Tailoring of glycopeptide scaffolds by the acyltransferases from the teicoplanin and A-40,926 biosynthetic operons

The teicoplanin acyltransferase (Atf) responsible for N-acylation of the glucosamine moiety to create the teicoplanin lipoglycopeptide scaffold has recently been identified. Here we use that enzyme (tAtf) and the cognate acyltransferase from the related A-40,926 biosynthetic cluster (aAtf) to evaluate specificity for glycopeptide scaffolds and for the acyl-CoA donor. In addition to acylation of 2-aminoglucosyl glycopeptide scaffolds with k(cat) values of 400-2000 min(-1), both Atfs transfer acyl groups to regioisomeric 6-aminoglucosyl scaffolds and to glucosyl scaffolds at rates of 0.2-0.5 min(-1) to create variant lipoglycopeptides. Using the teicoplanin glycosyltransferase tGtfA, tAtf, and GtfD, a glycosyltransferase from the vancomycin producer, it is possible to assemble a novel lipoglycopeptide with GlcNAc at beta-OH-Tyr(6) and an N(6)-acyl-glucosaminyl-vancosamine at Phegly(4). This study illustrates the utility of chemo- and regioselective acyltransferases and glycosyltransferases to create novel lipoglycopeptides.     

Composite PLA/PEG/nHA/Dexamethasone Scaffold Prepared by 3D Printing for Bone Regeneration

3D printing has become an essential part of bone tissue engineering and attracts great attention for the fabrication of bioactive scaffolds. Combining this rapid manufacturing technique with chemical precipitation, biodegradable 3D scaffold composed of polymer matrix (polylactic acid and polyethylene glycol), ceramics (nano hydroxyapatite), and drugs (dexamethasone (Dex)) is prepared. Results of water contact angle, differential scanning calorimeter, and mechanical tests confirm that incorporation of Dex leads to significantly improved wettability, higher crystallinity degree, and tunable degradation rates. In vitro experiment with mouse MC3T3‐E1 cells implies that Dex released from scaffolds is not beneficial for early cell proliferation, but it improves late alkaline phosphatase secretion and mineralization significantly. Anti‐inflammation assay of murine RAW 264.7 cells proves that Dex released from all the scaffolds successfully suppresses lipopolysaccharide induced interleukin‐6 and inducible nitric oxide synthase secretion by M1 macrophages. Further in vivo experiment on rat calvarial defects indicates that scaffolds containing Dex promote osteoinduction and osteogenic response and would be promising candidates for clinical applications.     

Quantitative analysis of conformational exchange contributions to 1H-15N multiple-quantum relaxation using field-dependent measurements. Time scale and structural characterization of exchange in a calmodulin C-terminal domain mutant

Multiple-quantum spin relaxation is a sensitive probe for correlated conformational exchange dynamics on microsecond to millisecond time scales in biomolecules. We measured differential 1H-15N multiple-quantum relaxation rates for the backbone amide groups of the E140Q mutant of the C-terminal domain of calmodulin at three static magnetic field strengths. The differential multiple-quantum relaxation rates range between -88.7 and 92.7 s(-1), and the mean and standard deviation are 7.0 +/- 24 s(-1), at a static magnetic field strength of 14.1 T. Together with values of the 1H and 15N chemical shift anisotropies (CSA) determined separately, the field-dependent data enable separation of the different contributions from dipolar-dipolar, CSA-CSA, and conformational exchange cross-correlated relaxation mechanisms to the differential multiple-quantum relaxation rates. The procedure yields precise quantitative information on the dominant conformational exchange contributions observed in this protein. The field-dependent differences between double- and zero-quantum relaxation rates directly benchmark the rates of conformational exchange, showing that these are fast on the chemical shift time scale for the large majority of residues in the protein. Further analysis of the differential 1H-15N multiple-quantum relaxation rates using previously determined exchange rate constants and populations, obtained from 15N off-resonance rotating-frame relaxation data, enables extraction of the product of the chemical shift differences between the resonance frequencies of the 1H and 15N spins in the exchanging conformations, deltasigma(H)deltasigma(N). Thus, information on the 1H chemical shift differences is obtained, while circumventing complications associated with direct measurements of conformational exchange effects on 1H single-quantum coherences in nondeuterated proteins. The method significantly increases the information content available for structural interpretation of the conformational exchange process, partly because deltasigma(H)deltasigma(N) is a signed quantity, and partly because two chemical shifts are probed simultaneously. The present results support the hypothesis that the exchange in the calcium-loaded state of the E140Q mutant involves conformations similar to those of the wild-type apo (closed) and calcium-loaded (open) states.     

