31P Magnetic relaxation studies of yeast transfer RNAPhe.

The molecular mechanism of thermal unfolding of yeast tRNA^Phe in 20 mM NaCl, 1 mM EDTA, and 10 mM MgSO₄, pH 7.1 ± 0.1, has been examined by ³¹P magnetic relaxation and the nuclear Overhauser effect methods at 40.48 MHz in the temperature range of 22.5–80°C. Two partially resolved ³¹P resonance peaks of yeast tRNA^Phe have been found to behave distinctively different in their longitudinal relaxation times. Individual intensities of the two partially resolved peaks have been quantitatively estimated by the use of relaxation data and the nuclear Overhauser effect as a function of temperature. The results of these observations largely support the earlier suggestion by Guéron and Shulman that the high- and low-field parts of the main ³¹P resonance cluster originate from phosphorus nuclei belonging to the double-helical and nonhelical regions of the tRNA, respectively. The spin-lattice relaxation of the phosphorus nucleus has been found to be determined dominantly by the dipolar interaction with the surrounding ribose protons at this observing frequency. Rotational correlation times for the two portions of the ribose-phosphate backbone of the tRNA have been separately deduced from the quantitative treatment of the ³¹P nuclear spin-lattice relaxation times (T₁) and the nuclear Overhauser effect. The result indicates that the two portions undergo internal motions at distinctively different rates of 10⁸–10¹⁰ sec^?1 order in the temperature range of 22.5–80°C, and that the thermal activation of these motions occurs at least in three distinctive steps, i.e., 22.5–31, 31–40, and 40–80°C. The rates of the internal motions and the associated activation energies in respective steps give some insight into the thermo-induced change of the yeast tRNA^Phe structure.     

New developments in first-principles excited-state dynamics simulations: unveiling the solvent specificity of excited anionic cluster relaxation and electron solvation

Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I^? (Solv)_n]^*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I^? (Solv)_n]^* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I^? (Solv)_n]^* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I^? (Solv)_n]^* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.     

Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water‐DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive‐biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time‐correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having ??ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO‐water mixtures. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 289–302, 2012.     

Proton and phosphorus magnetic relaxation studies on the dynamic structure of single-stranded polyriboadenylic acid

Proton and phosphorus-31 nuclear spin-lattice relaxation times (T₁) have been measured with the Fourier-transform method at 100 and 40.5 MHz, respectively, on single-stranded polyriboadenylic acid (poly(A)) in a neutral D₂O solution in the temperature range of 14–82°C. T₁ minimum is observed around 35–45°C for H(8), H(1′), and phosphorus resonances. Rotational correlation times have been deduced from the T₁ data, which indicate that the sugar–phosphate backbone as well as the base–sugar segment is undergoing rapid internal motion of 10^?8–10^?10 sec range. The molecular motion of the sugar–phosphate backbone as deduced from the phosphorus relaxation is well-characterized by a single activation enthalpy of 8.1 kal/mole for the whole temperature range of 14–82°C. Activation enthalpies of similar magnitude have been obtained for the motion of the adenine–ribose moiety from H(8) and H(1′) relaxation. The relative magnitude of T₁ for H(8) and H(1′) infers that the poly(A) nucleotide exists on the average as anti in the single-stranded form. The phosphorus T₁ value is consistent with a conformation such that both C(4′)–C(5′) and C(4′)–C(3′) bonds are nearly trans to their connected O–P bonds.     

