CN− secondary ions form by recombination as demonstrated using multi-isotope mass spectrometry of 13C- and 15N-labeled polyglycine

We have studied the mechanism of formation CN- secondary ions under Cs+ primary ion bombardment. We have synthesized 13C and 15N labeled polyglycine samples with the distance between the two labels and the local atomic environment of the 13C label systematically varied. We have measured four masses in parallel: 12C, 13C, and two of 12C14N, 13C14N, 12C15N, and 13C15N. We have calculated the 13C/12C isotope ratio, and the different combinations of the CN isotope ratios (27CN/26CN, 28CN/27CN, and 28CN/26CN). We have measured a high 13C15N- secondary ion current from the 13C and 15N labeled polyglycines, even when the 13C and 15N labels are separated. By comparing the magnitude of the varied combinations of isotope ratios among the samples with different labeling positions, we conclude the following: CN- formation is in large fraction due to recombination of C and N; the CO double bond decreases the extent of CN- formation compared to the case where carbon is singly bonded to two hydrogen atoms; and double-labeling with 13C and 15N allows us to detect with high sensitivity the molecular ion 13C15N-.     

Tracking Conformational Changes in Calmodulin in vitro,in Cell Extract,and in Cells by Electron Paramagnetic Resonance Distance Measurements

It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca²⁺ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.     

In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels

In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (T_M) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.     

Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides

β-Peptides are an interesting new class of transmembrane model peptides based on their conformationally stable and well-defined secondary structures. Herein, we present the synthesis of the paramagnetic β-amino acid β³-hTOPP (4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-d -β³-homophenylglycine) that enables investigations of β-peptides by EPR spectroscopy. This amino acid adds to the, to date, sparse number of β-peptide spin labels. Its performance was evaluated by investigating the helical turn of a 3₁₄-helical transmembrane model β-peptide. Nanometer distances between two incorporated β³-hTOPP labels in different environments were measured by using pulsed electron/electron double resonance (PELDOR/DEER) spectroscopy. Due to the semi-rigid conformational design, the label delivers reliable distances and sharp (one-peak) distance distributions even in the lipid bilayer. The results indicate that the investigated β-peptide folds into a 3.25₁₄ helix and maintains this conformation in the lipid bilayer.     

"Glass transition" near 200 K in the bacterial photosynthetic reaction center protein detected by studying the distances in the transient P+Q(A)- radical pair

The transient radical pair P(+)Q(A)(-) in the photosynthetic reaction center from Rhodobacter sphaeroides R26 was studied over a wide temperature range using out-of-phase electron spin-echo envelope modulation (ESEEM) spectroscopy. This method is sensitive to the magnetic dipole-dipole interaction between the two electron spins of the pair and allows precise determination of the distance in the pair P(+)Q(A)(-). The out-of-phase data were complemented by normal in-phase ESEEM spectra from the two stable radicals of P(+) and Q(A)(-). The results seem to indicate that the radical pair undergoes a noticeable molecular motion around 200 K that may be characterized by a change in the distance in the pair by approximately 0.3 nm. As the two cofactors, P(+) and Q(A)(-), are held in a well-defined relative position by the reaction center protein, this means that the protein becomes flexible at 200 K. This effect may be ascribed to a dynamic glass transition around 200 K. The relation with the temperature dependence of the back reaction of P(+)Q(A)(-) is discussed.     

SLIM: A Short‐Linked,Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.     

Reversible Dimerization of Human Serum Albumin

Pulsed Dipolar Spectroscopy (PDS) methods of Electron Paramagnetic Resonance (EPR) were used to detect and characterize reversible non-covalent dimers of Human Serum Albumin (HSA), the most abundant protein in human plasma. The spin labels, MTSL and OX063, were attached to Cys-34 and these chemical modifications of Cys-34 did affect the dimerization of HSA, indicating that other post-translational modifications can modulate dimer formation. At physiologically relevant concentrations, HSA does form weak, non-covalent dimers with a well-defined structure. Dimer formation is readily reversible into monomers. Dimerization is very relevant to the role of HSA in the transport, binding, and other physiological processes.     

SLIM: A Short-Linked,Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.     

CRYSTAL STRUCTURE OF 2，4—DINITROPHENYL—t—BUTYL NITRONE（DNPBN）

<正> C11H13 N3 O5·t-Bu- N = CHC6H3(NO2)2,Mr = 267. 27, Monoclinic space group C2/c,a= 18. 546(3),b = 5. 729(1),c= 27. 479(5) A,β= 118. 42(1)°/,F = 2567. 6(9)A3,F(000) = 1120,Z=8,Dx=1. 38g/cm3. The structure of DNPBN is akin to that of PBN reported by us except for shorter N - O and C = N bonds.     

Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels

The pulse DEER (Double Electron-Electron Resonance) technique is frequently applied for measuring nanometer distances between specific sites in biological macromolecules. In this work we extend the applicability of this method to high field distance measurements in a protein assembly with mixed spin labels, i.e. a nitroxide spin label and a Gd(3+) tag. We demonstrate the possibility of spectroscopic selection of distance distributions between two nitroxide spin labels, a nitroxide spin label and a Gd(3+) ion, and two Gd(3+) ions. Gd(3+)-nitroxide DEER measurements possess high potential for W-band long range distance measurements (6 nm) by combining high sensitivity with ease of data analysis, subject to some instrumental improvements.     

Self-assembly and Crystal Structure of a Novel Inorganic-organic Hybrid Coordination： {（C12H14N2）[Ag2I4]}n

1 INTRODUCTION The construction of low-dimensional organic- inorganic hybrid material with novel properties re- presents new directions in solid-state chemistry[1, 2]. Generally the physical properties of such low di- mensional compounds differ from tho…     

X-Ray Diffraction Studies of Bacteriorhodopsin. Determination of the Positions of Mercury Label at Several Engineered Cysteine Residues

Abstract— The single cysteine-containing bacteriorhodopsin mutants F27C, L100C, T170C, F171C and I222C were labeled with p -chloromercuribenzoic acid, which specifically reacts with sulfhydryl groups. These cysteines should be located at the cytoplasmic ends of the transmembrane helices A, C, F or G. We determined the positions of the bound mercury atoms by X-ray diffraction of purple membrane films, with better than 1 Å accuracy. The determined mercury positions were compared with the structural model from cryoelectron microscopy (N. Grigorieff, T. A. Ceska, K. H. Downing, J. M. Baldwin and R. Henderson, J. Mol. Biol 259, 393-421, 1996). Given that the distance between the mercury and the Cα atom of the cysteine in the xy plane must be shorter than 4.5 Å and that the mercury atom is located at the δ position, the positions obtained for the mercury labels agree with their expected positions from the structural model. The present results give a rationale for detecting structural changes upon illumination as shifts occur in the mercury label position.     

Site‐Directed Spin‐Labeling of DNA by the Azide–Alkyne ‘Click’ Reaction: Nanometer Distance Measurements on 7‐Deaza‐2′‐deoxyadenosine and 2′‐Deoxyuridine Nitroxide Conjugates Spatially Separated or Linked to a ‘dA‐dT’ Base Pair

Nucleobase‐directed spin‐labeling by the azide‐alkyne ‘click’ (CuAAC) reaction has been performed for the first time with oligonucleotides. 7‐Deaza‐7‐ethynyl‐2′‐deoxyadenosine ( 1 ) and 5‐ethynyl‐2′‐deoxyuridine ( 2 ) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4‐azido‐2,2,6,6‐tetramethylpiperidine 1‐oxyl (4‐azido‐TEMPO, 3 ) was performed by post‐modification in solution. Two spin labels ( 3 ) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a ‘dA‐dT’ base pair. Modification at the 5‐position of the pyrimidine base or at the 7‐position of the 7‐deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1–2 nm, were measured. The spin–spin distance was 1.8±0.2 nm for DNA duplex 17 ( dA*^7,10 ) ?11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin‐labeled ‘dA‐dT’ base pair 15 ( dA*⁷ ) ?16 ( dT*⁶ ). The ‘click’ approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.     

The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid,Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements

The development of ESR methods that measure long‐range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein‐backbone structure. Herein we present the double‐histidine (dHis) Cu²⁺‐binding motif as a rigid spin probe for double electron–electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X‐ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu²⁺ DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein‐backbone structure and flexibility.     

Synthesis and Crystal Structure of a Manganese Coordination Polymer [（phen）MnCl2]n

1 INTRODUCTION Polymeric manganese complexes with fascinating topological chemistry have received considerable interest[1, 2]. The complexation of phen with man- ganese ion gives rise to a wide variety of coordi- nation complexes; however, (phen)Mn coordina- tion polymers are rare since the chelation of phen results in 1 to 3 5-membered chelating rings, ob- structing the way towards the coordination poly- mer. Similar situation has also been observed for 2,2?-bipyridine (bpy) which has si…     

氯碘甲烷在A带的光解动力学

利用离子速度影像方法结合共振增强多光子电离(REMPI)技术研究了氯碘甲烷在A带的光解机理. 从266和277 nm的I*(5p 2P1/2)和I(5p 2P3/2)离子速度影像获得了碎片的平动能分布和角度分布. I和I*的平动能分布呈单高斯型, 可用软自由基近似来解释. I和I*是在排斥的势能面上直接解离产生的. 实验得到的各向异性参数β证实分子受激发后主要产生3Q0态, 并且3Q0和1Q1态之间存在非绝热转移. 波长越短, 这种非绝热转移越强. 在235 nm附近, Cl和Cl*各向同性的离子影像说明氯原子来自于CH2ICl的二次解离过程, 即CH2ICl先解离产生CH2Cl自由基, 自由基再解离产生氯原子.     