Biological Response of Osteoblastic and Chondrogenic Cells to Graphene-Containing PCL/Bioactive Glass Bilayered Scaffolds for Osteochondral Tissue Engineering Applications

Graphene-containing 13-93 bioactive glass and poly(ε-caprolactone)-based bilayer, electrically conductive scaffolds were prepared for osteochondral tissue repair. Biological response of osteoblastic MC3T3-E1 and chondrogenic ATDC5 cells to the composite scaffolds was assessed under mono-culture and co-culture conditions. Cytotoxicity was investigated using MTT assay, cartilage matrix production was evaluated by Alcian blue staining, and mineralization of both types of cells in the different culture systems was observed by Alizarin red S staining. Results showed that osteoblastic and chondrogenic cells utilized in the study did not show toxic response to the prepared scaffolds under mono-culture conditions and higher cell viability rates were obtained in co-culture conditions. Larger mineralized areas were determined under co-culture conditions and calcium deposition amount significantly increased compared with that in control group samples after 21 days. Additionally, the amount of glycosaminoglycans synthesized in co-culture was higher compared to mono-culture conditions. Electric stimulation applied under mono-culture conditions suppressed the viability of MC3T3-E1 cells whereas it enhanced the viability rates of ATDC5 cells. The study suggests that the designed bilayered osteochondral constructs have the potential for osteochondral defect repair.     

Polycaprolactone-polymethyl methacrylate electrospun blends for biomedical applications

Electrospinning is one of most versatile process to fabricate porous scaffolds in biomedical field. Synthetic polymers such as polycaprolactone (PCL) and polymethyl methacrylate (PMMA) provide excellent properties for biomedical applications due to their biocompatibility and tunable mechanical properties. PCL-PMMA electrospun blends combine compressive/tensile properties of individual polymers as well as biocompatibility/biodegradability. Together with porosity of scaffold, drug/nutrient supply is required in tissue regeneration and healing. High pressure CO₂ has been investigated to plasticize many biopolymers and impregnate drugs in scaffolds. This study explores several compositions of PCL-PMMA electrospun scaffolds for morphological and mechanical properties. These scaffolds are impregnated with hydrophilic (Rhodamine B) and hydrophobic (Fluorescein) dyes using high pressure CO₂ and air plasma treatment. Furthermore, release profiles of dyes have been studied from thin films and porous scaffolds to understand several controlling factors for controlled release applications. Results show dye-polymer interactions, CO₂ impregnation and stress relaxation of electrospun fibers are key factors in release profile from electrospun fibers. This study is a step forward in developing PCL-PMMA based electrospun scaffolds for drug delivery and tissue engineering.     

An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange

A series of experiments are presented that provide an exchange-free measure of dipole-dipole (15)N transverse relaxation, R(dd), that can then be substituted for (15)N R(1rho) or R(2) rates in the study of internal protein dynamics. The method is predicated on the measurement of a series of relaxation rates involving (1)H-(15)N longitudinal order, anti-phase (1)H and (15)N single-quantum coherences, and (1)H-(15)N multiple quantum coherences; the relaxation rates of all coherences are measured under conditions of spin-locking. Results from detailed simulations and experiments on a number of protein systems establish that R(dd) values are independent of exchange and systematic errors from dipolar interactions with proximal protons are calculated to be less than 1-2%, on average, for applications to perdeuterated proteins. Simulations further indicate that the methodology is rather insensitive to the exact level of deuteration so long as proteins are reasonably highly deuterated (>50%). The utility of the methodology is demonstrated with applications involving protein L, ubiquitin, and a stabilized folding intermediate of apocytochrome b(562) that shows large contributions to (15)N R(1rho) relaxation from chemical exchange.     

