Ronald T. Raines

Collagen Structure and Stability

Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen-the prototypical collagen fibril-has been revealed in detail. Artificial collagen fibrils that display some properties of natural collagen fibrils are now accessible using chemical synthesis and self-assembly. A rapidly emerging understanding of the mechanical and structural properties of native collagen fibrils will guide further development of artificial collagenous materials for biomedicine and nanotechnology.

Simple Chemical Transformation of Lignocellulosic Biomass into Furans for Fuels and Chemicals

Lignocellulosic biomass is a plentiful and renewable resource for fuels and chemicals. Despite this potential, nearly all renewable fuels and chemicals are now produced from edible resources, such as starch, sugars, and oils; the challenges imposed by notoriously recalcitrant and heterogeneous lignocellulosic feedstocks have made their production from nonfood biomass inefficient and uneconomical. Here, we report that N,N-dimethylacetamide (DMA) containing lithium chloride (LiCl) is a privileged solvent that enables the synthesis of the renewable platform chemical 5-hydroxymethylfurfural (HMF) in a single step and unprecedented yield from untreated lignocellulosic biomass, as well as from purified cellulose, glucose, and fructose. The conversion of cellulose into HMF is unabated by the presence of other biomass components, such as lignin and protein. Mechanistic analyses reveal that loosely ion-paired halide ions in DMA-LiCl are critical for the remarkable rapidity (1-5 h) and yield (up to 92%) of this low-temperature (<or=140 degrees C) process. The simplicity of this chemical transformation of lignocellulose contrasts markedly with the complexity of extant bioprocesses and provides a new paradigm for the use of biomass as a raw material for a renewable energy and chemical industries.

Hydrolytic Stability of Hydrazones and Oximes

Hydrazones and oximes are common conjugates, but are labile to hydrolysis. The hydrolytic stability of isostructural hydrazones and an oxime have been determined at pD 5.0–9.0. The hydrolysis of each adduct was catalyzed by acid. Rate constants for oxime hydrolysis were nearly 103-fold lower than those for simple hydrazones; a trialkylhydrazonium ion (formed after condensation) was even more stable than the oxime. The data suggest a general mechanism for conjugate hydrolysis.

Fermentable sugars by chemical hydrolysis of biomass

Abundant plant biomass has the potential to become a sustainable source of fuels and chemicals. Realizing this potential requires the economical conversion of recalcitrant lignocellulose into useful intermediates, such as sugars. We report a high-yielding chemical process for the hydrolysis of biomass into monosaccharides. Adding water gradually to a chloride ionic liquid-containing catalytic acid leads to a nearly 90% yield of glucose from cellulose and 70–80% yield of sugars from untreated corn stover. Ion-exclusion chromatography allows recovery of the ionic liquid and delivers sugar feedstocks that support the vigorous growth of ethanologenic microbes. This simple chemical process, which requires neither an edible plant nor a cellulase, could enable crude biomass to be the sole source of carbon for a scalable biorefinery.

Code for collagen's stability deciphered

The most abundant protein in animals is collagen. In connective tissue, this protein is present as chains wound in tight triple helices which are organized into fibrils of great tensile strength and thermal stability,. We propose a new explanation for this stability.

n→π* interactions in proteins

Hydrogen bonds between backbone amides are common in folded proteins. Here, we show that an intimate interaction between backbone amides likewise arises from the delocalization of a lone pair of electrons (n) from an oxygen atom to the antibonding orbital (π*) of the subsequent carbonyl group. Natural bond orbital analysis predicted significant n→π* interactions in certain regions of the Ramachandran plot. These predictions were validated by a statistical analysis of a large, non-redundant subset of protein structures determined to high resolution. The correlation between these two independent studies is striking. Moreover, the n→π* interactions are abundant, and especially prevalent in common secondary structures such as α-, 310-, and polyproline II helices, and twisted β-sheets. In addition to their evident effects on protein structure and stability, n→π* interactions could play important roles in protein folding and function, and merit inclusion in computational force fields.

Advances in Bioconjugation.

Bioconjugation is a burgeoning field of research. Novel methods for the mild and site-specific derivatization of proteins, DNA, RNA, and carbohydrates have been developed for applications such as ligand discovery, disease diagnosis, and high-throughput screening. These powerful methods owe their existence to the discovery of chemoselective reactions that enable bioconjugation under physiological conditions-a tremendous achievement of modern organic chemistry. Here, we review recent advances in bioconjugation chemistry. Additionally, we discuss the stability of bioconjugation linkages-an important but often overlooked aspect of the field. We anticipate that this information will help investigators choose optimal linkages for their applications. Moreover, we hope that the noted limitations of existing bioconjugation methods will provide inspiration to modern organic chemists.

A hyperstable collagen mimic

BACKGROUND Collagen is the most abundant protein in animals. Each polypeptide chain of collagen is composed of repeats of the sequence: Gly-X-Y, where X and Y are often L-proline (Pro) and 4(R)-hydroxy-L-proline (Hyp) residues, respectively. These chains are wound into tight triple helices of great stability. The hydroxyl group of Hyp residues contributes much to this conformational stability. The existing paradigm is that this stability arises from interstrand hydrogen bonds mediated by bridging water molecules. This model was tested using chemical synthesis to replace Hyp residues with 4(R)-fluoro-L-proline (Flp) residues. The fluorine atom in Flp residues does not form hydrogen bonds but does elicit strong inductive effects. RESULTS Replacing the Hyp residues in collagen with Flp residues greatly increases triple-helical stability. The free energy contributed by the fluorine atom in Flp residues is twice that of the hydroxyl group in Hyp residues. The stability of the Flp-containing triple helix far exceeds that of any untemplated collagen mimic of similar size. CONCLUSIONS Bridging water molecules contribute little to collagen stability. Rather, collagen stability relies on previously unappreciated inductive effects. Collagen mimics containing fluorine or other appropriate electron-withdrawing substituents could be the basis of new biomaterials for restorative therapies.

An electronic effect on protein structure

The well‐known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N‐formyl group (Hi−1−C′i−1=Oi−1), in which Hi−1 presents less steric hindrance than does Oi−1, likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n → π* interaction between the oxygen of the peptide bond (Oi−1), and the subsequent carbonyl carbon in the polypeptide chain (C′i) also contributes to this preference. The Oi−1 and C′i distance and Oi−1···C′i=Oi angle are especially favorable for such an n → π* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure.

Synthesis of Furfural from Xylose and Xylan

Rising fossil energy prices and environmental preservation call for alternative sources of energy, such as renewable fuels based on biomass.[1] Biofuels could reduce carbon dioxide emissions and decrease fuel prices, particularly if derived from nonfood biomass resources such as agricultural, forest, and landfill wastes. Hemicellulose, a mixture of polysaccharides containing xylose, arabinose, glucose, galactose, mannose, and other sugars, is typically the second-most-abundant component of biomass, after cellulose.[2] In grasses and hardwoods, xylan, a polymer of xylose, is often the primary hemicellulose. As a result, xylan conversion is critical for utilization of important biomass feedstocks such as bagasse, corn stover, Miscanthus, switchgrass, and poplar.