用多维NMR谱和圆二色CD光谱研究蛋白质亲环素A的结构稳定性

The structural stability of cyclophilin A （CypA） was investigated using H/D exchange and temperature coefficients of chemical shifts of amide protons, monitored by 213 heteronuclear NMR spectroscopy. Amide proton exchange rates were measured by H/D exchange experiments for slow-exchange protons and measured by SEA （Solvent Exposed Amides）-HSQC experiments for fast-exchange protons. Temperature coefficients of chemical shifts and hydrogen exchange rates of amide protons show reasonably good correlation with the protein structure. Totally, 44 out of 153 non-proline assigned residues still exist in 86 d of hydrogen-deuterium exchange at 4 ℃, suggesting that CypA structure should be highly stable. Residues in secondary structures of α2, β1, β2, β5, β6 and β7 might constitute the hydrophobic core of the protein. The change in free energy of unfolding （ △Gu^H2O ） of CypA was estimated to be （21.99± 1.53） kJ·mol^-1 by circular dichroism （CD）. The large free energy change is also an indicator of the high structural stability.     

Sodium controlled selective reactivity of protonated deoxy-oligonucleotides in the gas phase

Metastable fragmentation of the positively charged, hexameric oligonucleotides 5′-d(TTXYTT) (X and Y are dC, dG, or dA) and 5′-d(CTCGTT), 5′-d(TTCGTC) and 5′-d(CTCGTC) is studied after matrix assisted laser desorption/ionization (MALDI). The influence of the degree of sodiation, i.e., when the acidic protons are one by one exchanged against sodium ions, is systematically studied for the exchange of up to seven protons against sodium ions. Exchanging the acidic protons against sodium gradually quenches the backbone cleavage through the w and a-B channels, and quantitative quenching of these channels is generally achieved with the exchange of four protons against sodium ions. At the same time, the exchange of protons against sodium ions promotes the loss of a neutral, high proton affinity base. The formation of the w and a-B fragments is found to be highly dependent on the sequence of the central bases. A single mechanism consistent with these observations is proposed. In addition to the quenching of the classical w and a-B reaction channels, a drastic and abrupt on/off-switching of new reaction channels is observed as the degree of sodiation successively increases. These channels involve selective loss of the two central bases and the excision of a phosphodiester group and a sugar unit from the center of the oligonucleotides. Synchronously, the two terminal fragments recombine to form a tetramer containing the two terminal nucleosides from each end of the hexamer. Possible mechanism explaining these remarkable channels are discussed.     

Nitrogen-15 nuclear magnetic resonance spectroscopy. Differential rates of N?H proton-exchange reactions of hydrazine-carbothioamide and 4-methylhydrazine-carbothioamide in dimethyl sulfoxide

The proton-coupled nitrogen-15 NMR spectra of hydrazinecarbothioamide and 4-methylhydrazinecarbothioamide have been taken at the natural-abundance level in neutral, basic and acidic solutions at 25°C. The N? H proton-exchange reactions of the hydrazino-NH₂ groups in both compounds were found to be very rapid in the presence of acid, but quite slow in the presence of base. The hydrazino-NH protons of hydrazinecarbothioamide exhange six times and 200 times faster than the amide protons in the presence of either base or acid, respectively. Similarly, acid- and base-catalyzed N? H proton exchanges of the hydrazino-NH group of 4-methylhydrazinecarbothioamide were found to be two to three orders of magnitude faster than those of N-methylamido protons. These results can be rationalized by consideration of the effect of the lone pair on the hydrazino? NH₂ group on the reactivity of the adjacent ? NH? group.     

A molecular dynamics investigation of the titration of a trivalent aqueous ion

We carried out a series of molecular dynamics simulations of the hydrolysis of a model trivalent metal ion in aqueous solution. We use a dissociative model for water and examine the spontaneous speciation of M³⁺ into M(OH) _n ^(3-n)+ (n =1,4) both in neutral solution and as a function of added protons and hydroxide ions. The species distributions in neutral solution correspond reasonably well with those expected for real trivalent metal ions at neutral pH. However, the change in the species distributions as a function of either added protons or hydroxide ions is much less than expected with very large concentrations of protons or hydroxide ions required to shift the species equilibria in either direction. The influence of added protons and hydroxide ions on the species distributions appears to be proportional to the average charge of the hydrolysis couples, being highest for the 3+/2+ couple and lowest for the 1+/0 and 0/1- couples. Proton exchange rates vary with proton/hydroxide ion concentration giving a minimum at intermediate values ([H+]≈ 0.166) with increasing rates at both lower and higher pH.     

