(2) for OTS are formed, while for silicon dioxide the protein domains have a typical size of about 32 microm(2). In addition, more-rigid crystalline protein layers are formed on hydrophobic substrates. In situ AFM experiments reveal three different kinetic steps: adsorption, self-assembly, and crystalline-domain reorganization. These steps are corroborated by frequency-dissipation curves. Finally, it is shown that protein adsorption is a diffusion-driven process. Experiments at different protein concentrations demonstrate that protein adsorption saturates at 0.05 mg mL(-1) on silane-coated substrates and at 0.07 mg mL(-1) on hydrophilic silicon dioxide.

Effect of protein solution components in the adsorption of Herbaspirillum seropedicae GlnB protein on mica

The adsorption of proteins and its buffer solution on mica surfaces was investigated by atomic force microscopy (AFM). Different salt concentration of the Herbaspirillum seropedicae GlnB protein (GlnB-Hs) solution deposited on mica was investigated. This protein is a globular, soluble homotrimer (36kDa), member of PII-like proteins family involved in signal transducing in prokaryote. Supramolecular structures were formed when this protein was deposited onto bare mica surface. The topographic AFM images of the GlnB-Hs films showed that at high salt concentration the supramolecular structures are spherical-like, instead of the typical doughnut-like shape for low salt concentration. AFM images of NaCl and Tris from the buffer solution showed structures with the same pattern as those observed for high salt protein solution, misleading the image interpretation. XPS experiments showed that GlnB protein film covers the mica surface without chemical reaction.

Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal

Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48-54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton-Cabrera-Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299-358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications.

Structure and growth of ultrasmall protein microcrystals by synchrotron radiation: II. microGISAX and microscopy of lysozyme

The early steps of growth and nucleation of the lysozyme microcrystals by classical and nanotemplate-based hanging vapor diffusion methods are studied using microGISAXS at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Out-of-plane cuts in the Yoneda regions of the 2D scattering profiles point to the detection of ultrasmall lysozyme crystals by microGISAXS quite before than by light microscopy. Furthermore lysozyme crystal formation occurs quite earlier with the nanotemplate than with the classical method. Our data are compatible with two distinct modes of crystal nucleation and growth for P450sc and lysozyme.

Visualization of single receptor molecules bound to human rhinovirus under physiological conditions

Dynamic force microscopy (DFM) was used to image human rhinovirus HRV2 alone and complexed with single receptor molecules under near physiological conditions. Specific and site-directed immobilization of HRV2 on a model cell membrane resulted in a crystalline arrangement of virus particles with hexagonal symmetry and 35 nm spacing. High-resolution imaging of the virus capsid revealed about 20 resolvable structural features with 3 nm diameters; this finding is in agreement with protrusions seen by cryo-electron microscopy. Binding of receptor molecules to individual virus particles was observed after injection of soluble receptors into the liquid cell. Virus-receptor complexes with zero, one, two, or three attached receptor molecules were resolved. The number of receptor molecules associated to virions increased over time. Occasionally, dissociation of single receptor molecules from viral particles was also observed.

Crystallization of oxytetracycline from fermentation waste liquor: influence of biopolymer impurities

Organic impurities in the fermentation broth of antibiotic production impose great difficulties in the crystallization and recovery of antibiotics from the concentrated waste liquor. In the present laboratory study, the inhibitory effect of biopolymers on antibiotic crystallization was investigated using oxytetracycline (OTC) as the model antibiotic. Organic impurities separated from actual OTC fermentation waste liquor by ultrafiltration were dosed into a pure OTC solution at various concentrations. The results demonstrated that small organic molecules with an apparent molecular weight (AMW) of below 10,000 Da did not affect OTC crystallization significantly. However, large biopolymers, especially polysaccharides, in the fermentation waste caused severe retardation of crystal growth and considerable deterioration in the purity of the OTC crystallized. Atomic force microscopy (AFM) revealed that OTC nuclei formed in the solution attached to the surfaces of large organic molecules, probably polysaccharides, instead of being surrounded by proteins as previously thought. It is proposed that the attachment of OTC nuclei to biopolymers would prevent OTC from rapid crystallization, resulting in a high OTC residue in the aqueous phase. In addition, the adsorption of OTC clusters onto biopolymers would destabilize the colloidal system of organic macromolecules and promote particle flocculation. OTC crystallization would therefore take place with the precipitation of abundant organic impurities. Hence, the removal of polysaccharides and other biopolymers by ultrafiltration can be an effective means of improving the recovery of OTC and similar antibiotics by crystallization from the fermentation waste.

Turning protein crystallisation from an art into a science

Protein crystallisation has gained a new strategic and commercial relevance in the post-genomic era because of its pivotal role in structural genomics. Producing high-quality crystals has always been a bottleneck to structure determination and, with the advent of proteomics, this problem is becoming increasingly acute. The task of producing suitable crystals may be tackled using two approaches. The first relies on empirical techniques that are based mainly on trial and error, and what is perceived to be the 'art' of crystallisation. The second approach is aimed at gaining an understanding of the fundamental principles that govern crystallisation; this knowledge may be applied to design experimental methodology for producing high-quality crystals of medical and industrial interest.