Automated protein design and sequence optimisation: scoring functions and the search problem

Advances in molecular biology may mean that almost any protein sequence can be synthesised, but perhaps this has served to highlight the inadequacy of theoretical work. For a given protein fold, it is probably not possible to reliably predict an "ideal" sequence. We identify and survey several aspects of the problem. Firstly, it is not clear what is the best way to score a sequence-structure pair. Secondly, there is no consensus as to what the score function should represent (free energy or some abstract measure of sequence-structure compatibility). Finally, the number of possible sequences is astronomical and searching this space poses a daunting optimisation problem. These problems are discussed in the light of recent experimental successes.     

Properties and structures of porphyrexides

The molecular and crystal structures of porphyrexides, viz., 4-amino-2-imino-(1) and (Z)-2-amino-4-bromoimino-5,5-dimethyl-4,5-dihydro-1H-imidazole 1-oxyls (7), and their diamagnetic precursors were determined. Compound 1 is kinetically unstable because it is oxidized with atmospheric oxygen to form (E)-1,2-bis[1-amino-1-(cyanoimino)-2-methyl-propan-2-yl]diazene 1,2-dioxide. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 441–447, March, 2006.     

Heterometallic nickel(II) samarium(III) diethylenetriaminepentaacetate, a starting material for the preparation of samarium nickelate films

A reaction of samarium oxide, nickel oxocarbonate, and diethylenetriaminepentaacetic acid (H₅DTPA) taken in stoichiometric proportions in water gave SmNiDTPA · 10H₂O as a glassy solid. The formation of this heterometallic complex was confirmed by data from elemental analysis, IR spectroscopy, thermal analysis, and X-ray fluorescence analysis. An aqueous solution of the complex was used to deposit SmNiO₃ films onto a single-crystal SrTiO₃(001) substrate. The SmNiO₃ phase in films obtained upon 3-h annealing at 500°C was identified by powder X-ray diffraction. Films deposited from a solution of an equimolar mixture of monometallic samarium and nickel diethylenetriaminepentaacetates contained no samarium nickelate.     

The reaction of N-aminophthalimide with isothiocyanates

N-Aminophthalimide ( I ) reacted in refluxing isopropyl alcohol with a number of isothiocyanates to give the related 1:1 addition products, N-(3-substitutedthioureido)phthalimides III. On the other hand, heating I directly with an excess of neat arylisothiocyanates produced the N-arylphthalimides IV. As shown for IIIa, the 1:1 addition products are conveniently deblocked by the Ing-Manske procedure to yield the 4-substituted thiosemicarbazide.     

An improved procedure for the preparation of 2-amino-8-alkylpyrido-[2,3-d]pyrimidin-4(3H)-ones (8-alkyl-N5-deazapterins)

We report an improved procedure for the preparation of 8-alkyl-N5-deazapterins which allows clean preparation of all ring-methyl substituted compounds, including 5- and 7-methyl substituted compounds. The procedure was also successfully applied to the preparation of N5-deazapterins with improved yield over previous reports. The uv/visible and pKa data confirm the predicted increased basicity of 8-alkyl-N5-deazapterins compared with the N5-deazapterin parents, and indicate that N5-deazapterins protonate on N8 and 8-alkyl-N5-deazapterins protonate on N3.     

Homolytic dissociation of the carbon-element σ bonds by Grignard reagents

The reaction of 2-ethyl-3-tetrahydrofuryl thiocyanate (I) and triphenylacetonitrile (VIII) with methylmagnesium iodide in ether was studied using GC/MS, PMR and¹³C NMR spectroscopy. The reaction of (I) with CH₃MgI gives the product of the homolysis of the C-S bond, namely, bis(2-ethyl-3-tetrahydrofuryl) disulfide (II), in 81% yield. This reaction is assumed to be general in nature since triphenylacetonitrile (VIII) is also homolytically cleaved by the action of CH₃MgI to give triphenylmethane.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2886–2888, December, 1991.     

Structure of phenolic stabilizers for polymers VIII. Crystal structure of 2,2′-methylenebis(4-methyl-6-ter-butylphenol) monoacrylate

L. Ya. Karpov Scientific-Research Physicochemical Institute. Scientific-Research Institute of Rubber and Latex Goods. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 5, pp. 162–164, September–October, 1991.     

Effects of stereoisomerism in the mass spectra of 2,4-disubstituted thiacyclohexanes

The mass spectra of cis- (Ia-c) and trans-2-methyl-4-R-thiacyclohexanes (IIa-c; a R = n-C₄H₉, b R = n-C₅H₁₁, c R = Ph) were studied. It was established that [M-CH₃]⁺ ions, which correspond to the loss of a methyl group from the 2 position, are formed more readily in the case of the less stable trans isomers IIa-c than in the case of cis isomers Ia-c. The three-dimensional structures of the substances have no effect on the degree of elimination of the R substituent. The relative ionization energies (RIE) for Ia,b and IIa,b and the relative appearance energies (RAE) of the [M-CH₃]⁺ ions were measured by the electron impact method. It was found that the RIE are almost 0.05 eV lower and that the RAE of the [M-CH₃]⁺ ions are 0.1 eV lower for trans isomers IIa,b than for cis isomers Ia,b.Communication 4 from the series Ionization and appearance energies in organic chemistry, See [1] for Communication 3.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 333–338, March, 1981.