An NMR study of some N-arylaminopropenylylidenearylammonium salts

The preparation, characterisation and ¹H NMR spectra of some N-arylaminopropenylylidenearylammonium salts are reported. The NMR data show that in DMSO the cations exist as conjugated amino–imines, generally as the ‘all-trans’ geometrical isomer. An exception is found in the case of the 4-nitrophenyl derivative which produces a mixture of the ‘all-trans’ and ‘cis-trans’ isomers with slow exchange between them at room temperature. The relative stability of the ‘all-trans’ isomer increases as the salt becomes more ionic. By varying the temperature, pH and nature of the anion it is found that exchange of the N? H protons on the cation controls the appearance of spin-spin coupling between the N? H and 1,3-propene protons.     

The unusual hydrogen‐deuterium exchange of α‐carbon protons in N‐substituted glycine‐containing peptides

Hydrogens connected to α‐carbon (α‐C) of amino acid residues are usually resistant to hydrogen‐deuterium exchange (HDX) unless reaction conditions promote racemization. Although N‐methylglycine (sarcosine) residue has been found in biologically active peptide such as cyclosporine, to the best of our knowledge, the HDX of α‐C protons of this residue was not explored yet. Here, we presented a new and efficient methodology of α‐C deuteration in sarcosine residues under basic aqueous conditions. The deuterons, introduced at α‐C atom, do not undergo back‐exchange in acidic aqueous solution. The electrospray ionization‐MS and MS/MS experiments on proposed model peptides confirmed the HDX at α‐C and revealed the unexpected hydrogen scrambling in sarcosine‐containing peptides. Although the observed HDX of α‐C protons is only successful in N‐acylglycine when the amide possesses a certain degree of alkylation, it offers a new approach to the analysis of sarcosine‐containing peptides such as cyclosporine. Copyright © 2014 John Wiley & Sons, Ltd.     

Transverse Relaxation of Scalar‐Coupled Protons

In a preliminary communication (B. Baishya, T. F. Segawa, G. Bodenhausen, J. Am. Chem. Soc. 2009 , 131, 17538–17539), we recently demonstrated that it is possible to obtain clean echo decays of protons in biomolecules despite the presence of homonuclear scalar couplings. These unmodulated decays allow one to determine apparent transverse relaxation rates R₂^app of individual protons. Herein, we report the observation of R₂^app for three methyl protons, four amide H^N protons, and all 11 backbone H^α protons in cyclosporin A. If the proton resonances overlap, their R₂^app rates can be measured by transferring their magnetization to neighboring ¹³C nuclei, which are less prone to overlap. The R₂^app rates of protons attached to ¹³C are faster than those attached to ¹²C because of ¹³C–¹H dipolar interactions. The differences of these rates allow the determination of local correlation functions. Backbone H^N and H^α protons that have fast decay rates R₂^app also feature fast longitudinal relaxation rates R₁ and intense NOESY cross peaks that are typical of crowded environments. Variations of R₂^app rates of backbone H^α protons in similar amino acids reflect differences in local environments.     

Structural Studies of Antarctic Fish Antifreeze Glycoproteins by One- and Two-Dimensional NMR Spectroscopy

Abstract

The solution structure of antifreeze glycoproteins (AFGP's) of the polar fish Tetramatomus borchgrevinki has been investigated by 2D ¹ H NMR spectroscopy as well as molecular modeling calculations (MM2). The simple glycotripeptide repeating structure in the shorter AFGP's (fractions 7 & 8) makes the structural analysis amenable. The resonance assignments of AFGP's 7 & 8 were determined by two-dimensional NMR techniques (COSY, Relayed-COSY, Phase Sensitive DQCOSY, NOESY). Information about the protein secondary structure was obtained by the coupling constants between the back-bone amide and α-carbon protons (obtained by phase sensitive COSY). Additional three dimensional constraints were obtained from NOESY through-space connectivities. The three dimensional solution structures of several AFGP's glycotripeptide fragments were based on MM2 calculations. The model structure was compared with the experimental data. Exchange rates of amide protons measured by dynamical spectroscopy show that the threonine and some of the alanine amide protons have two different and distinct exchange rates. GalNAc and the C-terminal Ala' amide protons appear to show relatively slow exchznge rates. The results suggets that the amide protons are not involved in any strong intramolecular hydrogen bonding.     

