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PubMed1994

Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures.

A three-step method is presented to predict secondary structures of proteins, by utilizing aligned sequences of homologous proteins. Mean propensities and amino acid substitution patterns at a given site in the aligned sequences are first evaluated for four conformational states (i.e. alpha-helix, beta-strand, buried coil and exposed coil). Capping rules are applied in order to define boundaries of the secondary-structure segments more precisely. In the second step beta-strand is predicted by searching regions predicted as coil for the two patterns characteristic of alternating and fully buried beta-strands. The complete sequences of the solvent-accessibility classes predicted by substitution tables and propensities are also searched using Fourier transform methods for alpha-helical periodicity. After applying capping rules, the alpha-helices and beta-strands predicted in the second step replace, where appropriate, the conformational states predicted in the first step. Finally, in the third step, if one of the four conformational states is assigned to the residues at an equivalent site of aligned sequences in more than a given fraction of the proteins, such a state is reassigned to all the residues at that site. The method is applied to 13 protein families, which contain four folding types, alpha, beta, alpha/beta and alpha + beta. The accuracy of the prediction ranges from 60 to 79% (mean percentage over the 13 families is 69%). For comparison the Garnier-Osguthorpe-Robson (GOR) method is also applied to them. Although the mean prediction accuracy for the GOR method, 58%, can be improved to 63% by applying the second and third steps in this method, there remain four families with less than 55% accuracy. The mean accuracy is relatively higher and poor predictions are reduced in this method.

Amino Acid Sequence↗
PubMed2003

Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism.

The DNA base adenine and four monomethylated adenines were studied in solution at room temperature by femtosecond pump-probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S(1) state) populated by a UV pump pulse. In H(2)O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 +/- 0.03 ps and 8.8 +/- 1.2 ps. In contrast, signals from monomethylated adenines decay monoexponentially. The S(1) lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (tau = 4.23 +/- 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H(2)O at room temperature to be 22 +/- 4% (estimated standard deviation). To understand how the environment affects nonradiative decay, we performed the first solvent-dependent study of nucleobase dynamics on the ultrafast time scale. In acetonitrile, both lowest energy tautomers of adenine are present in roughly similar proportions as in water. The lifetimes of the 9-substituted adenines depend somewhat more sensitively on the solvent than those of the 7-substituted adenines. Transient signals for adenine in H(2)O and D(2)O are identical. These solvent effects strongly suggest that excited-state tautomerization is not an important nonradiative decay pathway. Instead, the data are most consistent with electronic energy relaxation due to state crossings between the optically prepared (1)pipi* state and one or more (1)npi* states and the electronic ground state. The pattern of lifetimes measured for the monomethylated adenines suggests a special role for the (1)npi* state associated with the N7 electron lone pair.

Adenine↗
PubMed2001

Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.

To investigate the structural and thermodynamic basis of the binding of solvent at internal sites within proteins a number of mutations were constructed in T4 lysozyme. Some of these were designed to introduce new solvent-binding sites. Others were intended to displace solvent from preexisting sites. In one case Val-149 was replaced with alanine, serine, cysteine, threonine, isoleucine, and glycine. Crystallographic analysis shows that, with the exception of isoleucine, each of these substitutions results in the binding of solvent at a polar site that is sterically blocked in the wild-type enzyme. Mutations designed to perturb or displace a solvent molecule present in the native enzyme included the replacement of Thr-152 with alanine, serine, cysteine, valine, and isoleucine. Although the solvent molecule was moved in some cases by up to 1.7 A, in no case was it completely removed from the folded protein. The results suggest that hydrogen bonds from the protein to bound solvent are energy neutral. The binding of solvent to internal sites within proteins also appears to be energy neutral except insofar as the bound solvent may prevent a loss of energy due to potential hydrogen bonding groups that would otherwise be unsatisfied. The introduction of a solvent-binding site appears to require not only a cavity to accommodate the water molecule but also the presence of polar groups to help satisfy its hydrogen-bonding potential. It may be easier to design a site to accommodate two or more water molecules rather than one as the solvent molecules can then hydrogen-bond to each other. For similar reasons it is often difficult to design a point mutation that will displace a single solvent molecule from the core of a protein.

Amino Acid Substitution↗
PubMed2004

Aqueous-phase, palladium-catalyzed cross-coupling of aryl bromides under mild conditions, using water-soluble, sterically demanding alkylphosphines.

