Diverse Structural Motifs Research Articles

Dipeptides as Microporous Materials

The synthesis and characterization of hydrophobic porous frameworks designed for a variety of applications has attracted significant research efforts over the last few years. The key idea in such studies is to design building elements which allow for controllable assembly and disassembly, and which may be extensively replaced and modified to give porous frameworks with various topologies and functions. The natural world often provides excellent examples of how to proceed with the design of materials; for example, the initial experiences with natural zeolites has led to very successful efforts to produce a wide variety of industrially relevant synthetic materials. Recently, supramolecular architectures based upon weaker interactions have motivated a number of studies; polypeptides that can build tubular and helical structures, frequently referred as nanotubes, have attracted considerable attention because of their biological relevancy as ion channels, membrane pores, etc. These naturally occurring and artificially created materials reveal a sophisticated complexity and are often difficult to characterize in detail. Thus, the lower oligomeric peptides, being both simpler model systems and cheaper, would appear to be useful as practical porous materials, especially since some dipeptides demonstrate the ability to host small organic molecules. Moreover, the ability of single crystals of the dipeptides to sustain guest solvent exchange and removal was reported. Herein we examine the structure and sorption properties of the two closely related dipeptides l-alanyl-lvaline (AV) and l-valyl-l-alanine (VA; Scheme 1), and show that these lower oligomers have considerable promise as novel porous materials. Moreover, the wide variety of amino acids available should allow the assembly of materials with quite diverse structural motifs containing significant void space. The two dipeptides AV and VA are microporous crystalline materials. Hexagonal prisms of the dipeptides were grown from water and characterized by single-crystal X-ray diffraction (XRD) analysis at room temperature (Table 1).

DNA binding and cleavage by the HNH homing endonuclease I-HmuI.

The structure of I-HmuI, which represents the last family of homing endonucleases without a defining crystallographic structure, has been determined in complex with its DNA target. A series of diverse protein structural domains and motifs, contacting sequential stretches of nucleotide bases, are distributed along the DNA target. I-HmuI contains an N-terminal domain with a DNA-binding surface found in the I-PpoI homing endonuclease and an associated HNH/N active site found in the bacterial colicins, and a C-terminal DNA-binding domain previously observed in the I-TevI homing endonuclease. The combination and exchange of these features between protein families indicates that the genetic mobility associated with homing endonucleases extends to the level of independent structural domains. I-HmuI provides an unambiguous structural connection between the His-Cys box endonucleases and the bacterial colicins, supporting the hypothesis that these enzymes diverged from a common ancestral nuclease.

Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein

The global fold of maltose-binding protein in complex with the substrate β-cyclodextrin was determined by solution NMR methods. The two-domain protein is comprised of a single polypeptide chain of 370 residues, with a molecular mass of 42 kDa. Distance information in the form of H N-H N, H N-CH 3 and CH 3-CH 3 NOEs was recorded on 15N, 2H and 15N, 13C, 2H-labeled proteins with methyl protonation in Val, Leu, and Ile (C δ1 only) residues. Distances to methyl protons, critical for the structure determination, comprised 77 % of the long-range restraints. Initial structures were calculated on the basis of 1943 NOEs, 48 hydrogen bond and 555 dihedral angle restraints. A global pair-wise backbone rmsd of 5.5 Å was obtained for these initial structures with rmsd values for the N and C domains of 2.4 and 3.8 Å, respectively. Direct refinement against one-bond 1H N- 15N, 13C α- 13CO, 15N- 13CO, two-bond 1H N- 13CO and three-bond 1H N- 13C α dipolar couplings resulted in structures with large numbers of dipolar restraint violations. As an alternative to direct refinement against measured dipolar couplings we have developed an approach where discrete orientations are calculated for each peptide plane on the basis of the dipolar couplings described above. The orientation which best matches that in initial NMR structures calculated from NOE and dihedral angle restraints exclusively is used to refine further the structures using a new module written for CNS. Modeling studies from four different proteins with diverse structural motifs establishes the utility of the methodology. When applied to experimental data recorded on MBP the precision of the family of structures generated improves from 5.5 to 2.2 Å, while the rmsd with respect to the X-ray structure (1dmb) is reduced from 5.1 to 3.3 Å.

Self-assembly of nanoparticles into structured spherical and network aggregates

Multi-scale ordering of materials is central for the application of molecular systems in macroscopic devices. Self-assembly based on selective control of non-covalent interactions provides a powerful tool for the creation of structured systems at a molecular level, and application of this methodology to macromolecular systems provides a means for extending such structures to macroscopic length scale. Monolayer-functionalized nanoparticles can be made with a wide variety of metallic and non-metallic cores, providing a versatile building block for such approaches. Here we present a polymer-mediated 'bricks and mortar' strategy for the ordering of nanoparticles into structured assemblies. This methodology allows monolayer-protected gold particles to self-assemble into structured aggregates while thermally controlling their size and morphology. Using 2-nm gold particles as building blocks, we show that spherical aggregates of size 97 +/- 17 nm can be produced at 23 degrees C, and that 0.5-1 microm spherical assemblies with (5-40) x 10(5) individual subunits form at -20 degrees C. Intriguingly, extended networks of approximately 50-nm subunits are formed at 10 degrees C, illustrating the potential of our approach for the formation of diverse structural motifs such as wires and rods. These findings demonstrate that the assembly process provides control over the resulting aggregates, while the modularity of the 'bricks and mortar' approach allows combinatorial control over the constituents, providing a versatile route to new materials systems.