Investigation of acid deuterium exchange in a number of isoquinoline and 4-hydroxyisoquinoline derivatives

The acid deuterium exchange of isoquinoline and 4-hydroxy- and 3-methyl-4-hydroxyisoquinolines at 145°C in 94% D₂SO₄ was investigated by PMR spectroscopy. The sequence of substitution and the rate constants for deuterium exchange of the protons of the isoquinoline ring were determined. The most reactive protons in isoquinoline and 3-methyl-4-hydroxyisoquinoline are those of the benzene ring, while the proton in the 3 position of the -pyridol ring is the most reactive in 4-hydroxyisoquinoline.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1647–1650, December, 1972.     

The Halogen–Samarium Exchange Reaction: Synthetic Applications and Kinetics

Fast I/Sm and Br/Sm exchanges take place when various aromatic or heterocyclic iodides and bromides are treated with nBu₂SmCl?4 LiCl and nBu₃Sm?5 LiCl, respectively. The resulting organosamarium reagents were efficiently quenched with aldehydes, ketones, and imines. Also, they undergo acylations when treated with N,N‐dimethylamides leading to ketones. The rate of the Br/Sm exchange for a typical aryl bromide was determined and found to be 8.5×10⁵ faster than the Br/Mg exchange, indicating that the rate of a metal‐exchange is related to the ionic character of the carbon–metal bond and to the metal electronegativity.     

Kernresonanz-spektroskopische Untersuchung protonierter Stickstoffverbindungen in Trifluoressigsäure

The nuclear magnetic resonance spectra of a series of protonated organic nitrogen compounds in trifluoroacetic acid solution have been studied. A direct correlation between the exchange rate of the ammonium protons and the acidity constant of the functional group is established. Substituted anilinium and pyridinium ions with pK values below 4 show coalescence for the signals of N^⊕? H protons and disappearence of the coupling with the α protons.     

HDX-ESI-MS reveals enhanced conformational dynamics of the amyloidogenic protein β 2-microglobulin upon release from the MHC-1

The light chain of the major histocompatibility complex class 1 (MHC-1), the protein β ₂-microglobulin (β ₂m), has amyloidogenic properties that arise only upon its dissociation from the MHC-1. Here hydrogen/deuterium exchange electrospray ionization mass spectrometry (HDX-ESI-MS) has been used to compare the solution dynamics of β ₂m in its MHC-1 bound state compared with those of β ₂m as a free monomer. The capability of tandem mass spectrometry to dissociate the MHC-1 into its individual constituents in the gas phase following deuterium incorporation in solution has permitted the direct observation of the exchange properties of MHC-1 bound β ₂m for the first time. The HDX-ESI-MS data show clearly that the H→D exchange of MHC-1 bound β ₂m follows EX2 kinetics and that about 20 protons remain protected from exchange after 17 days. Free from the MHC-1, monomeric β ₂m exhibits significantly different HDX behavior, which encompasses both EX1 and EX2 kinetics. The EX2 kinetics indicate a tenfold increase in the rate of exchange compared with MHC-1 bound β ₂m, with just 10 protons remaining protected from EX2 exchange and therefore exchanging only via the EX1 mechanism. The EX1 kinetics observed for unbound β ₂m are consistent with unfolding of its exchange-protected core with a t_1/2 of 68 min (pH 7, 37° C). Thus, upon dissociation from the stabilizing influence of the MHC-1, free β ₂m becomes highly dynamic and undergoes unfolding transitions that result in an aggregation-competent protein.     