Electron Spin Relaxation Rates for High-Spin Fe(III) in Iron Transferrin Carbonate and Iron Transferrin Oxalate

To optimize simulations of CW EPR spectra for high-spin Fe(III) with zero-field splitting comparable to the EPR quantum, information is needed on the factors that contribute to the line shapes and line widths. Continuous wave electron paramagnetic resonance (EPR) spectra obtained for iron transferrin carbonate from 4 to 150 K and for iron transferrin oxalate from 4 to 100 K did not exhibit significant temperature dependence of the line shape, which suggested that the line shapes were not relaxation determined. To obtain direct information concerning the electron spin relaxation rates, electron spin echo and inversion recovery EPR were used to measure T(1) and T(m) for the high-spin Fe(III) in iron transferrin carbonate and iron transferrin oxalate between 5 and 20-30 K. For comparison with the data for the transferrin complexes, relaxation times were obtained for tris(oxalato)ferrate(III). The relaxation rates are similar for the three complexes and do not exhibit a strong dependence on position in the spectrum. Extrapolation of the observed temperature dependence of the relaxation rates to higher temperatures gives values consistent with the conclusion that the CW line shapes are not relaxation determined up to 150 K.     

Quantitative measurement of differential 15N-H(alpha/beta)T2 relaxation rates in a perdeuterated protein by MAS solid-state NMR spectroscopy

Dynamic parameters become more and more accessible in the study of uniformly isotopically enriched proteins by MAS solid-state NMR. We demonstrate that T(2)-related relaxation properties can quantitatively be determined in a sample of a perdeuterated microcrystalline protein by the measurement of (15)N,(1)H dipole, (15)N CSA cross-correlated relaxation rates. We find that the measured cross-correlated relaxation rates are independent of the MAS rotation frequency, and therefore reflect local dynamic fluctuations of the protein structure.     

Electron spin relaxation in x-lithium phthalocyanine

Continuous-wave linewidths and spin susceptibilities, spin-spin relaxation rates (1/T2), and spin-lattice relaxation rates (1/T1) for two sources of x-LiPc were measured at 9.5 GHz between 15 and 298 K. Relaxation rates at 34 GHz were measured between 80 and 298 K. Room-temperature relaxation rates also were measured at 250 MHz, 1.9 GHz, and 2.76 GHz. The temperature dependences of linewidths and spin susceptibilities are characteristic of 1-D organic conductors. The ratio of populations of localized and delocalized electrons varies with sample preparation. For a single needle between 15 and about 200 K, 1/T2 is higher for the parallel orientation, but 1/T1 is higher for the perpendicular orientation, consistent with predictions based on dipolar interactions. Between about 60 and 150 K, which is the temperature regime in which spin susceptibility is changing rapidly with temperature, 1/T1 exhibits a non-monotonic dependence on temperature and is lower at 34 GHz than at 9.5 GHz. In other organic conductors, this dependence has been attributed to a bottleneck mechanism of relaxation. At higher temperatures, 1/T1 becomes less orientation-dependent. At room temperature, T1 increases rapidly between 250 MHz (3.0 micros) and 2.76 GHz (6.3 micros) and then shows less frequency dependence up to 34 GHz (9.8 micros). The relaxation rate near room temperature might have a substantial contribution from spin hopping perpendicular to the stacking axis of the molecules.     