Dynamics of a truncated prion protein,PrP(113–231), from 15N NMR relaxation: Order parameters calculated and slow conformational fluctuations localized to a distinct region

Prion diseases are associated with the misfolding of the prion protein (PrP^C) from a largely α‐helical isoform to a β‐sheet rich oligomer (PrP^Sc). Flexibility of the polypeptide could contribute to the ability of PrP^C to undergo the conformational rearrangement during PrP^C–PrP^Sc interactions, which then leads to the misfolded isoform. We have therefore examined the molecular motions of mouse PrP^C, residues 113–231, in solution, using ¹⁵N NMR relaxation measurements. A truncated fragment has been used to eliminate the effect of the 90‐residue unstructured tail of PrP^C so the dynamics of the structured domain can be studied in isolation. ¹⁵N longitudinal (T₁) and transverse relaxation (T₂) times as well as the proton‐nitrogen nuclear Overhauser effects have been used to calculate the spectral density at three frequencies, 0, ω_N, and 0.87ω_H. Spectral densities at each residue indicate various time‐scale motions of the main‐chain. Even within the structured domain of PrP^C, a diverse range of motions are observed. We find that removal of the tail increases T₂ relaxation times significantly indicating that the tail is responsible for shortening of T₂ times in full‐length PrP^C. The truncated fragment of PrP has facilitated the determination of meaningful order parameters (S²) from the relaxation data and shows for the first time that all three helices in PrP^C have similar rigidity. Slow conformational fluctuations of mouse PrP^C are localized to a distinct region that involves residues 171 and 172. Interestingly, residues 170–175 have been identified as a segment within PrP that will form a steric zipper, believed to be the fundamental amyloid unit. The flexibility within these residues could facilitate the PrP^C–PrP^Sc recognition process during fibril elongation.     

Effects of molecular association on structure and dynamics of a collagenous peptide

Peptide GVKGDKGNPGWPGAPY from the triple-helix domain of type IV collagen aggregates in solution at a critical aggregation concentration of 18 mM. This molecular self association process is investigated by ¹H- and ¹³C-nmr spectroscopy. As a function of increasing peptide concentration, selective ¹H resonances are cooperatively chemically shifted by up to 0.04 ppm to apparently saturable values at high concentration. Pulsed field gradient nmr was used to derive translation diffusion constants that, as the peptide concentration is increased, also cooperatively and monotonically decrease to an apparent limiting value. An average number of 6 monomer units per aggregate have been estimated from diffusion constant and ¹³C relaxation data. Comparative ¹H nuclear Overhauser effect spectroscopy (NOESY) spectra accumulated at high and low peptide concentrations suggest that average internuclear distances are decreased as a result of peptide association. ¹³C-nmr multiplet spin-lattice relaxation and ¹³C- {¹H} NOE effects on ¹³C-enriched glycine methylene positions in the peptide demonstrate that overall molecular tumbling and backbone internal motions are attenuated in the aggregate state. Lowering the solution pD from pD 6 to pD 2 disrupts the aggregate state, suggesting a role for electrostatic interactions in the association process. Based on thermodynamic considerations, hydrophobic interactions also probably act to stabilize the aggregate state. These data are discussed in terms of an nmr/NOE constrained computer-modeled structure of the peptide. © 1993 John Wiley & Sons, Inc.     

31P NMR relaxation measurements of the phosphate backbone of a double stranded hexadeoxynucleotide in solution: determination of the chemical shift anisotropy

The five phosphates of the deoxynucleotide d(CpGpTpApCpG)₂ have been assigned by two-dimensional heteronuclear NMR spectroscopy. The chemical shift anisotropy and correlation time of each phosphate group has been determined from measurements of the spin-lattice, spin-spin relaxation rate constants and the ³¹P-{¹H} nuclear Overhauser enhancement (NOE) at three magnetic field strengths (4.7 T, 9.4 T, and 11.75 T) and two temperatures (288 K and 298 K). As expected, the relaxation data require two mechanisms to account for the observed rate constants, i.e. dipole-dipole and chemical shift anisotropy. At 9.4 T and 11.75 T, the latter mechanism dominates the relaxation, leading to insignificant NOE intensities. The correlation time, chemical shift anisotropy and effective P-H distance were obtained from least-squares fitting to the data. Comparison of the fitted value for the correlation time with that obtained from ¹H measurements shows that the molecule behaves essentially as rigid rotor on the nanosecond timescale. Large amplitude motions observed in long segments of DNA are due to bending motions that do not contribute significantly to relaxation in short oligonucleotides.Abbreviations CSA chemical shift anisotropy - NOE nuclear Overhauser enhancement Offprint requests to: A. N. Lane     

