Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction

The study of micro- or nanocrystalline proteins by magic-angle spinning (MAS) solid-state NMR (SSNMR) gives atomic-resolution insight into structure in cases when single crystals cannot be obtained for diffraction studies. Subtle differences in the local chemical environment around the protein, including the characteristics of the cosolvent and the buffer, determine whether a protein will form single crystals. The impact of these small changes in formulation is also evident in the SSNMR spectra; however, the changes lead only to correspondingly subtle changes in the spectra. Here, we demonstrate that several formulations of GB1 microcrystals yield very high quality SSNMR spectra, although only a subset of conditions enable growth of single crystals. We have characterized these polymorphs by X-ray powder diffraction and assigned the SSNMR spectra. Assignments of the 13C and 15N SSNMR chemical shifts confirm that the backbone structure is conserved, indicative of a common protein fold, but side chain chemical shifts are changed on the surface of the protein, in a manner dependent upon crystal packing and electrostatic interactions with salt in the mother liquor. Our results demonstrate the ability of SSNMR to reveal minor structural differences among crystal polymorphs. This ability has potential practical utility for studying the formulation chemistry of industrial and therapeutic proteins, as well as for deriving fundamental insights into the phenomenon of single-crystal growth.     

Influence of Cyclodextrin Complexation on the in vitro Human Skin Penetration and Retention of the Sunscreen Agent, Oxybenzone

The objective of this study was to investigate the influence of cyclodextrins on the cutaneous availability of the sunscreen oxybenzone. The interaction between oxybenzone and hydrophilic α-, β- and γ-cyclodextrin derivatives was studied in water by phase-solubility analysis. Among the available cyclodextrins, hydroxypropyl-β-cyclodextrin (HP-β-CD) and especially sulfobutylether-β-cyclodextrin (SBE-β-CD) had the greatest solubilizing activity. Ethanol–water solutions containing oxybenzone free or complexed with HP-β-CD or SBE-β-CD were applied to human skin in Franz diffusion cells and the amount of sunscreen permeated into the different cutaneous compartments was determined by HPLC. As much as 20.5% of the oxybenzone applied dose diffused within the skin tissue after 6 h application. Between 39.4% and 54.9% of the penetrated UV filter was localized in the stratum corneum, with no significant difference between uncomplexed oxybenzone or its complex with HP-β-CD. Conversely, the amount retained in the stratum corneum was markedly decreased (ca. 50%) by complexation with SBE-β-CD. Considerable quantities of oxybenzone accumulated into the viable epidermis (5.7% of the applied dose) and dermis (6.2% of the applied dose) from the preparation containing the free UV filter. The sunscreen penetration to the deeper living layers of the skin was remarkably lower (1.0% and 2.0% of applied dose for epidermis and dermis, respectively) upon application of the sunscreen complexed with SBE-β-CD, whereas HP-β-CD had no effect. In addition, photostability experiments demonstrated that SBE-β-CD complexation did not alter the sunscreen photochemical properties.     

Visualising the onset of viscous fingering in chromatography columns

Viscous fingering is an important fluid transport phenomenon that manifests itself when two fluids having different viscosities move in the same direction. Their interface is unstable and a complex fingering pattern may arise. This phenomenon is important in chromatography because it may lead to a decrease or even a failure in separations. The onset of viscous fingering was visually observed by packing a glass column with particles having the same refractive index as the mobile phase and injecting plugs of dye solutions having viscosities different from that of the mobile phase. Severe fingering effects are observed if the viscosity difference exceeds 0.17 cP. However, for smaller viscosity differences, band distortions are observed that may affect retention data, band efficiency, and band resolution. Careful attention should be paid to matching the mobile phase viscosity and that of the injection plug when accurate chromatographic information is required.     

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Modeling Sub- and Super-ambient Heat Capacities of the Group Iva Compounds Despite the Lanthanide Contraction

This paper is concerned with the estimation of heat capacities in the IVA 3d-transition element compounds using especially Zr and Hf compounds as examples. Most prediction schemes routinely tacitly assume that volumes and masses trend in parallel. However, the lanthanide contraction here ensures for ZrX/HfX systems — and generally elsewhere — that this is not so in this portion of the periodic table. Available methods such as Latimer's, Volumetric Priority, Komada-Westrum, Grimvall's, and Sommers' are compared on IVA elements and compounds. Only the Sommers approach has volumetric input. It provides the best prediction.This revised version was published online in November 2005 with corrections to the Cover Date.     

Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold

The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.     

Synthetic erythropoietic proteins: tuning biological performance by site-specific polymer attachment

Chemical synthesis in combination with precision polymer modification allows the systematic exploration of the effect of protein properties, such as charge and hydrodynamic radius, on potency using defined, homogeneous conjugates. A series of polymer-modified synthetic erythropoiesis proteins were constructed that had a polypeptide chain similar to the amino acid sequence of human erythropoietin but differed significantly in the number and type of attached polymers. The analogs differed in charge from +5 to -26 at neutral pH and varied in molecular weight from 30 to 54 kDa. All were active in an in vitro cell proliferation assay. However, in vivo potency was found to be strongly dependent on overall charge and size. The trends observed in this study may serve as starting points for the construction of more potent synthetic EPO analogs in the future.     

Bis(cyclopentadienyl)titanium complexes of naphthalene-1,8-dithiolates, biphenyl 2,2'-dithiolates, and related ligands

Titanocene 1,8-dithiolato-naphthalene and titanocene 2,2'-dithiolato biphenyl are produced by the reaction of naphtho[1,8-cd]-1,2-dithiole [or the biphenyl] with titanocene dicarbonyl (Ti(II)) in toluene at room temperature. The pro-ligands 2,7-di(tert-butyl)naphtho[1,8-cd]-1,2-dithiole, 5,6-dihydroacenaphtho[5,6-cd]-1,2-dithiole, 4,5-dithioacephenanthrylene, and 13,14-dithiapicene have been used in similar reactions with titanocene dicarbonyl to investigate the effect of steric bulk and of varying the naphthalene backbone on the final complex. The resulting Cp(2)TiS(2)Ar complexes (Ar = naphthalene) have been shown by temperature-dependent (1)H NMR spectroscopy to exist in solution in an envelope conformation with the six-membered TiS(2)C(3) rings undergoing inversion on the NMR time scale while the similar Cp(2)TiS(2)Ar complexes (Ar = biphenyl, binaphthalene) interconvert more rapidly. Titanocene 2,2'-disulfinato biphenyl has been synthesized by the salt elimination reaction of titanocene dichloride (Ti(IV)) and the disodium salt of biphenyl 2,2'-disulfinic acid. Finally, the effect of using pro-ligands where the sulfur atoms have been mono- or di-oxidized has been studied, and an interesting oxygen elimination reaction is observed for the S=O fragments but not for the SO(2) groups. All complexes have been characterized spectroscopically and seven X-ray structures are reported.     

In situ preparation of protein-"smart" polymer conjugates with retention of bioactivity

Protein-polymer conjugates are widely used in biotechnology and medicine, and new methods to prepare the bioconjugates would be advantageous for these applications. In this report, we demonstrate that bioactive "smart" polymer conjugates can be synthesized by polymerizing from defined initiation sites on proteins, thus preparing the polymer conjugates in situ. In particular, free cysteines, Cys-34 of bovine serum albumin (BSA) and Cys-131 of T4 lysozyme V131C, were modified with initiators for atom transfer radical polymerization (ATRP) either through a reversible disulfide linkage or irreversible bond by reaction with pyridyl disulfide- and maleimide-functionalized initiators, respectively. Initiator conjugation was verified by electrospray-ionization mass spectroscopy (ESI-MS), and the location of the modification was confirmed by muLC-MSMS (tandem mass spectrometry) analysis of the trypsin-digested protein macroinitiators. Polymerization of N-isopropylacrylamide (NIPAAm) from the protein macroinitiators resulted in thermosensitive BSA-polyNIPAAm and lysozyme-polyNIPAAm in greater than 65% yield. The resultant conjugates were characterized by gel electrophoresis and size exclusion chromatography (SEC) and easily purified by preparative SEC. The identity of polymer isolated from the BSA conjugate was confirmed by (1)H NMR, and the polydispersity index was determined by gel permeation chromatography (GPC) to be as low as 1.34. Lytic activities of the lysozyme conjugates were determined by two standard assays and compared to that of the unmodified enzyme prior to polymerization; no statistical differences in bioactivity were observed.