The nucleotide sequence coding for major outer membrane protein OmpA of Shigella dysenteriae
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Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...
A palladium-catalyzed domino aminopalladation/C-H functionalization sequence has been developed, and provides access to functionalized phenanthridines and isoquinolines. The use of butyronitrile as the solvent is determinant to the success of the domino pr ...
Protein synthesis is one of the central elements in every living cell. For this process, mRNAs coding for genes are simultaneously competing for the same translation machinery (ribosomes and amino acids). But the ultimate determinants of cellular functions ...
The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in ...
Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...
We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded ...
The conformation of model Arg(Ala)(4)X(Ala)(4)Lys+2H and Arg(Gly)(4)X(Gly)(4)Lys+2H peptides has been systematically investigated as a function of the central amino acid X through a combined experimental and theoretical approach. Mass spectrome ...
Microcystins (MCs) are toxic heptapeptides found in cyanobacteria and share the common structure cyclo(-D-Ala1-L- X2-D-isoMeAsp3-L-Z4-Adda5-D-isoGlu6-Mdha7). The letters X and Z in the general formula above represent a wide range of L-amino acids that occu ...
Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework ...
Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for tr ...