Frequency dependence of the proton magnetic relaxation in aqueous solutions iof haemoproteins

The longitudinal proton magnetic relaxation times T₁ were measured for ferri (met)-and carbonmonoxy-bovine haemoglobin and equine myoglobin in 0.1 M KH₂PO₄ aqueous solutions near pH 6 at 5°C and 35°C from 1.5- to 60-MHz Larmor frequencies. It is concluded that the correlation time τ_C for the dipole–dipole interaction of electron and nuclear spins is in fact the electron (ferric) spin relaxation time τ_S being close to 1.5 × 10^?10 sec for both metHb and metMb at 5°C. At 35°C the paramagnetic relaxation rates are not determined solely by the relaxation of protons exchanging from the haem pocket with bulk solvent. Hence, τC at 35°C cannot be calculated from the dispersion data obtained at this temperature. The relevance of this for the determination of interspin distances r is discussed.     

Dielectric relaxation of DNA solutions. III. Effects of DNA concentration, protein contamination, and mixed solvents

As a continuation of previous papers [Biopolymers (1976) 15 , 879; (1978) 17 , 1508], the low-frequency dielectric relaxation of DNA solutions was studied with a four-electrode cell and the simultaneous two-frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration C_p, and the dielectric increment is proportional to C_p. The critical concentration is approximately 0.02% of DNA for molecular weight M_r 2 × 10⁶ and 0.2% for M_r 4.5 × 10⁵ in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi-permanent dipole due to counterion fluctuation.     

13C nuclear magnetic resonance studies on selectively labeled bacterial biofilms

Bacterial biofilms of Pseudomonas aeruginosa selectively labeled by introduction of 2-¹³C-glycerol was studied by solid-state and high-resolution nuclear magnetic resonance. The ¹³C nuclei were mainly integrated into mannuronate and guluronate, the two monomer units forming the bacterial alginate. The signal for the C5 position of the mannuronate, which was easily identified and well separated from other peaks, was analyzed for molecular mobility. The result indicated a high degree of motional freedom within the molecular network of the alginate. Despite the fact that the alginate was part of a solid aqueous gel phase, the reorientation mechanism of the monomer units came close to isotropic tumbling. Solid-state spectra of biofilms labeled in the described manner may serve as a valuable tool for noninvasive analyses of molecular mobility of the alginate component under various influences, thereby revealing important structural information. In addition, the effect of a monovalent electrolyte (LiCl) on the molecular mobility of alginate fragments in an aqueous solution was studied by determining the spin–lattice relaxation times, line widths and line shapes under variations of the ion concentration. The presence of ions accelerated overall motions but left rapid local motions virtually unaffected. Journal of Industrial Microbiology & Biotechnology (2001) 26, 62–69. Received 26 January 2000/ Accepted in revised form 30 August 2000     

NMR relaxation processes of 31P in macromolecules

³¹P-Nmr relaxation parameters (spin-lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well-defined (145 ± 3 base-pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of ³¹P chemical shift anisotropy as well as by ¹H-³¹P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least-square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ₀ = 6.5 × 10^?7 sec for the end-to-end motion, (2) the ratio of diffusion constants D_∥/D_⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log ? χ² distribution function of correlation times [Scheafer, J. (1973) Macromolecules 6 , 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10^?9 sec and a distribution parameter p = 14.     

