A dimensional analysis of the benzylic hydroxylase active site in mortierella isabellina

The spatial limits of the active site in the benzylic hydroxylase enzyme of the fungus Mortierella isabellina were investigated. Several molecular probes were used in incubation experiments to determine the acceptability of each compound by this enzyme. The yields of benzylic alcohols provided information on the acceptability of the particular compound into the active site, and the enantiomeric excess values provided information on the "fit" of acceptable substrates. Measurements of the molecular models were made using Cambridge Scientific Computing Inc. CSC Chem 3D Plus modeling program. i The dimensional limits of the aromatic binding pocket of the benzylic hydroxylase were tested using suitably substituted ethyl benzenes. Both the depth (para substituted substrates) and width (ortho and meta substituted substrates) of this region were investigated, with results demonstrating absolute spatial limits in both directions in the plane of the aromatic ring of 7.3 Angstroms for the depth and 7.1 Angstroms for the width. A minimum requirement for the height of this region has also been established at 6.2 Angstroms. The region containing the active oxygen species was also investigated, using a series of alkylphenylmethanes and fused ring systems in indan, 1,2,3,4-tetrahydronaphthalene and benzocycloheptene substrates. A maximum distance of 6.9 Angstroms (including the 1.5 Angstroms from the phenyl substituent to the active center of the heme prosthetic group of the enzyme) has been established extending directly in ii front of the aromatic binding pocket. The other dimensions in this region of the benzylic hydroxylase active site will require further investigation to establish maximum allowable values. An explanation of the stereochemical distributions in the obtained products has also been put forth that correlates well with the experimental observations.

Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

Generator Matrix Based Search for Extremal Self-Dual Binary Error-Correcting Codes

Self-dual doubly even linear binary error-correcting codes, often referred to as Type II codes, are codes closely related to many combinatorial structures such as 5-designs. Extremal codes are codes that have the largest possible minimum distance for a given length and dimension. The existence of an extremal (72,36,16) Type II code is still open. Previous results show that the automorphism group of a putative code C with the aforementioned properties has order 5 or dividing 24. In this work, we present a method and the results of an exhaustive search showing that such a code C cannot admit an automorphism group Z6. In addition, we present so far unpublished construction of the extended Golay code by P. Becker. We generalize the notion and provide example of another Type II code that can be obtained in this fashion. Consequently, we relate Becker's construction to the construction of binary Type II codes from codes over GF(2^r) via the Gray map.