ORGANIZING FORCES AND CONFORMATIONAL ACCESSIBILITY IN THE UNFOLDED STATE OF PROTEINS

For over fifty years, the unfolded state of proteins had been thought to be featureless and random. Experiments by Tanford and Flory confirmed that unfolded proteins possessed the same dimensions as those predicted of a random flight chain in good solvent. In the late eighties and early nineties, however, researchers began to notice structural trends in unfolded proteins. Some experiments showed that the unfolded state was very similar to the native state, while others indicated a conformational preference for the polyproline II helix in unfolded proteins. As a result, a paradox developed. How can unfolded proteins be both random and nonrandom at the same time? Current experiments and most theoretical simulations cannot characterize the unfolded state in high detail, so we have used the simplified hard sphere model of Richards to address this question. By modeling proteins as hard spheres, we can not only determine what interactions are important in the unfolded state of proteins, but we can address the paradox directly by investigating whether nonrandom behavior is in conflict with random coil statistics. Our simulations identify hundreds of disfavored conformations in short peptides, each of which proves that unfolded proteins are not at all random. Some interactions are important for the folded state of proteins as well. For example, we find that an α-helix cannot be followed directly by a β-strand because of steric considerations. The interactions outlined here limit the conformational possibilities of an unfolded protein far beyond what would be expected for a random coil. For a 100-residue protein, we find that approximately 9 orders of magnitude of conformational freedom are lost because of iii local chain organization alone. Furthermore, we show that the existence of this organization is compatible with random coil statistics. Although our simulations cannot settle the controversy surrounding the unfolded state, we can conclude that new methods of characterizing the unfolded state are needed. Since unfolded proteins are not random coils, the methods developed for describing random coils cannot adequately describe the complexities of this diverse structural ensemble

\u3csup\u3e1\u3c/sup\u3eH, \u3csup\u3e15\u3c/sup\u3eN, and \u3csup\u3e13\u3c/sup\u3eC Chemical Shift Assignments of the Regulatory Domain of Human Calcineurin

Calcineurin (CaN) plays an important role in T-cell activation, cardiac system development and nervous system function. Previous studies have demonstrated that the regulatory domain (RD) of CaN binds calmodulin (CaM) towards the N-terminal end. Calcium-loaded CaM activates the serine/threonine phosphatase activity of CaN by binding to the RD, although the mechanistic details of this interaction remain unclear. It is thought that CaM binding at the RD displaces the auto-inhibitory domain (AID) from the active site of CaN, activating phosphatase activity. In the absence of calcium-loaded CaM, the RD is disordered, and binding of CaM induces folding in the RD. In order to provide mechanistic detail about the CaM–CaN interaction, we have undertaken an NMR study of the RD of CaN. Complete 13C, 15N and 1H assignments of the RD of CaN were obtained using solution NMR spectroscopy. The backbone of RD has been assigned using a combination of 13C-detected CON-IPAP experiments as well as traditional HNCO, HNCA, HNCOCA and HNCACB-based 3D NMR spectroscopy. A 15N-resolved TOCSY experiment has been used to assign Hα and Hβ chemical shifts

Surface Plasmon Resonance, Formation Mechanism, and Surface Enhanced Raman Spectroscopy of Ag+-Stained Gold Nanoparticles

A series of recent works have demonstrated the spontaneous Ag+ adsorption onto gold surfaces. However, a mechanistic understanding of the Ag+ interactions with gold has been controversial. Reported herein is a systematic study of the Ag+ binding to AuNPs using several in-situ and ex-situ measurement techniques. The time-resolved UV-vis measurements of the AuNP surface plasmonic resonance revealed that the silver adsorption proceeds through two parallel pseudo-first order processes with a time constant of 16(±2) and 1,000(±35) s, respectively. About 95% of the Ag+ adsorption proceeds through the fast adsorption process. The in-situ zeta potential data indicated that this fast Ag+ adsorption is driven primarily by the long-range electrostatic forces that lead to AuNP charge neutralization, while the time-dependent pH data shows that the slow Ag+ binding process involves proton-releasing reactions that must be driven by near-range interactions. These experimental data, together with the ex-situ XPS measurement indicates that adsorbed silver remains cationic, but not as a charged-neutral silver atom proposed by the anti-galvanic reaction mechanism. The surface-enhanced Raman activities of the Ag+-stained AuNPs are slightly higher than that for AuNPs, but significantly lower than that for the silver nanoparticles (AgNPs). The SERS feature of the ligands on the Ag+-stained AuNPs can differ from that on both AuNPs and AgNPs. Besides the new insights to formation mechanism, properties, and applications of the Ag+-stained AuNPs, the experimental methodology presented in this work can also be important for studying nanoparticle interfacial interactions