Conformation and dynamic structure of poly(inosinic acid) in neutral aqueous solution by 1H-, 2H-, 13C-, and 31P-NMR spectroscopy

The conformation and dynamic structure of single-stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies: ¹H (90 and 250 MHz), ²H (13.8 MHz), ¹³C (75.4 MHz), and ³¹P (36.4 and 111.6 MHz). Measurements of the proton-proton coupling constants and of the ¹H and ¹³C chemical shifts versus temperature show that the ribose is flexible and that base-base stacking is not very significant for concentrations varying from 0.04 to 0.10M in the monomer unit. On the other hand, the proton T₁ ratios between the sugar protons, T₁ (H₁′)/T₁ (H₃′), indicate a predominance of the anti orientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation time T₂. For a given temperature between 22 and 62°C, the ¹³C-{¹H} NOE value is practically the same for seven protonated carbons (C₂, C₈, C_1′, C_2′, C_3′, C_4′, C_5′). This is also true for the T₁ ratio of the corresponding protons. Thus, the motion of the ribose–base unit can be considered as isotropic and characterized by a single correlation time, τ_c, for all protons and carbons. The τ_c values determined from either the ¹³C-{¹H} NOE or proton T₁ ratios, T₁(90 MHz)/T₁(250 MHz), and/or deuterium transverse relaxation time T₂ agree well. The molecular motion of the sugar-phosphate backbone (O-P-O) and the chemical-shift anisotropy (CSA) were deduced from T₁ (³¹P) and ³¹P-{¹H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ ? σ?). Activation energies of 2–6 kcal/mol for the motion of the ribose–base unit and the sugarphosphate backbone were evaluated from the proton and phosphorus relaxation data.     

Interaction of the antimalarial drug fluoroquine with DNA,tRNA, and poly(A): 19F-NMR chemical-shift and relaxation,optical absorption,and fluorescence studies

The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and ¹⁹F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (T_m) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the ¹⁹F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D₂O vs H₂O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. ¹⁹F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T₁), ¹⁹F{¹H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine–DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.     

Solution three-dimensional structure of surfactin: A cyclic lipopeptide studied by 1H-nmr,distance geometry,and molecular dynamics

The solution three-dimensional structure of the protonated [Leu7]-surfactin, an hepta-peptide extracted from Bacillus subtilis, has been determined from two-dimensional ¹Hnmr performed in ²H₆-dimethylsulfoxide and combined with molecular modeling. Experimental data included 9 coupling constants, 61 nuclear Overhauser effect derived distances, NH temperature coefficients, and ¹³C relaxation times. Two distance geometry (DISMAN) protocols converged toward models of the structure and the best of them were refined by restrained and unrestrained molecular dynamics (GROMOS). Two structures in accord with the set of experimental constraints are presented. Both are characterized by a “horse saddle” topology for ring atoms on which are attached the two polar Glu and Asp side chains showing an orientation clearly opposite to that of the C_11–13 aliphatic chain. Amphipathic and surface properties of surfactin are certainly related to the existence of such minor polar and a major hydrophobic domains. The particular “claw” configuration of acidic residues observed in surfactin gives important clues for the understanding of its cation binding and transporting ability. © 1994 John Wiley & Sons, Inc.     

Orientational interactions in low-concentration DNA solutions

The rotational relaxation tiem τ₃ of DNA molecules (M_w ? 5 × 10⁶) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher-molecular-weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ₃ increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10^?3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M-13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45 , 1891–1894]. These results may be discussed in terms of the Doi-Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36 , 607–611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74 , 918–932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ₃ and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high-molecular-weight elongated molecules are studied.     

Infinite dilution viscoelastic properties of poly(gamma-benzyl-L-glutamate) in m-cresol.

The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ-benzyl-L -glutamate) in m-cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights M_r are 6.4 × 10⁴–17 × 10⁴. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with M_r > 10⁵ is interpreted in terms of three mechanisms appearing from low to high frequencies: end-over-end rotation, flexural deformation, and side-chain motion. For a sample with M_r < 10⁵, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side-chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].     

Nuclear spin-relaxation studies of hydrated elastin.