Sterically demanding, water-soluble alkylphosphines have been used in combination with various palladium salts in Suzuki, Sonogashira, and Heck couplings of aryl bromides under mild conditions in aqueous solvents. The tert-butyl-substituted ligands 2-(di-tert-butylphosphino)ethyltrimethylammonium chloride (t-Bu-Amphos) and 4-(di-tert-butylphosphino)-N,N-dimethylpiperidinium chloride (t-Bu-Pip-phos) in combination with palladium(II) salts were found to give catalysts that were significantly more active than catalysts derived from tri(3-sulfonatophenyl)phosphine trisodium (TPPTS). Suzuki couplings of unactivated aryl bromides occurred efficiently at room temperature in water/acetonitrile and water/toluene biphasic mixtures or in neat water. Notably, Suzuki couplings of hydrophilic aryl bromides gave high yields without using organic solvents for the reaction or purification. This methodology has been applied to a highly efficient synthesis of diflunisal. The catalyst derived from t-Bu-Amphos was recycled three times in Suzuki couplings in water/toluene before catalyst activity began to significantly drop. The average yield of four cycles was >80% per cycle. Heck and Sonogashira couplings were carried out under mild conditions (50 and 80 degrees C, respectively) with unactivated aryl bromides to give coupled products in high yield.

Journal Article↗
PubMed2005

Study of the effect of the peptide loading and solvent system in SPPS by HRMAS-NMR.

The SPPS methodology has continuously been investigated as a valuable model to monitor the solvation properties of polymeric materials. In this connection, the present work applied HRMAS-NMR spectroscopy to examine the dynamics of an aggregating peptide sequence attached to a resin core with varying peptide loading (up to 80%) and solvent system. Low and high substituted BHAR were used for assembling the VQAAIDYING sequence and some of its minor fragments. The HRMAS-NMR results were in agreement with the swelling of each resin, i.e. there was an improved resolution of resonance peaks in the better solvated conditions. Moreover, the peptide loading and the attached peptide sequence also affected the spectra. Strong peptide chain aggregation was observed mainly in highly peptide loaded resins when solvated in CDCl3. Conversely, due to the better swelling of these highly loaded resins in DMSO, improved NMR spectra were acquired in this polar aprotic solvent, thus enabling the detection of relevant sequence-dependent conformational alterations. The more prominent aggregation was displayed by the VQAAIDYING segment and not by any of its intermediary fragments and these findings were also corroborated by EPR studies of these peptide-resins labelled properly with an amino acid-type spin probe.

Amino Acid Sequence↗
PubMed2004

Theoretical study of the vinyl allene oxide to cyclopent-2-en-1-one rearrangement: mechanism, torquoselectivity and solvent effects.

Density-functional calculations in the gas phase and solvent (PCM) at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level were performed to study a series of six reactions that involve the rearrangement of vinyl allene oxides to cyclopent-2-en-1-ones along two distinct mechanistic pathways, namely concerted and stepwise. Calculations predict that stepwise pathways are highly competitive processes that occur via biradical/zwitterionic intermediates. Torquoselectivity is predicted to result from the concerted pathway leading to a stereodefined 4,5-disubstituted cyclopent-2-en-1-ones that should have memory of the starting terminal double-bond geometry and oxide configuration. The stepwise pathway cannot show torquoselectivity as cyclization of the planar oxidopentadienyl zwitterion can follow enantiomorphous conrotations. The concerted/stepwise mechanistic preference depends mainly on the olefin geometry and is further modulated by epoxide substitution. The influence of the solvent (PCM model for dichloromethane or water) is moderate, although the greater (de)stabilization of the polarized oxidopentadienyl zwitterions along the stepwise mechanism does alter the kinetic preferences exhibited by the systems in vacuo. Results with system 1e suggest that, if vinyl allene oxide II having a double bond with Z-geometry, an intermediate in the biogenesis of epi-jasmonic acid IV, is processed along an in stepwise mechanism following ring opening, the enzyme allene oxide cyclase must enforce enantiofacial torquoselectivity.

Computational Biology↗
PubMed2002

Probing backbone hydrogen bonds in the hydrophobic core of GCN4.