Analysis and parametric optimization of 1H off-resonance relaxation NMR experiments designed to map polypeptide self-recognition and other noncovalent interactions

The measurement of 1H off-resonance nonselective relaxation rates (R(theta,ns)) has been recently proposed as an effective method to probe peptide self-recognition, opening new perspectives in the understanding of the prefibrillization oligomerization processes in amylodogenesis. However, a full analysis and parametric optimization of the NMR experiments designed to measure R(theta,ns) relaxation rates is still missing. Here we analyze the dependence of the R(theta,ns) rates upon three critical parameters: the tilt angle of the effective field during the spin lock, the static magnetic field, and finally the repetition delay. Our analysis reveals that the tilt angle theta = 35.5 degrees not only minimizes spin-diffusion, but also avoids experimental artifacts such as J-transfer and poor adiabaticity. In addition, we found that when the dominant relaxation mechanism is caused by uncorrelated pairwise 1H dipole-1H dipole interactions the R(35.5 degrees,ns) rate is not significantly affected by static field variations, suggesting a wide applicability of the 1H off-resonance nonselective relaxation experiment. Finally, we show that the self-recognition maps based on the comparative analysis of the R(35.5 degrees,ns) rates can tolerate decreases in the interscan delays without significantly compromising the identification of critical self-association loci. These considerations not only provide a better understanding of the 1H off-resonance nonselective relaxation, but they also serve as guidelines for the optimal setup of this experiment.     

1H NMR relaxation in glycerol solutions of nitroxide radicals: effects of translational and rotational dynamics

(1)H spin-lattice relaxation rates in glycerol solutions of selected nitroxide radicals at temperatures between 200 K and 400 K were measured at 15 MHz and 25 MHz. The frequency and temperature conditions were chosen in such a way that the relaxation rates go through their maximum values and are affected by neither the electron spin relaxation nor the electron-nitrogen nucleus hyperfine coupling, so that the focus could be put on the mechanisms of motion. By comparison with (1)H spin-lattice relaxation results for pure glycerol, it has been demonstrated that the inter-molecular electron spin-proton spin dipole-dipole interactions are affected not only by relative translational motion of the solvent and solute molecules, but also by their rotational dynamics as the interacting spins are displaced from the molecular centers; the eccentricity effects are usually not taken into account. The (1)H relaxation data have been decomposed into translational and rotational contributions and their relative importance as a function of frequency and temperature discussed in detail. It has been demonstrated that neglecting the rotational effects on the inter-molecular interactions leads to non-realistic conclusions regarding the translational dynamics of the paramagnetic molecules.     

Mapping polypeptide self-recognition through (1)H off-resonance relaxation

1H NMR relaxation rates provide a readily available and sensitive probe ideally suited to investigate the weak (KD approximately micromolar to millimolar range) interactions that frequently mediate polypeptide oligomerization in the early steps of amyloid fibrillogenesis. However, the measurement of transverse and longitudinal 1H relaxation rates is experimentally challenging due to J-transfer and selectivity problems in CPMG and inversion-recovery experiments, respectively. We show here that these problems are effectively circumvented by measuring nonselective off-resonance relaxation rates using an effective field tilted by 35.5 degrees . When applied to the Halpha spins of the Abeta (12-28) peptide, the proposed experiment provides a residue-resolution self-recognition map which is fully consistent with previous independent mutational studies. The method is anticipated to be widely applicable not only to the fast growing family of amyloidogenic peptides but also to the screening and mapping of protein-ligand interactions in general.     

Interaction of the human prion PrP(106-126) sequence with copper(II), manganese(II), and zinc(II): NMR and EPR studies

