Energetics and role of the hydrophobic interaction during photoreaction of the BLUF domain of AppA

A recently developed method for time-resolved thermodynamic measurements was used to study the photochemical reaction(s) of the BLUF domain of AppA (AppA-BLUF), which has a dimeric form in the ground state, in terms of the energetics and heat capacity changes (DeltaC(p)) in different time domains. The enthalpy change (DeltaH) of the first intermediate that forms within 1 ns after photoexcitation was 38 (+/-8) kJ mol(-1) at 298 K. The heat capacity change (DeltaC(p)) upon formation of this intermediate was positive [1.4 (+/-0.3) kJ mol(-1) K(-1)]. This positive DeltaC(p) suggests that the hydrophobic surface area of AppA-BLUF exposed to the bulk solvent increased. After this initial transition, a dimerization reaction with another ground-state dimer (i.e., tetramer formation) takes place. Upon this reaction, the energy was stabilized to 26 (+/-6) kJ mol(-1) at 298 K. Interestingly, the dimer formation was accompanied by a larger but negative DeltaC(p) [-6.0 (+/-1) kJ mol(-1) K(-1)]. This negative DeltaC(p) might indicate buried hydrophobic residues at the interface of the dimer and/or the existence of trapped water at the interface. We suggest that hydrophobic interactions are the main driving force for the formation of the dimer upon photoactivation of AppA-BLUF.     

Deciphering the origins of observed heat capacity changes for aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA a-sites: a calorimetric, computational, and osmotic stress study

Isothermal titration calorimetry (ITC), computational, and osmotic stress techniques have been used to characterize the changes in heat capacity, solvent-accessible surface, and hydration that accompany the binding of the aminoglycoside paromomycin to both prokaryotic and eukaryotic rRNA A-site model oligonucleotides. Regarded as a whole, the results of these studies suggest that the intrinsic heat capacity change (DeltaC(p)) for the binding of paromomycin to each rRNA A-site is near zero, with the negative DeltaC(p) observed for the binding of the drug to the prokaryotic rRNA A-site being dictated by the coupled destacking of the adenine residues at positions 1492 and 1493. In this connection, DeltaC(p) provides a useful calorimetric signature for assessing the relative impacts of novel and existing A-site targeting ligands on rRNA conformation, which, in turn, should provide a useful analytical tool for facilitating the drug design process, since aminoglycoside-induced destacking of A1492 and A1493 is thought to be a determining factor in the mistranslational and antimicrobial activities of the drugs.     

LINC02532 Contributes to Radiosensitivity in Clear Cell Renal Cell Carcinoma through the miR-654-5p/YY1 Axis

Background: Studies have shown that long non-coding RNAs (lncRNAs) play essential roles in tumor progression and can affect the response to radiotherapy, including in clear cell renal cell carcinoma (ccRCC). LINC02532 has been found to be upregulated in ccRCC. However, not much is known about this lncRNA. Hence, this study aimed to investigate the role of LINC02532 in ccRCC, especially in terms of radioresistance. Methods: Quantitative real-time PCR was used to detect the expression of LINC02532, miR-654-5p, and YY1 in ccRCC cells. Protein levels of YY1, cleaved PARP, and cleaved-Caspase-3 were detected by Western blotting. Cell survival fractions, viability, and apoptosis were determined by clonogenic survival assays, CCK-8 assays, and flow cytometry, respectively. The interplay among LINC02532, miR-654-5p, and YY1 was detected by chromatin immunoprecipitation and dual-luciferase reporter assays. In addition, in vivo xenograft models were established to investigate the effect of LINC02532 on ccRCC radioresistance in 10 nude mice. Results: LINC02532 was highly expressed in ccRCC cells and was upregulated in the cells after irradiation. Moreover, LINC02532 knockdown enhanced cell radiosensitivity both in vitro and in vivo. Furthermore, YY1 activated LINC02532 in ccRCC cells, and LINC02532 acted as a competing endogenous RNA that sponged miR-654-5p to regulate YY1 expression. Rescue experiments indicated that miR-654-5p overexpression or YY1 inhibition recovered ccRCC cell functions that had been previously impaired by LINC02532 overexpression. Conclusions: Our results revealed a positive feedback loop of LINC02532/miR-654-5p/YY1 in regulating the radiosensitivity of ccRCC, suggesting that LINC02532 might be a potential target for ccRCC radiotherapy. This study could serve as a foundation for further research on the role of LINC02532 in ccRCC and other cancers.     

