Stability of collagen heterotrimer with same charge pattern and different charged residue identities.

Salt bridges are important factors in maintaining the stability of proteins, and their contribution to protein folding has received much attention. Although the interaction energies, or stabilizing contributions, of individual salt bridges have been measured in various proteins, a systematic assessment of various types of salt bridges in a relatively uniform environment is still a valuable analysis. Here, we used a collagen heterotrimer as a host-guest platform to construct 48 heterotrimers with the same charge pattern. A variety of salt bridges were formed between the oppositely charged residues Lys, Arg, Asp, and Glu. The melting temperature (Tm) of the heterotrimers was measured with circular dichroism. The atomic structures of 10 salt bridges were shown in three x-ray crystals of heterotrimer. Molecular dynamics simulation based on the crystal structures indicated that strong, intermediate, and weak salt bridges have distinctive N-O distances. A linear regression model was used to predict the stability of heterotrimers with high accuracy (R2 = 0.93). We developed an online database to help readers understand how a salt bridge stabilizes collagen. This work will help us better understand the stabilizing mechanism of salt bridges in collagen folding and provide a new strategy to design collagen heterotrimers.

2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems.

Poly(A-T)-rich sequences have been applied as stems of DNA dumbbell tiles for construction of single crystalline 2D DNA lattice arrays in slightly acidic solutions. These arrays show much higher stability and better organised crystalline lattice structures than those assembled from DNA dumbbell tiles with randomly sequenced stems in slightly alkaline environments. DNA nanotechnology probably provides a useful platform to study the mechanical properties of DNA duplexes with specific sequences.

How electrostatic networks modulate specificity and stability of collagen.

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Synthesis and conformational analysis of linear homo- and heterooligomers from novel 2-C-branched sugar amino acids (SAAs).

Sugar amino acids (SAAs), as biologically interesting structures bearing both amino and carboxylic acid functional groups represent an important class of multifunctional building blocks. In this study, we develop an easy access to novel SAAs in only three steps starting from nitro compounds in high yields in analytically pure form, easily available by ceric (IV) mediated radical additions. Such novel SAAs have been applied in the assembly of total nine carbopeptoids with the form of linear homo- and heterooligomers for the structural investigations employing circular dichroism (CD) spectroscopy, which suggest that the carbopeptoids emerge a well-extended, left (or right)-handed conformation similar to polyproline II (PPII) helices. NMR studies also clearly demonstrated the presence of ordered secondary structural elements. 2D-ROESY spectra were acquired to identify i+1 NH ↔ i C 1 H, i C 2 H correlations which support the conformational analysis of tetramers by CD spectroscopy. These findings provide interesting information of SAAs and their oligomers as potential scaffolds for discovering new drugs and materials.

Parallels between DNA and collagen - comparing elastic models of the double and triple helix.

Multi-stranded helices are widespread in nature. The interplay of polymeric properties with biological function is seldom discussed. This study probes analogies between structural and mechanical properties of collagen and DNA. We modeled collagen with Eulerian rotational and translational parameters of adjacent rungs in the triple-helix ladder and developed statistical potentials by extracting the dispersion of the parameters from a database of atomic-resolution structures. The resulting elastic model provides a common quantitative way to describe collagen deformations upon interacting with integrins or matrix metalloproteinase and DNA deformations upon protein binding. On a larger scale, deformations in Type I collagen vary with a periodicity consistent with the D-periodic banding of higher-order fibers assemblies. This indicates that morphologies of natural higher-order collagen packing might be rooted in the characteristic deformation patterns.

Selective Catalytic B-H Arylation of o-Carboranyl Aldehydes by a Transient Directing Strategy.