The synthetic peptide encompassing residues 106-126 (PrP106-126, KTNMKHMAGAAAAGAVVGGLG) of the human prion protein was considered for its binding properties toward copper(II), manganese(II) and zinc(II) at pH 5.7. 1H and 13C 1D spectra, 1H spin-lattice relaxation rates, and 1H-15N and 1H-13C HSQC 2D experiments were obtained in the absence and in the presence of metal ions. While Zn(II) was found to yield negligible effects upon any NMR parameter, metal-peptide association was demonstrated by the paramagnetic effects of Cu(II) and Mn(II) upon 1D and 2D spectra. Delineation of structures of metal complexes was sought by interpreting the paramagnetic effect on 1H spin-lattice relaxation rates. Exchange of peptide molecules from the metal coordination sphere was shown to provide sizable contribution to the observed relaxation rates. Such contribution was calculated in the case of Cu(II); whereas the faster paramagnetic rates of peptide molecules bound to Mn(II) were determining spin-lattice relaxation rates almost exclusively dominated by exchange. Proton-metal distances were therefore evaluated in the case of the Cu(II) complex only and used as restraints in molecular dynamics calculations where from the structure of the complex was obtained. The peptide was shown to bind copper through the imidazole nitrogen and the ionized amide nitrogen of His-111 and the amino-terminal group with the terminal carboxyl stabilizing the coordination sphere through ionic interactions. The data were interpreted as to demonstrate that the hydrophobic C-terminal region was not affecting the copper-binding properties of the peptide and that this hydrophobic tail is left free to interact with other target molecules. As for the complex with Mn(II), qualitative information was obtained on carbonyl oxygens of Gly-124 and Leu-125, beyond the terminal Gly-126 carboxyl, being at close distance from the metal ion, that also interacts, most likely, through a hydrogen bond of metal-bound water, with the imidazole ring of His-111.     

Compressive mechanical properties and biodegradability of porous poly(caprolactone)/chitosan scaffolds

Porous polycaprolactone(PCL)/chitosan(CH) scaffolds with large pore sizes and high porosities were fabricated via a particle-leaching technique using hexafluoro-2-propanol as a shared solvent and salt (sodium chloride) particles as porogen. By optimizing processing conditions, numerous PCL/CH scaffolds with CH proportion lower than 50 wt% and similar pore parameters were built. These scaffolds were further evaluated for their compressive mechanical properties and biodegradation behaviors. It was found that their compressive modulus and stress at 10% strain were basically maintained in their dry state in contrast to their individual components, and these scaffolds still showed well-defined compressive characteristics and dimension stability even in their hydrated state compared with pure chitosan scaffolds. After being exposed to PBS or enzymatic degradation systems in vitro for various periods up to 10 weeks, it was observed that degradation of the PCL component could be accelerated at various rates depending on the compositions of the scaffolds and the media, and the chiosan component could effectively buffer the acidic degradation products of the PCL component.     

An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates

Rotating-frame relaxation rates, R(1)(rho), are often measured in NMR studies of protein dynamics. We show here that large systematic errors can be introduced into measured values of heteronuclear R(1)(rho) rates using schemes which are usually employed to suppress cross-correlation between dipole-dipole and CSA relaxation mechanisms. For example, in a scalar-coupled two-spin X-H spin system the use of (1)H WALTZ16 decoupling or (1)H pulses applied at regularly spaced intervals leads to a significant overestimation of heteronuclear R(1)(rho) values. The problem is studied experimentally and theoretically for (15)N-(1)H and (13)C-(1)H spin pairs, and simple schemes are described which eliminate the artifacts. The approaches suggested are essential replacements of existing methodology if accurate dynamics parameters are to be extracted from spin-lock relaxation data sets.     

Oxygen consumption rate of cells in 3D culture: the use of experiment and simulation to measure kinetic parameters and optimise culture conditions

Understanding the basal O(2) and nutrient requirements of cells is paramount when culturing cells in 3D tissue models. Any scaffold design will need to take such parameters into consideration, especially as the addition of cells introduces gradients of consumption of such molecules from the surface to the core of scaffolds. We have cultured two cell types in 3D native collagen type I scaffolds, and measured the O(2) tension at specific locations within the scaffold. By changing the density of cells, we have established O(2) consumption gradients within these scaffolds and using mathematical modeling have derived rates of consumption for O(2). For human dermal fibroblasts the average rate constant was 1.19 × 10(-17) mol cell(-1) s(-1), and for human bone marrow derived stromal cells the average rate constant was 7.91 × 10(-18) mol cell(-1) s(-1). These values are lower than previously published rates for similar cells cultured in 2D, but the values established in this current study are more representative of rates of consumption measured in vivo. These values will dictate 3D culture parameters, including maximum cell-seeding density and maximum size of the constructs, for long-term viability of tissue models.     