Thermodynamic studies on the interaction of antibodies with beta-amyloid peptide

Antibodies against beta-amyloid peptides (Abetas) are considered an important therapeutic opportunity in Alzheimer's disease. Despite the vast interest in Abeta no thermodynamic data on the interaction of antibodies with Abeta are available as yet. In the present study we use isothermal titration calorimetry (ITC) and surface plasmon resonance to provide a quantitative thermodynamic analysis of the interaction between soluble monomeric Abeta(1-40) and mouse monoclonal antibodies (mAb). Using four different antibodies directed against the N-terminal, middle, and C-terminal Abeta epitopes, we measured the thermodynamic parameters for the binding to Abeta. Each antibody species was found to have two independent and equal binding sites for Abeta with binding constants in the range of 10(7) to 10(8) M(-1). The binding reaction was essentially enthalpy driven with a reaction enthalpy of DeltaH(0)(Abeta) approximately -19 to -8 kcal/mol, indicating the formation of tight complexes. The loss in conformational freedom was supported by negative values for the reaction entropy DeltaS(0)(Abeta). We also measured the heat capacity change of the 1mAb:2Abeta reaction. DeltaC(0)(p, abeta) was large and negative but could not be explained exclusively by the hydrophobic effect. The free energy of binding was found to be linearly correlated with the size of the epitope.     

Microcalorimetric study on the influence of temperature on bacterial coaggregation

Binding isotherms and heats of interaction have been determined at 15, 25, and 40 degrees C for a coaggregating and a non-coaggregating oral bacterial pair. Heats of interaction were measured upon three consecutive injections of streptococci into an actinomyces suspension using isothermal titration calorimetry. After each injection, the number of streptococci injected remaining free in suspension was quantified microscopically and the degree of binding between the two bacterial strains was established. The coaggregating pair shows positive cooperative binding. The highest cooperativity, at 25 degrees C, correlates with a strong, macroscopically visible coaggregation. The non-coaggregating pair shows low cooperativity and lacks macroscopically visible coaggregation. Interactions between the coaggregating partners seem to be mainly due to specific, enthalpically saturable and favorable binding sites. Even though the enthalpic part of the interaction is saturated, cooperativity increases with consecutive injections, implying that the coaggregation phenomenon is driven by entropy gain. The change in heat capacity (DeltaC(p)) is positive for the non-coaggregating pair from 15-40 degrees C as well as for the coaggregating pair beyond 25 degrees C. At lower temperatures the coaggregating pair causes a negative DeltaC(p). The decrease in heat capacity together with an increase in entropy is considered to be indicative of hydrophobic interactions playing an important role in the formation of large coaggregates as observed for the coaggregating pair at 25 degrees C.     

Binding affinities for models of biologically available potential Cu(II) ligands relevant to Alzheimer's disease: an ab initio study

A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.     

温度对丙烯腈-丙烯酸甲酯水相沉淀共聚合竞聚率的影响

应用气相色谱法研究了温度对丙烯腈-丙烯酸甲酯水相沉淀共聚合竞聚率的影响,测得30℃时r_1=0.96,r_2=1.18;40℃时r_1=0.83,r_2=1.17;50℃时r_1=0.70,r_2=1.17;60℃时r_1=0.68,r_2=1.10,竞聚串与反应温度的关系为:1nr_1=-4.043+1207/T,1nr_2=-0.01360+51.68/T。发现共聚物沉淀粒子的表面吸附作用对该共聚体系竞聚率的温度依赖性有很大影响。     

The relevance of carbohydrate hydrogen-bonding cooperativity effects: a cooperative 1,2-trans-diaxial diol and amido alcohol hydrogen-bonding array as an efficient carbohydrate-phosphate binding motif in nonpolar media