Backbone amide hydrogen bonds play a central role in protein secondary and tertiary structure. Previous studies have shown that substitution of a backbone ester (-COO-) in place of a backbone amide (-CONH-) can selectively destabilize backbone hydrogen bonds in a protein while maintaining a similar conformation to the native backbone structure. The majority of these studies have focused on backbone substitutions that were accessible to solvent. The GCN4 coiled coil domain is an example of a stable alpha-helical dimer that possesses a well-packed hydrophobic core. Amino acids in the a and d positions of the GCN4 helix, which pack the hydrophobic core, were replaced with the corresponding alpha-hydroxy acids in the context of a chemoselectively ligated heterodimer. While the overall structure and oligomerization state of the heterodimer were maintained, the overall destabilization of the ester analogues was greater (average DeltaDeltaG of 3+ kcal mol(-1)) and more variable than previous studies. Since burial of the more hydrophobic ester should stabilize the backbone and reduce the DeltaDeltaG, the increased destabilization must come from another source. However, the observed destabilization is correlated with the protection factors for individual amide hydrogens from previous hydrogen exchange experiments. Therefore, our results suggest that backbone engineering through ester substitution is a useful approach for probing the relative strength of backbone hydrogen bonds.

Anilino Naphthalenesulfonates↗
PubMed2003

Acetylenic quinoxalinoporphyrazines as photosensitisers for photodynamic therapy.

A range of lipo- and hydrophilic derivatives of the new class of octaalkynyl tetra-[6,7]-quinoxalinoporphyrazines (TQuiPors), analogues of the naphthalocyanines, were prepared in two steps starting from functionalised hexa-1,5-diyne-3,4-diones. Divalent zinc and magnesium ions were introduced into the macrocyclic core. Whereas the triisopropylsilyl-, 3,5-di-tert-butylphenyl- and 4-triisopropylsilyloxyphenyl-terminated acetylenic TQuiPors are lipophilic and hence soluble in standard organic solvents, a polyethylene glycol-substituted derivative was found to dissolve in DMSO as well as in ethanol/water mixtures. The new chromophores are characterised by intense UV/Vis/NIR absorptions, most notably by bands at 770 nm with extinction coefficients exceeding 500 000 M(-1) cm(-1). With a view to possible photodynamic therapy applications, the potency of the chromophores to sensitise the formation of singlet oxygen was examined, both qualitatively using a 1,3-diphenylisobenzofuran assay, and quantitatively by the determination of the singlet oxygen quantum yields. It was found that all TQuiPors produce singlet oxygen when irradiated in the presence of air. In particular, the octaalkynyl Zn-TQuiPor generates singlet oxygen with a quantum yield of 56 %, thereby rivalling, and, in conjunction with its absorption profile, even exceeding the standards set by established PDT agents. The photostabilities of the TQuiPors were assessed and generally found to be satisfactory, but dependent on the solvent and the wavelength of the incident light.

Indoles↗
PubMed2005

Small-angle neutron scattering on a core-shell colloidal system: a contrast-variation study.

Small-angle neutron scattering (SANS) measurements are reported on a sterically stabilized, core-shell colloidal system using contrast variation. Aqueous dispersions of polystyrene particles bearing grafted poly(ethylene glycol) (PEG) have been studied over a large range of particle concentrations and two different solvent conditions for the PEG polymer. SANS data are analyzed quantitatively by modeling the particles as core-shell colloids. In a good solvent and under particle contrast conditions, an effective hard-sphere interaction captures excluded-volume interactions up to high concentrations. Contrast variation, through isotopic substitution of both the core and solvent, expedite a detailed study of the PEG layer, both in the dilute limit and as a function of the particle concentration. Upon diminishing the solvent quality, subtle changes in the PEG layer translate into attractions among particles of moderate magnitude.

Journal Article↗
PubMed2004

Negative ion-atmospheric pressure photoionization-mass spectrometry.

The ionization mechanism in the novel atmospheric pressure photoionization mass spectrometry (APPI-MS) in negative ion mode was studied thoroughly by the analysis of seven compounds in 17 solvent systems. The compounds possessed either gas-phase acidity or positive electron affinity, whereas the solvent systems had different polarities and gas-phase acidities and some of them positive electron affinities. The analytes that possessed gas-phase acidity formed deprotonated ions in proton transfer; in addition, fragments and solvent adducts were observed. The compounds of positive electron affinity formed negative molecular ions by electron capture or charge exchange and substitution products of form [M - X + O](-) by substitution reactions. The efficiency of deprotonation was decreased if the solvent used possessed higher gas-phase acidity than the analyte. Solvents of positive electron affinity captured thermal electrons and deteriorated the ionization of all the analytes. Also, the proportion of substitution products was affected by the solvent. Finally, the performances of negative ion APPI and negative ion APCI were compared. The sensitivity for the studied compounds was better in APPI, but the formation of substitution products was lower in APCI.