The nuclear magnetic spin-lattice and transverse relaxation processes for the ¹H and ²D nuclei in purified elastin (ligamentum nuchae), exchanged and hydrated with excess D₂O, have been studied in the temperature range 276°–340°K. The ²D relaxation results clearly show the presence of D²O (1) external to the bulk elastin sample, (2) in spaces within the bulk elastin, and (3) as an integral part of the protein on a molecular level. It is shown from these measurements that the protein on a molecular level. It is shown from these measurements that the water content of the protein itself changes from ～0.8 g D₂O/g dry elastin at ～280°K to ～0.2 g D₂O/g dry elastin at ～335°K, a decrease of 400%. The D₂O content of the interfiber spaces decreases by less than 20% over the same temperature range. This fact throws considerable doubt on the validity of the values of β, the thermal expansion coefficient of elastin, used by other workers in discussion of the elastic mechanism in elastin. The elastin proton transverse relaxation shows the presence of three regions in elastin having different degrees of molecular mobility. These are assigned to protons associated with the crosslinks, a fairly mobile, hydrophobic, and low-water-content region, and a more mobile higher water-content region. The temperature variation of the relative proportions of these three regions is explained in terms of a hypothetical temperature-composition phase diagram in which the two mobile regions are represented as two partially miscible phases with different negative temperature coefficients of ‘solubility’ in water. The implications of these observations for current views of the nature of elastin are assessed. It is concluded that the spin-relaxation results are consistent with a multiphase structural model for elastin. An approximate sorption isotherm for the water/elastin system is reported and shows the relatively weak nature of the water/elastin interaction.     

Comparative Analyses of Coding and Noncoding DNA Regions Indicate that Acropora (Anthozoa: Scleractina) Possesses a Similar Evolutionary Tempo of Nuclear vs. Mitochondrial Genomes as in Plants

Evidence suggests that the mitochondrial (mt)DNA of anthozoans is evolving at a slower tempo than their nuclear DNA; however, parallel surveys of nuclear and mitochondrial variations and calibrated rates of both synonymous and nonsynonymous substitutions across taxa are needed in order to support this scenario. We examined species of the scleractinian coral genus Acropora, including previously unstudied species, for molecular variations in protein-coding genes and noncoding regions of both nuclear and mt genomes. DNA sequences of a calmodulin (CaM)-encoding gene region containing three exons, two introns and a 411-bp mt intergenic spacer (IGS) spanning the cytochrome b (cytb) and NADH 2 genes, were obtained from 49 Acropora species. The molecular evolutionary rates of coding and noncoding regions in nuclear and mt genomes were compared in conjunction with published data, including mt cytochrome b, the control region, and nuclear Pax-C introns. Direct sequencing of the mtIGS revealed an average interspecific variation comparable to that seen in published data for mt cytb. The average interspecific variation of the nuclear genome was two to five times greater than that of the mt genome. Based on the calibration of the closure of Panama Isthmus (3.0 mya) and closure of the Tethy Seaway (12 mya), synonymous substitution rates ranged from 0.367% to 1.467% Ma⁻¹ for nuclear CaM, which is about 4.8 times faster than those of mt cytb (0.076–0.303% Ma⁻¹). This is similar to the findings in plant genomes that the nuclear genome is evolving at least five times faster than those of mitochondrial counterparts. I-Ping Chen and Chung-Yu Tang, co-first author (equal contribution)     

Properties of a 110000 molecular weight protein in rat liver hnRNP particles

Particles carrying heterogeneous nuclear RNA (30–40 S-particles) were isolated from rat liver nuclei and the particle proteins separated by sodium dodecylsulfate gel electrophoresis. Some properties of a 110000 molecular weight component (P 110/103) were studied in detail: (i) P 110/103 was labeled to a 4–5 times higher specific activity than the major particle proteins in the presence of [¹⁴C]-amino acidsin vivo. (ii) In nuclei incubated with [³H]- or [³²P]-nicotinamide adenine dinucleotide P 110/103 was labeled presumably by ADP-ribosylation. (iii) A protein with the same molecular weight as P 110/103 and isolated from the nuclear extract by affinity chromatography was phosphorylated in vitro.Abbreviations hnRNA heterogeneous nuclear RNA - hnRNP and mRNP ribonucleoproteins which contain hnRNA respectively mRNA     

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy

Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D ¹H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.