Residue types, structural states

However, this is not so easy without the tertiary structure of the enzyme. The possible clues are the homology search with functionally resembling enzymes and computer simulation of the tert-structure of the enzyme. The characteristic features of AMDase are (i) the reaction proceeds via an enolate-type transition state, (ii) the cysteine residue plays an essential role and (iii) the reaction involves an inversion of configuration on the a-carbon of the carboxyl group. 

In the statistical method of Chou and Fasman (Chou and Fasman, 1978), the propensities for a residue type to adopt three structural states a-helix (

), p-sheet () and turn () conformations are calculated for all of the 20 amino acids according to... 

The classic Chou-Fasman technique (64) is a statistical or probabilistic one. It divides the compositional frequency of a particular amino acid type within a given secondary structural type by its composition within all the sequences of all the proteins in the data base considered. If the so-called "conformational preference" is above 1.00, the amino acid shows a structural bias for a given secondary structure below 1.00 indicates a structural avoidance and, of course, 1.00 displays neutrality. These 20 propensities over three structural states (a, coil or turn) are used to predict sequence spans if a cluster of consecutive preferences along the sequence consists of four or more residues and shows a mean preference greater than some threshold. 

The left-hand side of this expression is the energy of the sequence S adopting the conformation C, relative to some reference state. The right-hand side is the sum of the database-derived probabilities multiplied by the quantity /. In the purely statistical frameworks / = 1, and when statistical mechanics are used / = —kT. P (cj) is the probability that a specific sequence component s (individual residues, residue pairs or triplets) adopts a specific structural state c (defined by values of backbone angles, or spatial distances between atoms or residues). The indices i and j indicate the position or positions along the polypeptide chain of the sequence components and the structural states, respectively. P(Cj) represents the probability that any sequence component adopts a structural state c at position j along the polypeptide chain, and is compiled by considering all amino acid types as equivalent. This sequence-nonspecific probability is a normalization factor, applied in order to factor out many-body effects. 

Scheme 1). Introduction of a jt bond into the molecular structure of 1 furnishes homoallylic amine 2 and satisfies the structural prerequisite for an aza-Prins transform.4 Thus, disconnection of the bond between C-2 and C-3 affords intermediate 3 as a viable precursor. In the forward sense, a cation ji-type cyclization, or aza-Prins reaction, could achieve the formation of the C2-C3 bond and complete the assembly of the complex pentacyclic skeleton of the target molecule (1). Reduction of the residual n bond in 2, hydro-genolysis of the benzyl ether, and adjustment of the oxidation state at the side-chain terminus would then complete the synthesis of 1. 

The aldehyde oxidoreductase from Desulfovibrio gigas shows 52% sequence identity with xanthine oxidase (199, 212) and is, so far, the single representative of the xanthine oxidase family. The 3D structure of MOP was analyzed at 1.8 A resolution in several states oxidized, reduced, desulfo and sulfo forms, and alcohol-bound (200), which has allowed more precise definition of the metal coordination site and contributed to the understanding of its role in catalysis. The overall structure, composed of a single polypeptide of 907 amino acid residues, is organized into four domains two N-terminus smaller domains, which bind the two types of [2Fe-2S] centers and two much larger domains, which harbor the molybdopterin cofactor, deeply buried in the molecule (Fig. 10). The pterin cofactor is present as a cytosine dinucleotide (MCD) and is 15 A away from the molecular surface,... 

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