Journal Article↗
PubMed2000

Studies on the synthetic compatibility of aryloxime linkers in the solid-phase synthesis of 3-aminobenzisoxazoles.

Further exploration of the scope of our solid-phase method for the synthesis of 3-aminobenzisoxazoles (using the Kaiser oxime resin 1) is described. The effects of base, leaving group, and solvent on the nucleophilic aromatic substitution based resin-loading reaction are discussed. Representative aryloxime intermediates were subjected to a variety of acidic conditions commonly used in protecting group removal to establish the acid stability profile of this linker. Regioselectivity was evaluated with various di- and trifluorobenzonitriles, which gave single benzisoxazole products after loading and cyclorelease reactions. Substituent effects observed in the course of the acid stability and regioselectivity studies suggest that the nitrile plays a critical role in the oxime hydrolysis mechanism. Finally, to establish the compatibility of the aryloxime linker with a variety of useful on-resin synthetic transformations, functionalized substrates were loaded onto resin 1, and carbon-nitrogen, carbon-oxygen, and carbon-carbon bond-forming reactions were successfully executed.

Amides↗
PubMed1984

Butyryl-CoA dehydrogenase from Megasphaera elsdenii. Specificity of the catalytic reaction.

The absorption coefficient of butyryl-CoA dehydrogenase from Megasphaera elsdenii at 450 nm is determined as 14.4 mM-1 X cm-1 in the CoA-free form and 14.2 mM-1 X cm-1 in the CoA-liganded form (both yellow). The latter value is considerably higher than the earlier published estimate. Phenazine ethosulphate offers great advantages over phenazine methosulphate as a coupling dye in the catalytic assay despite giving lower Vmax. values (506 min-1 as compared with 1250 min-1 under the conditions used). The phenazine ethosulphate assay is used to establish a pH optimum of 8.05 for oxidation of 100 microM-butyryl-CoA. The rates of oxidation of a range of straight-chain, branched-chain and alicyclic acyl thioesters are used to provide the following information. Only straight-chain acyl groups containing 4-6 carbon atoms are easily accommodated by the postulated hydrophobic pocket of the enzyme. C-3-substituted acyl-CoA thioesters are not oxidized at a significant rate, suggesting that the C-3 pro-S-hydrogen atom of straight-chain substrates is partially exposed to the solvent. Acyl-CoA thioesters with substitutions at C-2 are oxidized, though at a lower rate than their straight-chain counterparts. This implies that the C-2 pro-S-hydrogen atom of straight-chain substrates is partially exposed to the solvent. Saturated alicyclic carboxylic acyl-CoA thioesters with 4-7 carbon atoms in the ring are oxidized, with maximal activity for the cyclohexane derivative. This implies that optimal oxidation requires a true trans orientation of the two departing hydrogen atoms. The strain imposed by bound unsaturated alicyclic acyl thioesters strikingly perturbs the flavin visible-absorption spectrum, with the exception of the cyclohex-2-ene derivative, which forms a complex with similar spectral properties to those of the crotonyl-CoA complex. In the thiol moiety of thioester substrates the amide bond of N-acetylcysteamine is essential for both binding and catalysis. The adenosine structure contributes substantially to strong binding, but is less important in determining the catalytic rate.

Acyl Coenzyme A↗
PubMed2006

Substitution and chemical environment effects on the absorption spectrum of indigo.

The UV/visible spectra of a series of indigo derivatives have been evaluated by using ab initio methods. The combination of the Polarizable continuum model for estimating bulk solvent effects with the TD-B3LYP6-311 + G(2d,p)B3LYP6-311G(d,p) level of approximation, leads to an accurate description of the wavelength of maximum absorption of indigoids compounds. Using this procedure, we have assessed the effects of both the surroundings (solvent and solid state) and the substitution pattern. For the latter, we obtained a mean absolute deviation of only 7 nm (0.02 eV) compared to experiment, for a set of 86 molecules/solvents.

Journal Article↗
PubMed1997

Trans- and Cis-Water Reactivities in d(6) Octahedral Ruthenium(II) Pentaaqua Complexes: Experimental and Density Functional Theory Studies(1)(,)(2).

