Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination

The high sensitivity of modern NMR instrumentation, in combination with full deuteration, enabled the measurement of long-range NOEs between amide protons in a fully deuterated protein corresponding to distances up to 8A. These are beyond the limit normally observed in protonated samples. Such long-distance NOEs could be observed using long mixing times, which became possible due to reduced spin diffusion and T1 relaxation of the amide protons in the fully deuterated sample. This information was used in combination with secondary structure restraints derived from secondary chemical shifts for structure calculations. With these backbone amide proton NOEs only, a unique fold could be obtained with positional root mean square deviations from the average of 1.30 and 2.25 A for backbone and heavy atoms, respectively. Despite the low density of restraints, no mirror image problems were observed. Addition of sidechain NOE information increased the precision of the ensemble and in particular of the core packing. The structures obtained in this way were close to the published crystal structure. NOE completeness analysis revealed that the cumulative completeness is still more than 80% for an 8.0 A cut-off distance.     

Analysis of class I phosphoinositide 3-kinase autophosphorylation sites by mass spectrometry

This article describes the identification of the autophosphorylation sites of the G protein-sensitive class I phosphoinositide 3-kinase isoforms beta and gamma by mass spectrometry. Since discrimination and suppression effects prevented the immediate detection and sequencing of phosphopeptides in complex mixtures, a strategy was applied that involved (32)P-radiolabeling of the phosphoproteins, cleavage of the phosphoproteins with several proteases and/or cyanogen bromide, separation of the resulting peptide mixtures by micro-reversed-phase liquid chromatography, and mass spectrometric analysis of fractions containing phosphopeptides. As a result the primary autophosphorylation sites of phosphoinositide 3-kinase p110beta and p110gamma subunits could be unambiguously assigned to the C-terminal Ser 1070 and Ser 1101, respectively.     

Thioformaldehyde S-methylide and thioacetone S-methylide: an ab initio MO study of structure and cycloaddition reactivity

The mechanisms of cycloaddition of thioformaldehyde S-methylide and thioacetone S-methylide, as models for an alkyl-substituted ylide, to thioformaldehyde and thioacetone, as well as to ethene as a model for a C=C double bond have been studied by ab initio calculations. Restricted and unrestricted B3LYP/6-31G* calculations were performed for the geometries of ground states, transition structures, and intermediates. Although basis sets with more polarization functions were tested, the 6-31G* basis set was applied throughout. Single-point CASPT2 calculations are reported for analysis of the unsubstituted system. The stabilities of structures with high biradical character seem to be overestimated by DFT methods in comparison to CASPT2. The general trends of the results are independent of the level of theory. Thioformaldehyde adds to thioformaldehyde S-methylide without activation energy, and the activation energies for two-step biradical pathways to 1,3-dithiolane are low. C,S biradicals are more stable than C,C biradicals. The two-step cycloaddition is not competitive with the concerted cycloaddition. Methyl substitution in the 1,3-dipole and the dipolarophile does not change the mechanistic relationships. TSs for the concerted formation of the regioisomeric cycloadducts of thioacetone Smethylide and thioacetone were located. Concerted addition remains the preferred reaction. The reactivity of the C=S double bond is high relative to that of the C=C double bond.     

Ancillary ligand effect on single-site styrene polymerization: isospecificity of group 4 metal bis(phenolate) catalysts

Styrene is polymerized isospecifically by group 4 metal complexes that contain a C2-symmetrically coordinated 1,4-dithiabutane-linked bis(phenolato) ligand activated by methylaluminoxane.     

Studies on the conformation of α-arylcinnamic acids and their esters: Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate and methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate

The conformations of stereoisomers of -arylcinnamic acids and their esters are discussed based on crystal structures of the E and Z forms of 2,3-bis(3,4-dimethoxyphenyl)propenoic acid and its methyl ester. In the E forms of the cinnamic acid and the cinnamic acid ester, the plane of the -aryl substituent is approximately perpendicular to that of the rest of the molecule. In the Z forms the plane of the carboxyl or methoxycarbonyl group is approximately perpendicular to that of the ethylenic group, and both the aromatic group planes are significantly twisted out of the ethylenic group plane. Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁/n with a = 8.1697(5), b = 11.3882(9), c = 19.7766(9) Å, = 90.058(4)°, V = 1840.0(2) ų, and Z = 4), monoclinic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁/n with a = 11.183(2), b = 5.640(2), c = 29.737(7) Å, = 99.19(2)°, V = 1851.4(9) ų, and Z = 4), and orthorhombic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁2₁2₁ with a = 8.849(4), b = 24.288(9), c = 8.734(3) Å, V = 1877(1) ų, and Z = 4) are reported.     

Determination of Interatomic Potentials for the X0(+), A0(+), and B1 States of HgKr from Fluorescence and Excitation Spectra

We present an analysis of the A0(+)(6(3)P(1))-->X0(+)(6(1)S(0)) bound-bound and bound-free fluorescence spectrum, and of the A0(+)(6(3)P(1))<--X0(+)(6(1)S(0)) and B1(6(3)P(1))<--X0(+)(6(1)S(0)) bound-bound excitation spectrum of the HgKr van der Waals molecule. The A-->X fluorescence spectrum, which was observed for the first time, as well as the excitation spectra were recorded using a pulsed supersonic molecular beam crossed with a pulsed dye laser beam. An analysis of the A(v')<--X(v"), B(v')<--X(v"), and A(v'=8)-->X(v") bound-bound bands indicates that a Morse function combined with a long-range approximation represents the interatomic potential energy curve of the A, B, and X states below the dissociation limit. In the simulation of the A(v'=8)-->X bound-free spectrum the Morse, Lennard-Jones (n-6), and Maitland-Smith (n(0), n(1)) functions were tested, and the Maitland-Smith (11.39, 10.50) potential was found to be a good representation of the repulsive part of the X-state PE curve above the dissociation limit, over the internuclear separation range R=2.85-3.55 ?. The spectroscopic characteristics for the A, B, and X states obtained in this work are compared with other available experimental and theoretical results. Copyright 2001 Academic Press.     

Solving Nonconvex Planar Location Problems by Finite Dominating Sets

It is well-known that some of the classical location problems with polyhedral gauges can be solved in polynomial time by finding a finite dominating set, i.e. a finite set of candidates guaranteed to contain at least one optimal location.In this paper it is first established that this result holds for a much larger class of problems than currently considered in the literature. The model for which this result can be proven includes, for instance, location problems with attraction and repulsion, and location-allocation problems.Next, it is shown that the approximation of general gauges by polyhedral ones in the objective function of our general model can be analyzed with regard to the subsequent error in the optimal objective value. For the approximation problem two different approaches are described, the sandwich procedure and the greedy algorithm. Both of these approaches lead - for fixed - to polynomial approximation algorithms with accuracy for solving the general model considered in this paper.