Nuclear spin relaxation of sodium cations in bacteriophage Pf1 solutions

The nuclear magnetic resonance (NMR) spectra for the I=3/2 23Na cation dissolved into filamentous bacteriophage Pf1 solutions display line splittings and relaxation times consistent with an interaction between the 23Na nuclear quadrupole moment and the electric field gradient produced by the negatively charged Pf1 particles. The 23Na NMR line splittings and relaxation rates corresponding to magnetization recovery and single, double, and triple quantum coherence decays are measured in Pf1 solutions and compared to theoretical values. The deviation of the observed dc spectral density J0 from the equal first harmonic J(omega0) and second harmonic J(2omega0) values as J(omega0)=J(2omega0) not equal to J0 in these solutions suggests that ion migration in the electric field gradient of the Pf1 particles produces an anisotropic relaxation mechanism. Correlation functions and thus spectral densities for this process are calculated from solutions to the Fokker-Planck equation for radial motion in an electric potential and used to estimate measured relaxation rates. Appropriate electric potentials are generated from the solutions to the Poisson-Boltzmann equation for a charged Pf1 particle in aqueous phase, functions that lead to theoretical estimates of NMR line splittings consistent with experimental observations.     

I2分子B(ν′=43)能级在超音速射流中振动弛豫速率的定量测量

利用改变观察场位置的方法, 用LIF法定量测量了超音速射流中I_2B(υ’=43)能极的振动弛豫速率. 首次获得了Ar, N_2和CO等分子的驰豫截面. 结果表明, 低温射流中振动弛豫速率呈负温度关系, 对载气He和H_2, 主要弛豫过程是△υ=-1通道, 但对Ar, N_2和CO等载气, 多振动量子传输很显著, 特别是对双原子分子, 最可几弛豫通道不再是△υ=-1过程. 这违反了能隙定律.这种现象可用亚稳态络合物的形成来解释。     

Proton spin-lattice relaxation studies. N-aryl-1-isoindolinones

Proton spin-lattice relaxation rates (R₁ values) have been measured, at 270 MHz, for a series of N-aryl isoindolinones. A normalization procedure has been used to enable comparison of R₁ values in different compounds by minimizing the effects on relaxation rates of changes in motional correlation times accompanying changes in substitution patterns. A substantial (4.3-fold) dynamic range of R₁ values has been observed, and individual values have been correlated with the molecular environments of the nuclei. There is evidence for an interring relaxation process.     

Long-range magnetization transfer between uncoupled nuclei by dipole-dipole cross-correlated relaxation: a precise probe of beta-sheet geometry in proteins

Interference between dipolar interactions in covalently linked (13)C-(1)H and nonlinked (1)H-(1)H pairs can be used to generate antiphase magnetization between noncoupled spins. The buildup rate of such antiphase terms is highly sensitive to local geometry, in particular the interproton distance and the (13)C-(1)H-(1)H internuclear angle. These rates have been measured for opposing C(alpha)H(alpha) pairs in antiparallel beta-sheets in the third Igg-binding domain of protein G (GB3) and in HIV protease, complexed with the inhibitor DMP323. For GB3, good agreement with the 1.1-A crystal structure is found. However, this agreement rapidly deteriorates with decreasing resolution of the corresponding X-ray structure. For HIV protease, two separate crystal structures that differ by less than 0.2 A from one another exhibit lower agreement in their predicted cross-correlated relaxation rates relative to one another than is found between experimental rates and the average of the rates predicted for the two structures. These data indicate that quantitative measurement of these cross-correlated relaxation rates can provide highly accurate structural information in macromolecules.