Feasibility of Manufacturing Strand-Based Wood Composite Treated with β-Cyclodextrin–Boric Acid for Fungal Decay Resistance

The feasibility of using β-cyclodextrin (βCD) as an eco-friendly carrier of boric acid for the protection of strand-based wood composites against decay fungi was evaluated. The formation of a βCD–boric acid (βCD–B) complex was confirmed by the appearance of the boron–oxygen bond by using attenuated total reflection–Fourier transform infrared spectroscopy. Chemical shifts of around 6.25 and 1.41 ppm were also observed in 1H Nuclear Magnetic Resonance (NMR) and 11B NMR spectra, respectively. The βCD–B preservatives at two levels (5 and 10 wt.%) were uniformly blended with southern pine strands that were subsequently sprayed with polymeric methylene diphenyl diisocyanate (pMDI) resin. The blended strands were formed into a loose mat by hand and consolidated into 25 × 254 × 12 mm oriented strand boards (OSB) using a hot-press. The OSB panels were cut to end-matched internal bonding (IB) strength and fungal decay resistance test specimens. The vertical density profiles (VDPs) of the IB specimens were measured using an X-ray based density profiler and the specimens with statistically similar VDPs were selected for the IB and decay tests. The IB strength of the treated specimens was lower than the control specimens but they were above the required IB strength of heavy-duty load-bearing boards for use in humid conditions, specified in the BS EN 300:2006 standard. The reduced IB of preservative-treated OSB boards could be explained by the destabilized resin upon the addition of the βCD–B complex, as indicated by the differential scanning calorimetry (DSC) results. The resistance of the OSB panels against two brown-rot fungi (i.e., G. trabeum or P. placenta) was evaluated before and after accelerated leaching cycles. The treated OSBs exposed to the fungi showed an average mass loss of lower than 3% before leaching, while the untreated OSBs had 49 and 35% mass losses due to decay by G. trabeum or P. placenta, respectively. However, upon the leaching, the treatment provided protection only against G. trabeum to a certain degree (average mass loss of 15%). The experimental results suggest that protection efficacy against decay fungi after leaching, as well as the adhesion of the OSB strands, can be improved by increasing the amount of pMDI resin

Using Hydrogen–Deuterium Exchange to Monitor Protein Structure in the Presence of Gold Nanoparticles

The potential applications of protein-functionalized gold nanoparticles (AuNPs) have motivated many studies characterizing protein–AuNP interactions. However, the lack of detailed structural information has hindered our ability to understand the mechanism of protein adsorption on AuNPs. In order to determine the structural perturbations that occur during adsorption, hydrogen/deuterium exchange (HDX) of amide protons was measured for two proteins by NMR. Specifically, we measured both slow (5–300 min) and fast (10–500 ms) H/D exchange rates for GB3 and ubiquitin, two well-characterized proteins. Overall, amide exchange rates are very similar in the presence and absence of AuNPs, supporting a model where the adsorbed protein remains largely folded on the AuNP surface. Small differences in exchange rates are observed for several loop residues, suggesting that the secondary structure remains relatively rigid while loops and surface residues can experience perturbations upon binding. Strikingly, several of these residues are close to lysines, which supports a model where positive surface residues may interact favorably with AuNP-bound citrate. Because these proteins appear to remain folded on AuNP surfaces, these studies suggest that it may be possible to engineer functional AuNP-based nanoconjugates without the use of chemical linkers