Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Rare earth exchanged (Ce3+, La3+ and RE3+) H-Y zeolites as solid acid catalysts for the synthesis of linear alkyl benzenes

Rare earth exchanged H–Y zeolites were prepared by simple ion exchange methods at 353 K and have been characterized using different physicochemical techniques. A strong peak around 58 ppm in the 27Al{1H} MAS NMR spectra of these zeolites suggests a tetrahedral coordination for the framework aluminium. Small peak at or near 0 ppm is due to hexa-coordinated extra-framework aluminium and a shoulder peak near 30 ppm is a penta-coordinated aluminium species; [Al(OH)4]−. The vapor-phase benzene alkylation with 1-decene and 1-dodecene was investigated with these catalytic systems. Under the reaction conditions of 448 K, benzene/olefin molar ratio of 20 and time on stream 3 h, the most efficient catalyst was CeH–Y which showed more than 70% of olefin conversion with 48.5% 2-phenyldecane and 46.8%, 2-phenyldodecane selectivities with 1-decene and 1-dodecene respectively.

Novel organic porous solids with channel and layered structures from 1,3,5-triazine-2,4,6-triaminehexaacetic acid and its calcium salt

Single crystals of a symmetrically substituted molecule, 1,3,5-triazine-2,4,6-triaminehexaacetic acid, (TTHA) and its Ca2+ salt have been synthesized, the analysis of which reveals the existence of novel channel type cavities and helical packing organizations in the crystals.

The fate of the initiator tRNAs is sensitive to the critical balance between interacting proteins

Formylation of the initiator tRNA is essential for normal growth of Escherichia coil, The initiator tRNA containing the U35A36 mutation (CUA anticodon) initiates from UAG codon, However, an additional mutation at position 72 (72A --> G) renders the tRNA (G72/U35A36) inactive in initiation because it is defective in formylation, In this study, we isolated U1G72/U35A36 tRNA containing a wobble base pair at 1-72 positions as an intragenic suppressor of the G72 mutation. The U1G72/U35A36 tRNA is formylated and participates in initiation. More importantly, we show that the mismatch at 1-72 positions of the initiator tRNA, which was thus far thought to be the hallmark of the resistance of this tRNA against peptidyl-tRNA hydrolase (PTH), is not sufficient, The amino acid attached to the initiator tRNA is also important in conferring protection against PTH. Further, we show that the relative levels of PTH and IF2 influence the path adopted by the initiator tRNAs in protein synthesis. These findings provide an important clue to understand the dual function of the single tRNA(Met) in initiation and elongation, in the mitochondria of various organisms.

Crystal structure of L-lysyl-L-glutamic acid dihydrate

L-Lysyl-L-glutamic acid dihydrate, C11N3O5H21·2H2O, crystallizes in the monoclinic space group P21 with a = 12.474(2), b = 5.020(1), c = 13.157(2) Å, β= 114.69(1)° and Z = 2. The crystal structure was solved by direct methods and refined to an R value of 0.037 using full matrix least-squares method. The molecule exists as a double zwitterion with both the amino and carboxyl groups ionised. The peptide has a folded conformation with its Lys residue trans and Glu residue gauche−gauche+. The side chains of the Lys and Glu residues correspond to all trans and folded (g−g−g−) conformations respectively. The terminal carboxyl group forms hydrogen bonds with the ξ-amino group of the lysine side chain. The head-to-tail interaction often seen in peptide crystals is absent in the present structure. In the extended crystal structure water molecules form channels along the b direction and are enclosed within helically arranged hydrogen bonds formed by the lysine side chain and the peptide backbone.

Selective para metalation of unprotected 3-methoxy and 3,5-dimethoxy benzoic acids with n-butyl lithium-potassium tert-butoxide (LIC-KOR): synthesis of 3,5-dimethoxy-4-methyl benzoic acid

The potassium salt of 3-methoxy and 3,5-dimethoxy benzoic acids undergoes deprotonation at the position para to the carboxylate group selectively when treated with LIC-KOR in THF at -78 degrees C and it has been extended to the synthesis of 3,5-dimethoxy-4-methyl benzoic acid. (C) 2000 Elsevier Science Ltd. All rights reserved.

Charge Density Analysis of Crystals of Nicotinamide with Salicylic Acid and Oxalic Acid: An Insight into the Salt to Cocrystal Continuum

Charge density analysis from both experimental and theoretical points of view on two molecular complexes: one is formed between nicotinamide and salicylic acid, and the other formed between nicotinamide and oxalic acid brings out the quantitative topological features to distinguish a cocrystal from a salt.

Thermal decomposition studies on copolyurethanes based on hydroxyl terminated polybutadiene and poly(12-hydroxy stearic acid-co-TMP) ester polyol

Thermal degradation of copolyurethanes based on hydroxyl terminated polybutadiene (HTPB) and poly(12-hydroxy stearic acid-co-TMP) ester polyol (PEP) with varying compositions has been studied by thermo-gravimetric and pyrolysis-GC techniques. The copolyurethanes were found to decompose in multiple stages and the kinetic parameters were found to be dependent on the method of their evaluation. The activation energy for the initial stage of decomposition was found to increase, and for the main stage decreases with the increase in PEP content. The pyrolysis-GC studies on the ammonium perchlorate filled copolyurethanes (solid propellants) showed that the major products during the pyrolysis were C-2, C-3 hydrocarbons and butadiene. The amount of C-2 fraction in the pyrolyslate increased with solid loading, as well as with the HTPB content in the copolyurethanes. A linear relationship apparently exists between the amount of C-2 fraction and the burn rates of the solid propellants. (C) 2000 Elsevier Science Ltd. All rights reserved.