Carbohydrates with suitably positioned intramolecularly hydrogen-bonded hydroxyl and amide groups have the potential to act as efficient bidentate phosphate binders by taking advantage of sigma- and/or ,sigma,pi-H-bonding cooperativity in nonpolar solvents. Donor-donor 1,2-trans-diaxial amido alcohol (1) and diol (3), in which one of the donor centres is cooperative, are very efficient carbohydrate-phosphate binding motifs. We have proven and quantified the key role of hydrogen-bonding centres indirectly involved in complexation, which serve to generate an intramolecular H-bond (six-membered cis H-bond) in 1 and 3. This motif enhances the donor nature of the H-bonding centres that are directly involved in complexation. A comparison of the thermodynamic parameters of the complexes formed between phosphate and a cooperative (1-Phos) or anti-cooperative (2-Phos) bidentate H-bonded motif of a carbohydrate has allowed us to quantify the energetic advantage of H-bonding cooperativity in CDCl3 and CDCl3/CCl4 (1:1.3) (Delta Delta G degrees=-2.2 and -2.0 kcal mol(-1), respectively). The solvent dependences of the entropy and enthalpy contributions to binding provide a valuable example of the delicate balance between entropy and enthalpy that can arise for a single process, providing effective cooperative binding in terms of Delta G degrees.     

Selective binding of monovalent cations to the stacking G-quartet structure formed by guanosine 5'-monophosphate: a solid-state NMR study

We report a solid-state multinuclear ((23)Na, (15)N, (13)C, and (31)P) NMR study on the relative affinity of monovalent cations for a stacking G-quartet structure formed by guanosine 5'-monophosphate (5'-GMP) self-association at pH 8. Two major types of cations are bound to the 5'-GMP structure: one at the surface and the other within the channel cavity between two G-quartets. The channel cation is coordinated to eight carbonyl oxygen atoms from the guanine bases, whereas the surface cation is close to the phosphate group and likely to be only partially hydrated. On the basis of solid-state (23)Na NMR results from a series of ion titration experiments, we have obtained quantitative thermodynamic parameters concerning the relative cation binding affinity for each of the two major binding sites. For the channel cavity site, the values of the free energy difference (Delta G degrees at 25 degrees C) for ion competition between M(+) and Na(+) ions are K(+) (-1.9 kcal mol(-1)), NH(4)(+) (-1.8 kcal mol(-1)), Rb(+) (-0.3 kcal mol(-1)), and Cs(+) (1.8 kcal mol(-1)). For the surface site, the values Delta G degrees are K(+) (2.5 kcal mol(-1)), NH(4)(+) (-1.3 kcal mol(-1)), Rb(+) (1.1 kcal mol(-1)), and Cs(+) (0.9 kcal mol(-1)). Solid-state NMR data suggest that the affinity of monovalent cations for the 5'-GMP structure follows the order NH(4)(+) > Na(+) > Cs(+) > Rb(+) > K(+) at the surface site and K(+) > NH(4)(+) > Rb(+) > Na(+) > Cs(+) > Li(+) at the channel cavity site. We have found that the cation-induced stability of a 5'-GMP structure is determined only by the affinity of monovalent cations for the channel site and that the binding of monovalent cations to phosphate groups plays no role in 5'-GMP self-ordered structure. We have demonstrated that solid-state (23)Na and (15)N NMR can be used simultaneously to provide mutually complementary information about competitive binding between Na(+) and NH(4)(+) ions.     

Binding cooperativity of two different Lewis acid groups at the edge of ferrocene

