Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

A flexible protein-peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexibility of protein side chains was as important as ligand flexibility for successful protein-peptide docking. On the basis of mean field theory, a transferable potential was designed to evaluate distance-dependent protein-ligand interactions and atomic solvation energies. The potential parameters were developed using a self-consistent process based on only 10 known complex structures. The effectiveness of each intermediate potential was judged on the basis of a Z score, approximating the gap between the energy of the native complex and the average energy of a decoy set. The Z score was determined using experimentally determined native structures and decoys generated by docking with the intermediate potentials. Using 6600 generated decoys and the Z score optimization criterion proposed in this work, the developed potential yielded an acceptable correlation of R(2) = 0.77, with binding free energies determined for known MHC I complexes (Class I Major Histocompatibility protein HLA-A(*)0201) which were not present in the training set. Test docking on 25 complexes further revealed a significant correlation between energy and dRMS, important for identifying native-like conformations. The near-native structures always belonged to one of the conformational classes with lower predicted binding energy. The lowest energy docked conformations are generally associated with near-native conformations, less than 3.0 Angstrom dRMS (and in many cases less than 1.0 Angstrom) from the experimentally determined structures.     

Electronic structures and spectral and acid-base properties of pyrrol-, thiophen-, and furananthrones

The IR spectra, electronic absorption and luminescence spectra, solvatochromism, and basicities of compounds of the 6H-dibenz[cd,g]indol-6-one, 6H-anthra[9,1-bc] thiophen-6-one, and 6H-anthra[9,1-bc]furan-6-one groups were studied. The interrelationship between the indicated properties and such structural factors as the 1,10-anthraquinoid structure, the presence of a -surplus heteroring, and the presence of substituents was examined.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 486–493, April, 1985.     

Narrow band quantitative and multivariate electroencephalogram analysis of peri-adolescent period

ABSTRACT: BACKGROUND: The peri-adolescent period is a crucial developmental moment of transition from childhood to emergent adulthood. The present report analyses the differences in Power Spectrum (PS) of the Electroencephalogram (EEG) between late childhood (24 children between 8 and 13 years old) and young adulthood (24 young adults between 18 and 23 years old). RESULTS: The narrow band analysis of the Electroencephalogram was computed in the frequency range of 0--20 Hz. The analysis of mean and variance suggested that six frequency ranges presented a different rate of maturation at these ages, namely: low delta, delta-theta, low alpha, high alpha, low beta and high beta. For most of these bands the maturation seems to occur later in anterior sites than posterior sites. Correlational analysis showed a lower pattern of correlation between different frequencies in children than in young adults, suggesting a certain asynchrony in the maturation of different rhythms. The topographical analysis revealed similar topographies of the different rhythms in children and young adults. Principal Component Analysis (PCA) demonstrated the same internal structure for the Electroencephalogram of both age groups. Principal Component Analysis allowed to separate four subcomponents in the alpha range. All these subcomponents peaked at a lower frequency in children than in young adults. CONCLUSIONS: The present approaches complement and solve some of the incertitudes when the classical brain broad rhythm analysis is applied. Children have a higher absolute power than young adults for frequency ranges between 0-20 Hz, the correlation of Power Spectrum (PS) with age and the variance age comparison showed that there are six ranges of frequencies that can distinguish the level of EEG maturation in children and adults. The establishment of maturational order of different frequencies and its possible maturational interdependence would require a complete series including all the different ages.     

Dissociations of Complexes Between Monovalent Metal Ions and Aromatic Amino Acid or Histidine

The fragmentations of [AA + M]⁺ complexes, where AA = Phe, Tyr, Trp, or His, and M is a monovalent metal (Li, Na, or Ag), have been exhaustively studied through collision-induced dissociation (CID) and through deuterium labeling. Dissociations of the Li- and Ag-containing complexes gave a large number of fragment ions; by contrast, the sodium/amino acid complexes have lower binding energies, and dissociation resulted in much simpler spectra, with loss of the entire ligand dominating. Unambiguous assignments of these fragment ions were made and formation mechanisms are proposed. Of particular interest are fragmentations in which the charge was retained on the organic fragment and the metal was lost, either as a metal hydride (AgH) or hydroxide (LiOH) or as the silver atom (Ag^?).

Synthesis of 3-substituted 2-hydroxybenz[f]indolequinones and benz[f]isatinquinone - A new π-acceptor system

Starting from 2,3-dichloro-1,4-naphthaquinone a series of 2-hydroxy-1-methylbenz[f]indolequinones bearing benzyl-, amino- and hydroxy substituents in position 3 , and benz[f]isatinquinone have been synthesised and their reactions have been studied.     

Cyclization of 4,5‐Diamino Pyrazole Derivatives and Their Antibacterial Activities

A convenient synthesis of intermediate 4,5‐diamino‐3‐aryl‐1‐phenylpyrazoles 4a – 4c was reported. The different cyclization reactions were carried out with chalcone, 2‐mercaptoacetic acid and p‐anisialdehyde, ethyl chloroformate, glyoxal and thiourea to afford different N and S containing heterocycles. The reaction conditions were compared by conventional heating and microwave irradiation. The structures of the cyclization products were determined by analytical and spectroscopic data. All the synthesized compounds were screened for antibacterial activities in vitro.     

Synthesis of Polyfunctionally Substituted Fused Pyrimidine Derivatives as Antimicrobial Agents

A variety of pyrimidine derivatives 2—4 and annulated pyrimidine derivatives 5—17 have been synthesized via a sequence of heterocyclization reaction of readily available 6-naphthyl-4-oxo-2-thioxo-1,2,3,4-tetrahydroprimi-     

Synthesis and characterization of triphenylmethylphosphonium transition metal salts

Triphenylmethylphosphonium salts, [PPh3Me]aMXn (M=Cu2+, Co2+, Mn2+, Ni2+ Fe3+ Pb2+ and Hg2+; X=Cl or I; a=1 or 2 and n=3 or 4) prepared by reacting PPh3MeX with the metal dihalide in EtOH sol-utions, have been characterized by electronic, Raman, far i.r. and Mo¨ssbaur spectra and by their magnetic properties as well as by elemental analyses. The copper complexes [PPh3Me]2CuCl4 and [PPh3Me]2Cu3Cl8 were characterized by X-ray crystallography and the structures are described. Powder diffraction patterns have shown that the cobalt and manganese tetrachloride complexes are isomorphous. Investigation by d.s.c. measurements showed that the complexes exhibit structural phase transitions.