The Role of Ate Complexes in the Lithium‐Sulfur,Lithium‐Selenium and Lithium‐Tellurium Exchange Reactions

Hypervalent ate complexes are presumptive intermediates in the metal‐halogen, metal‐tellurium, and related exchange reactions. The effect of o,o′‐biphenyldiyl vs. diphenyl substitution on formation of tellurium ate complexes was studied by a kinetic technique and by NMR spectroscopy. Only a modest increase in the association constant (K_ate) was measured. When Li/M exchanges of o,o′‐biphenyldiyl sulfides and selenides were made intramolecular by means of a m‐terphenyl framework ( 12‐S, 12‐Se, 21 ), enormous increases (>10⁹) in the rate of Li/S and Li/Se exchange were observed compared to acyclic models. Apparently, these systems are ideally preorganized to favor the T‐shaped geometry of the hypervalent intermediates. For the selenium systems, ate complex intermediates ( 20‐Se, 26 ) were detected spectroscopically in THF‐ or THF/HMPA‐containing solutions. A DNMR study showed that Li/Se exchange was substantially faster than exchange of the lithium reagents with the ate complex. Therefore, these ate complexes are not on the actual Li/Se exchange pathway.     

Relationships between NMR shifts and interaction energies in biphenyls,alkanes, aza-alkanes,and oxa-alkanes with X─H…H─Y and X─H…Z (X,Y = C or N; Z = N or O) hydrogen bonding

Hydrogen–hydrogen C─H^…H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom–atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact (“in”) and the other is not (“out”), show a rough correlation with the corresponding C─H^…H─C exchange energies. The “in” and “in,in” isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H^…H─N hydrogen bonded, whereas the “out” and “in,out” isomers display X─H^…N hydrogen bonds (X = C or N). Oxa-alkanes and the “in” isomers of aza–oxa-alkanes are X─H^…O hydrogen bonded. There is a very good general correlation, including both N─H^…H─Y (Y = C or N) and N─H^…Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For “in” CH protons, the data for the different C─H^…H─Y and C─H^…Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.     

Pyranosyl-RNA (‘p-RNA’): NMR and Molecular-Dynamics Study of the Duplex Formed by Self-pairing of Ribopyranosyl-(C-G-A-A-T-T-C-G)

The solution structure of the duplex formed by self-pairing of the p-RNA octamer β-D -ribopyranosyl-(2′→4′)-(CGAATTCG) was studied by NMR techniques and, independently, by molecular-dynamics calculations. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles β and ? in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base-pair axis forms an angle of ca. 40° with the backbone. The resulting interstrand π-π stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps molecular-dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. For the backbone torsion angle ?, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle β, a systematic difference of ca. 25° remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.     

Nitrogen-15 nuclear magnetic resonance spectroscopy. N?H proton exchange reactions of urea and substituted ureas

Proton-coupled nitrogen-15 NMR spectra of urea, N-methylurea, N,-N′-dimethylurea, N-methyl-N′-benzylurea and N-phenylurea have been obtained at natural abundance level in neutral, basic and acidic solutions at 25°C. Base-catalyzed N? H proton exchange of the ? NH₂ group of N-methylurea in water was found to be 1.5 times faster than that for the -NH- group, while the corresponding acid-catalyzed exchange is 7.5 times faster. Comparison of urea and N,-N′-dimethylurea in water shows urea to be 10 times faster in base but 2 times slower in acid. The ratio of the base-catalyzed N? H proton exchanges of the two -NH- groups of N-methyl-N′-benzylurea in dimethyl sulfoxide is close to unity, whereas the CH₃NH- group exchanges 4 times faster in acid. Similarly, the C₆H₅NH- group of N-methyl-N′-phenylurea exchanges 50 times faster than the CH₃NH- group in base and about 3 orders of magnitude slower in acid. The results are rationalized by consideration of steric and electronic effects.     

Fast Proton Exchange in Histidine: Measurement of Rate Constants through Indirect Detection by NMR Spectroscopy

Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH₃⁺ amino protons and the labile NH^ε2 and NH^δ1 protons of the imidazole ring by indirect detection through nitrogen‐15 as a function of temperature (272 K<T<293 K) and pH (1.3<pH<4.9) of uniformly nitrogen‐15‐ and carbon‐13‐labeled L ‐histidine ? HCl ? H₂O. Exchange rates up to 8.5×10⁴ s^?1 could be determined (i.e., lifetimes as short as 12 μs). The three chemical shifts δ_Hi of the invisible exchanging protons H_i and the three one‐bond scalar coupling constants ¹J(N,H_i) could also be determined accurately.     