Liquid-liquid distribution of ion-associates of dichlorocuprate(I) with quaternary ammonium counter-ions

The dichlorocuprate(I) anion CuCl(-)(2) can be extracted as its ion-associates Q(+).CuCl(-)(2) with quaternary ammonium cations (Q(+)) into chloroform. The extraction constants K(ex) have been determined, and the log K(ex) values found for the various counter-ions used are 1.93 for (C(3)H(7))(4)N(+), 4.10 for (C(4)H(9))(4)N(+), 6.57 for (C(5)H(11))(4)N(+), 1.57 for C(8)H(17)N(+) (CH(3))(3), 2.83 for C(10)H(21)N(+) (CH(3))(3) 4.12 for C(12)H(25)N(+) (CH(3))(3) and 5.21 for C(14)H(29)N(+)(CH(3))(3), respectively. A linear relationship was found between log K(ex) and the total number of carbon atoms in Q(+); from the slope of the line, the contribution of a methylene group to log K(ex) was calculated to be 0.59. The extractability with alkyltrimethylammonium cations was larger than that with symmetrical tetra-alkylammonium cations and the difference in log K(ex) for two cations (one of each type) with the same number of carbon atoms was about 0.4. From the extraction constants obtained, the extractability of CuCl(-)(2) was found to lie between that of ReO(-)(4) and ClO(-)(4).     

Fe(CO)5 thin films adsorbed on Au(111) and on self-assembled organic monolayers: I. Structure

The adsorption of Fe(CO)(5) onto Au(111)/mica and C(4), C(8), C(12), and C(16) SAMs/Au(111)/mica surfaces has been studied using infrared spectroscopy to elucidate the coverage-dependent structures of these films and the intermolecular couplings that determine the form of the spectra. For all substrates, the first layer is composed of molecules physisorbed with one axial and two equatorial carbonyl groups directed toward the substrate; subsequent layers are preferentially oriented with the C(3) molecular axis aligned perpendicular to the substrate (i.e., one axial carbonyl group directed toward the substrate). The axial vibrational band systematically shifts to higher frequencies with increasing surface coverage because of the effects of intermolecular coupling of the quasiparallel transition dipole moments. The strong effects of dipolar coupling are also witnessed by the trends of the band positions when the distance to the image plane is systematically varied using highly organized self-assembled organic substrates; no band shifts are observed when dilute Fe(CO)(5) is embedded in Xe matrixes under identical experimental conditions. The as-deposited films are structurally stable below 125 K on Au(111)/mica surfaces and below 100 K on the organic self-assembled monolayers. The instability of the films above these temperatures demonstrates that the as-adsorbed films do not form thermodynamically well-defined phases but are structurally metastable. The results presented herein and in the companion paper provide a consistent framework to interpret the spectroscopy of these systems that resolves outstanding issues concerning these films and provides a structural model that explains the dynamic properties of these films during exposure to low-energy electron beams.     

Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin?

Molecular dynamics (MD) simulations have been widely used to analyze dynamic conformational equilibria of folded proteins, especially in relation to NMR observables. However, this approach found little use in the studies of disordered proteins, where the sampling of vast conformational space presents a serious problem. In this paper, we demonstrate that the latest advances in computation technology make it possible to overcome this limitation. The experimentally validated (calibrated) MD models allow for new insights into structure/dynamics of disordered proteins. As a test system, we have chosen denatured ubiquitin in solution with 8 M urea at pH 2. High-temperature MD simulations in implicit solvent have been carried out for the wild-type ubiquitin as well as MTSL-tagged Q2C, D32C, and R74C mutants. To recalibrate the MD data (500 K) in relation to the experimental conditions (278 K, 8 M urea), the time axes of the MD trajectories were rescaled. The scaling factor was adjusted such as to maximize the agreement between the simulated and experimental (15)N relaxation rates. The resulting effective length of the trajectories, 311 μs, ensures good convergence properties of the MD model. The constructed MD model was validated against the array of experimental data, including additional (15)N relaxation parameters, multiple sets of paramagnetic relaxation enhancements (PREs), and the radius of gyration. In each case, a near-quantitative agreement has been obtained, suggesting that the model is successful. Of note, the MD-based approach rigorously predicts the quantities that are inherently dynamic, i.e., dependent on the motional correlation times. This cannot be accomplished, other than in empirical fashion, on the basis of static structural models (conformational ensembles). The MD model was further used to investigate the relative translational motion of the MTSL label and the individual H(N) atoms. The derived segmental diffusion coefficients proved to be nearly uniform along the peptide chain, averaging to D = 0.49-0.55 × 10(-6) cm(2)/s. This result was verified by direct analysis of the experimental PRE data using the recently proposed Ullman-Podkorytov model. In this model, MTSL and H(N) moieties are treated as two tethered spheres undergoing mutual diffusion in a harmonic potential. The fitting of the experimental data involving D as a single adjustable parameter leads to D = 0.45 × 10(-6) cm(2)/s, in good agreement with the MD-based analyses. This result can be compared with the range of estimates obtained from the resonance energy transfer experiments, D = 0.2-6.0 × 10(-6) cm(2)/s.     

Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment

Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.