The binding properties of heteronuclear bidentate Lewis acids, in which an organoboron and an organotin moiety are attached adjacent to each other at one of the Cp rings of ferrocene, have been studied. Treatment of [1,2-fc(SnMe2Cl)(BClMe)] (1-Cl) (fc = ferrocenediyl) with one equivalent of pyridine or 4-dimethylaminopyridine (DMAP) resulted in diastereoselective complexation of boron. Adducts 2 and 3 have been studied by multinuclear NMR, and the stereoselectivity of complexation was further confirmed by single crystal X-ray diffraction of 2. The importance of cooperative effects that involve an intramolecular B-ClSn interaction on the diastereoselectivity is evident from comparison with binding studies on the phenyl-substituted analogue [1,2-fc(SnMe2Cl)(BPhMe)] (1-Ph). Complexation of 1-Ph led to diastereomeric mixtures of adducts 4 and 5, respectively, which were identified by multinuclear NMR including NOESY experiments. The solid-state structure of one of the diastereomers of 5 was confirmed by X-ray crystallography. Facile isomerization was found in solution and the barrier of activation was determined by VT NMR studies (4: Delta(#)(298) = 54.9+/-0.4 kJ mol(-1); 5: Delta(#)(298) = 70.3+/-0.1 kJ mol(-1)). Competitive binding of pyridine to 1-Cl and [FcB(Cl)Me] (Fc = ferrocenyl) showed that cooperative effects between tin and boron lead to significant Lewis acidity enhancement. Binding of a second nucleophile in the presence of excess of base occurred also at boron. The novel zwitterionic complexes [1,2-fc(BMe(py)2)(SnMe2Cl2)] (6) and [1,2-fc(BMe(dmap)(2))(SnMe(2)Cl2)] (7) formed, which consist of boronium cation and stannate anion moieties. The structure of 7 in the solid-state was confirmed by X-ray crystallography. Multinuclear NMR data and competition experiments indicate weak binding of chloride to tin in 7 and partial dissociation in solution.     

Correlation between thermodynamic and kinetic fragilities in nonpolymeric glass-forming liquids

A phenomenological relationship between reduced excess heat capacity of supercooled liquid DeltaC(p)(exc)(T(g))DeltaS(m) at the glass transition temperature T(g), fragility index m, and reduced glass transition temperature T(rg)=T(g)T(m), where T(m) is the melting (liquidus) temperature, was derived for fragile nonpolymeric glass-forming liquids under the assumptions that the fragile behavior of these liquids is described by the Vogel-Fulcher-Tammann (VFT) equation; the excess heat capacity of liquid is inversely proportional to the absolute temperature and the VFT temperature T(0) is equal to the Kauzmann temperature T(K). It was found that DeltaC(p)(exc)(T(g))DeltaS(m) is a composite function of m and T(rg), which indicates that the empirical correlation DeltaC(p)(exc)(T(g))DeltaS(m)=0.025m recently identified by Wang et al. [J. Chem Phys. 125, 074505 (2006)] is probably valid only for liquids which have nearly the same values of T(rg).     

Theoretical determination of highly excited states of K2 correlated adiabatically above K4p + K4p

The electronic structure of the K(2) molecule is revisited to describe the 36 highly excited states dissociating into the three limits K(4s) + K(4f), K(4s) + K(6p), and K(4s) + K(5d), which have not yet been investigated theoretically. Potential energy curves and spectroscopic constants are (re)displayed for the 98(1,3)Lambda(g,u) ((+,-)) molecular states correlated adiabatically to the limits up to K(4s) + K(5d). For the 10 states dissociating adiabatically into K(4p) + K(4p) and limits above for which experimental data are available, averaged errors of present results are found to be Delta R(e) = 0.07a(0), Delta T(e) = 50 cm(-1), Delta omega(e) = 0.8 cm(-1) and Delta D(e) = 60 cm(-1). Full energy data are available at the following address http://lasim.univ-lyon1.fr/allouche/k2.html     

Low-lying electronic states of FeNC and FeCN: a theoretical journey into isomerization and quartet/sextet competition

