Multiple Sequence Alignment.

The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments, although many biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, to serve as a helpful guide or starting point for researchers who aim to construct a reliable MSA.

Altering the regioselectivity of cytochrome P450 CYP102A3 of Bacillus subtilis by using a new versatile assay system.

A novel monooxygenase (CYP102A3) has been discovered within the Bacillus subtilis genome that reveals a similarity of 76 % to the well-known cytochrome P450 BM-3 of B. megaterium (CYP102A1). Both enzymes are natural fusion proteins consisting of a heme domain and a FAD/FMN-reductase domain. Because of their high turnover rates, these biocatalysts are of special interest for industrial applications, but show only limited regioselectivity. In this work, the regioselectivity of CYP102A3 was changed by directed evolution and protein design to hydroxylate substrates not only in different subterminal, but also to a high extent, in terminal carbon chain positions. To enable a high-throughput screening procedure, a very versatile assay was developed that is capable of discriminating between terminal and subterminal hydroxylation of carbon chains. A double mutant of CYP102A3 was obtained that produces 48 % octan-1-ol as the main product of the reaction.