Carboranyl aldehydes are among the most useful synthons in derivatization of carboranes. However, compared to the utilization of carboranyl carboxylic acids in selective B-H bond functionalizations, the synthetic application of carboranyl aldehydes is limited due to the weakly coordinating nature of the aldehyde group. Herein, the direct arylation of o-carboranyl aldehydes has been developed via Pd-catalyzed cage B-H bond functionalization. With the help of glycine to generate a directing group (DG) in situ, a series of cage B(4,5)-diarylated- and B(4)-monoarylated-o-carboranyl aldehydes were obtained in good to excellent yields with high selectivity. A wide range of functional groups are tolerated. The aldehyde group in the B-H arylated products could be readily removed or transformed into o-carboranyl methanol. A plausible catalytic cycle for B-H arylation was proposed based on control experiments and stoichiometric reactions, including the isolation of a key bicyclic palladium complex.

Small circular DNA molecules act as rigid motifs to build DNA nanotubes.

Small circular DNA molecules with designed lengths, for example 64 and 96 nucleotides (nt), after hybridization with a few 32-nt staple strands respectively, can act as rigid motifs for the construction of DNA nanotubes with excellent uniformity in ring diameter. Unlike most native DNA nanotubes, which consist of longitudinal double helices, nanotubes assembled from circular DNAs are constructed from lateral double helices. Of the five types of DNA nanotubes designed here, four are built by alternating two different rings of the same ring size, while one is composed of all the same 96-nt rings. Nanotubes constructed from the same 96-nt rings are 10-100 times shorter than those constructed from two different 96-nt rings, because there are fewer hinge joints on the rings.

Periodical assembly of repetitive RNA sequences synthesized by rolling circle transcription with short DNA staple strands to RNA-DNA hybrid nanowires.

The long single-stranded RNAs produced from Rolling Circle Transcription (RCT) were used as scaffolds to be folded with a few short DNA staples into RNA-DNA hybrid nanowires.

RCA strands as scaffolds to create nanoscale shapes by a few staple strands.

Thousands of nucleotide(nt)-long single strand DNAs, generated from rolling-circle-amplification (RCA), were used as scaffolds to create DNA nanoscale wires and plates with a few short staple strands by following the origami design principle with a crossover at 1.5 turns. The core sequence of the circle template, for producing tens and hundreds of tandemly repeated copies of it by RCA, was designed according to Seeman's sequence design principle for nucleic acid structural engineering (Seeman, N. C. J. Biomol. Struct. Dyn. 1990, 8, 573). The significance for folding the RCA products into nanoscale shapes lies in the design flexibility of both staple and scaffold strand codes, simplicity of a few short staple strands to fold the periodic sequence of RCA products, and lower cost.

Microwave irradiated click reactions on silicon surfaces via derivertization of covalently grafted poly(PEGMA) brushes.

Two surface chemistry approaches were realized to complete click reactions at covalently grafted polymer brushes of poly(poly(ethylene glycol) monomethacrylate) on a planar silicon surface (Si-g-P(PEGMAOH)). On one hand, the hydroxyls from Si-g-P(PEGMA-OH) brushes can be replaced by chlorines of thionyl chloride and then chlorines can be substituted with azides of sodium azide to achieve azide-terminated (Si-g-P(PEGMA-N(3))) brushes. On the other hand, the terminal acetylene (Si-g-P(PEGMA-CH(2)C[triple bond]CH)) brushes can be prepared easily by reaction between Si-g-P(PEGMA-OH) and propargyl bromide. Model compounds of acetylene-terminated propargylamine, propiolic acid, and 10-undecynoic acid as well as azide-terminal benzyl azide were chosen to investigate the surface click reactions catalyzed with Cu(II)/sodium L-ascorbate by microwave irradiation under very mild conditions at 30°C for 1h. The stepwise modifications were characterized by two surface-sensitive techniques, Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) and X-ray Photoelectron Spectroscopy (XPS), and their spectra were analyzed in detail. The triazole ring v(H-C=) stretching at 3139 cm(-1) and the XPS high-resolution scan of N 1s directly confirm the click reactions. By quantifying their infrared spectra before and after click reactions, we conclude that the click reactions on silicon surfaces by microwave irradiation possess high yield and efficiency. Hence, the microwave irradiated click reaction approaches might open convenient avenues to fabricate functional and hybrid organic/silicon devices.