The hexaaqua complex of ruthenium(II) represents an ideal starting material for the synthesis of isostructural compounds with a [Ru(H(2)O-ax)(H(2)O-eq)(4)L](2+) general formula. We have studied a series of complexes, where L = H(2)O, MeCN, Me(2)SO, H(2)C=CH(2), CO, and F(2)C=CH(2). We have evaluated the effect of L on the cyclic voltammetric response, on the rate and mechanism of exchange reaction of the water molecules, and on the structures calculated with the density functional theory (DFT). As expected, the formal redox potential, E degrees '(+2/+3), increases with the pi-accepting capabilities of the ligands. For L = N(2), the oxidation to Ru(III) is followed by a fast substitution of dinitrogen by a solvent molecule, revealing the poor stability of the Ru(III)-N(2) bond. The water exchange reactions have been followed by (17)O NMR spectroscopy. The variable-pressure and variable-temperature kinetic studies made on selected examples are all in accordance with a dissociative activation mode for exchange. The positive activation volumes obtained for the axial and equatorial water exchange reactions on [Ru(H(2)O)(5)(H(2)C=CH(2))](2+) (DeltaV(ax)() and DeltaV(eq)() = +6.5 +/- 0.5 and +6.1 +/- 0.2 cm(3) mol(-)(1)) are the strongest evidence of this conclusion. The increasing cis-effect series was established according to the lability of the equatorial water molecules and is as follows: F(2)C=CH(2) congruent with CO < Me(2)SO < N(2) < H(2)C=CH(2) < MeCN < H(2)O. The increase of the lability is accompanied by a decrease of the E degrees ' values, but no change was found in the calculated Ru-H(2)O(eq) bond lengths. The increasing trans-effect series, established from the lability of the axial water molecule, is the following: N(2) << MeCN < H(2)O < CO < Me(2)SO < H(2)C=CH(2) < F(2)C=CH(2). A variation of the Ru-H(2)O(ax) bond lengths is observed in the calculated structures. However, the best correlation is found between the lability and the calculated Ru-H(2)O(ax) bond energies. It appears, also, that a decrease of the electronic density along the Ru-O(ax) bond and the increase of the lability can be related to an increase of the pi-accepting capability of the ligand. For L = N(2), the calculations have shown that the Ru(II)-N(2) bond is weak. Consequently, the water exchange reaction proceeds through a different mechanism, where first the N(2) ligand is substituted by one water molecule to produce the hexaaqua complex of Ru(II). The water exchange takes place on this compound before re-formation of the [Ru(H(2)O)(5)N(2)](2+) complex.

Journal Article↗
PubMed1988

Sequence analysis of end-labeled DNA fragments by solvolysis in hot aqueous piperidine solutions.

One-lane DNA sequencing by solvolysis in hot aqueous piperidine solutions, originally described for 5'-32P-labeled DNA (B. Ambrose and R. Pless (1985) Biochemistry 24, 6194-6200), is extended to 3'-labeled fragments. A salt-free sample for electrophoresis can be obtained by using 1 M LiCl in the solvolysis mixture and removing this salt from the dried hydrolysate by washing with ethanol. Rate and distribution of DNA cleavage in hot aqueous piperidine, containing 0.3 M NaCl, are studied in dependence of temperature, solvent, amine concentration, and reaction time. An increase in temperature strongly accelerates overall DNA degradation, but leaves the distribution of cleavage essentially unchanged. When 50% aqueous ethanol is substituted for water as the reaction solvent, the overall cleavage is slower, and scission at G-sites is enhanced relative to cleavage at the other bases. A rise in the piperidine concentration strongly accelerates the reaction, except at very high amine concentration. Cleavage at A-, G-, and C-sites increases steadily with reaction time, while the T-cleavage observed takes place primarily at the very beginning of the solvolysis.

Autoradiography↗
PubMed2000

Further studies of the thermal and photochemical diels-alder reactions of N-methyl-1,2,4-triazoline-3,5-dione (MeTAD) with naphthalene and some substituted naphthalenes

MeTAD thermally reacted with naphthalene (2) and methylated naphthalenes to give equilibrium mixtures of starting materials and [4 + 2] cycloadducts. Methyl substitution on the naphthalene ring generally increased both the amount of cycloadduct formed and the rate of cycloaddition relative to 2. The isolated cycloadducts were all thermally labile and quantitatively reverted to the parent naphthalene in the presence of 2,3-dimethyl-2-butene as a trap for liberated MeTAD. The rates of the cycloreversion reactions were affected by substitution patterns but not appreciably by solvent. A mechanism for the cycloaddition reaction is presented that proposes the involvement of a charge-transfer complex. Photochemically, MeTAD demonstrated lower regioselectivity in its reactions with substituted naphthalenes relative to the corresponding thermal reactions.

Journal Article↗