With several levels of multireference and restricted open-shell single-reference electronic structure theory, optimum structures, relative energetics, and spectroscopic properties of the low-lying (6)Delta, (6)Pi, (4)Delta, (4)Pi, and (4)Sigma(-) states of linear FeNC and FeCN have been investigated using five contracted Gaussian basis sets ranging from Fe[10s8p3d], C/N[4s2p1d] to Fe[6s8p6d3f2g1h], C/N[6s5p4d3f2g]. Based on multireference configuration interaction (MRCISD+Q) results with a correlation-consistent polarized valence quadruple-zeta (cc-pVQZ) basis set, appended with core correlation and relativistic corrections, we propose the relative energies: T(e)(FeNC), (6)Delta(0)<(6)Pi (2300 cm(-1))<(4)Delta (2700 cm(-1))<(4)Pi (4200 cm(-1))<(4)Sigma(-); and T(e)(FeCN), (6)Delta(0)<(6)Pi (1800 cm(-1))<(4)Delta (2500 cm(-1))<(4)Pi (2900 cm(-1))<(4)Sigma(-). The (4)Delta and (4)Pi states have massive multireference character, arising mostly from 11sigma-->12sigma promotions, whereas the sextet states are dominated by single electronic configurations. The single-reference CCSDT-3 (coupled cluster singles and doubles with iterative partial triples) method appears to significantly overshoot the stabilization of the quartet states provided by both static and dynamical correlation. The (4,6)Delta and (4,6)Pi states of both isomers are rather ionic, and all have dipole moments near 5 D. On the ground (6)Delta surface, FeNC is predicted to lie 0.6 kcal mol(-1) below FeCN, and the classical barrier for isocyanide/cyanide isomerization is about 6.5 kcal mol(-1). Our data support the recent spectroscopic characterization by Lei and Dagdigian [J. Chem. Phys. 114, 2137 (2000)] of linear (6)Delta FeNC as the first experimentally observed transition-metal monoisocyanide. Their assignments for the ground term symbol, isotopomeric rotational constants, and the Fe-N omega(3) stretching frequency are confirmed; however, we find rather different structural parameters for (6)Delta FeNC:r(e)(Fe-N)=1.940 A and r(N-C)=1.182 A at the cc-pVQZ MRCISD+Q level. Our results also reveal that the observed band of FeNC originating at 27 236 cm(-1) should have an analog in FeCN near 23 800 cm(-1) of almost equal intensity. Therefore, both thermodynamic stability and absorption intensity factors favor the eventual observation of FeCN via a (6)Pi<--(6)Delta transition in the near-UV.     

Dihydrogen trioxide clusters, (HOOOH)n (n = 2-4), and the hydrogen-bonded complexes of HOOOH with acetone and dimethyl ether: implications for the decomposition of HOOOH

Hydrogen-bonded gas-phase molecular clusters of dihydrogen trioxide (HOOOH) have been investigated using DFT (B3LYP/6-311++G(3df,3pd)) and MP2/6-311++G(3df,3pd) methods. The binding energies, vibrational frequencies, and dipole moments for the various dimer, trimer, and tetramer structures, in which HOOOH acts as a proton donor as well as an acceptor, are reported. The stronger binding interaction in the HOOOH dimer, as compared to that in the analogous cyclic structure of the HOOH dimer, indicates that dihydrogen trioxide is a stronger acid than hydrogen peroxide. A new decomposition pathway for HOOOH was explored. Decomposition occurs via an eight-membered ring transition state for the intermolecular (slightly asynchronous) transfer of two protons between the HOOOH molecules, which form a cyclic dimer, to produce water and singlet oxygen (Delta (1)O 2). This autocatalytic decomposition appears to explain a relatively fast decomposition (Delta H a(298K) = 19.9 kcal/mol, B3LYP/6-311+G(d,p)) of HOOOH in nonpolar (inert) solvents, which might even compete with the water-assisted decomposition of this simplest of polyoxides (Delta H a(298K) = 18.8 kcal/mol for (H 2O) 2-assisted decomposition) in more polar solvents. The formation of relatively strongly hydrogen-bonded complexes between HOOOH and organic oxygen bases, HOOOH-B (B = acetone and dimethyl ether), strongly retards the decomposition in these bases as solvents, most likely by preventing such a proton transfer.     

激酶ABL与肉豆蔻酰位点小分子作用机理的分子动力学模拟及自由能计算

采用分子动力学方法研究激酶ABL 与ATP 位点小分子imatinib、P16 及变构位点小分子STJ、MS7、MS9、3YY、MYR等的结合, 并用GBSA (generalized Born surface area)方法将结合自由能分解到各残基. 自由能计算结果表明, 小分子STJ、MS7、MS9 有利于imatinib 与ABL 结合; 小分子STJ、MS7、MS9 与激酶ABL的结合自由能接近, 绝对值均大于ABL 与3YY、MYR 的结合自由能. 能量分解表明, ABL 残基ILE502、VAL506、LEU510与STJ和MYR的相互作用是αI 螺旋处于弯曲状态的重要原因. 模拟过程中ABL肉豆蔻酰口袋残基均方根偏差(RMSD)变化值表明, STJ等小分子抑制剂与ABL结合后降低了肉豆蔻酰口袋残基的柔性.