Electrochemical reactions with protonations at equilibrium: Part VI. The homogeneous electron exchange reaction between a monoelectronic and A 1 e, 1 H+ system

The rate of homogeneous electron exchange between a 1 e redox couple and a 1 e, 1 H⁺ redox system is studied theoretically when the protonations are much faster than the electron exchange reactions, i.e. when they can be assumed to be at equilibrium. It is shown that the whole system is equivalent to a reaction between two simple 1 e couples, with apparent rate constants for the electron exchange. Variations of these constants are complex functions of the difference of the standard potentials of the monoelectronic system and those of the 1 e, 1 H⁺ system. They also vary with pH in a less complicated way. The reaction path and the reaction sequence (order of addition or loss of electrons and protons) are studied. A potential-pH diagram, which allows the results to be visualized, is given. It is shown that it is not possible to accelerate at the same time the reduction and oxidation of the members of the square scheme by the same monoelectronic system. Applications to redox polymer electrodes are discussed.     

Enolate Stabilization by Anion–π Interactions: Deuterium Exchange in Malonate Dilactones on π‐Acidic Surfaces

Of central importance in chemistry and biology, enolate chemistry is an attractive topic to elaborate on possible contributions of anion–π interactions to catalysis. To demonstrate the existence of such contributions, experimental evidence for the stabilization of not only anions but also anionic intermediates and transition states on π‐acidic aromatic surfaces is decisive. To tackle this challenge for enolate chemistry with maximal precision and minimal uncertainty, malonate dilactones are covalently positioned on the π‐acidic surface of naphthalenediimides (NDIs). Their presence is directly visible in the upfield shifts of the α‐protons in the ¹H NMR spectra. The reactivity of these protons on π‐acidic surfaces is measured by hydrogen–deuterium (H–D) exchange for 11 different examples, excluding controls. The velocity of H–D exchange increases with π acidity (NDI core substituents: SO₂R>SOR>H>OR>OR/NR₂>SR>NR₂). The H–D exchange kinetics vary with the structure of the enolate (malonates>methylmalonates, dilactones>dithiolactones). Moreover, they depend on the distance to the π surface (bridge length: 11–13 atoms). Most importantly, H–D exchange depends strongly on the chirality of the π surface (chiral sulfoxides as core substituents; the crystal structure of the enantiopure (R,R,P)‐macrocycle is reported). For maximal π acidity, transition‐state stabilizations up to ?18.8 kJ mol^?1 are obtained for H–D exchange. The Brønsted acidity of the enols increases strongly with π acidity of the aromatic surface, the lowest measured pK_a=10.9 calculates to a ΔpK_a=?5.5. Corresponding to the deprotonation of arginine residues in neutral water, considered as “impossible” in biology, the found enolate–π interactions are very important. The strong dependence of enolate stabilization on the unprecedented seven‐component π‐acidity gradient over almost 1 eV demonstrates quantitatively that such important anion–π activities can be expected only from strong enough π acids.     

Lanthanide‐Based T2ex and CEST Complexes Provide Insights into the Design of pH Sensitive MRI Agents

The CEST and T₁ /T₂ relaxation properties of a series of Eu³⁺ and Dy³⁺ DOTA‐tetraamide complexes with four appended primary amine groups are measured as a function of pH. The CEST signals in the Eu³⁺ complexes show a strong CEST signal after the pH was reduced from 8 to 5. The opposite trend was observed for the Dy³⁺ complexes where the r_2ex of bulk water protons increased dramatically from ca. 1.5 mm ⁻¹ s⁻¹ to 13 mm ⁻¹ s⁻¹ between pH 5 and 9 while r₁ remained unchanged. A fit of the CEST data (Eu³⁺ complexes) to Bloch theory and the T_2ex data (Dy³⁺ complexes) to Swift–Connick theory provided the proton‐exchange rates as a function of pH. These data showed that the four amine groups contribute significantly to proton‐catalyzed exchange of the Ln³⁺‐bound water protons even though their pK _a’s are much higher than the observed CEST or T_2ex effects. This demonstrated the utility of using appended acidic/basic groups to catalyze prototropic exchange for imaging tissue pH by MRI.