Bioinformatics for Semi-Predictive Functional in silico designs of Synthetic Genes and Clusters become more and more reality. |
Dear Customers,
You for sure know that the difference between high yield of protein expressed and the yield of small molecules are just two sides of the same coin. The specific activity of the protein is mainly dependent on the autonomous re-folding power intrinsically encoded in the amino acid sequence of a protein, the supporting activity of helper proteins like the professional Chaperons are needed. Those proteins like many membrane proteins which do not have a strong tendency for autonomous re-folding are heavily dependent on the co-translational folding properties directed by the ribosomal kinetics along the messenger RNA. There is an increasing knowledge documented in various recent publications about approaching a rational and at least semi-predictive way to handle big and complex sequences in this respect.Figure-1.
The proper function of proteins like enzymes is determined by its general
folding properties. Correct folding into a functional protein structure can
be (1) autonomously, supported by (2) Chaperones or (3)
highly dependent from the ribosomal co-translational speed or both. Robust
refolding enzymes like RNase (Anfinsen) have the ability for correct
folding information intrinsically encoded. Therefore these are autonomously
refolding into its functional structure. In contrast are the folding sensitive
proteins. These fall in two classes. For the one type co-expression of
chaperones which are supportive for the folding process are binding to proteins
in statu nascendi for the stabilization of meta-structures which are favourable
to finally promote functional folding. In parallel to protein neo-genese,
co-translational folding processes can be highly dependent from the correct fine
tuning of the ribosomal kinetics along the RNA message and in addition
associated with chaperones. For the heterologous expression of enzymes and other
proteins the adaptation of the codon usage as well as the micro and macro
evolution for the creation of biodiversity and in addition the chaperon
co-expression are versatile approaches for achieving a high specificactivity of
the protein function like catalysts
ATG:biosynthetics is specialist in bio-synthetics pathway systems on Pro- as well as in Eukaryotes.
Continuously we are developing and providing the up-to-date knowledge in the field mirrored in our development of algorithms.
We are offering services like :
- identification of high expression group genes
- identification and delineation of specific sub-tables
- balanced codon use and codon sampling
- tRNA - adaption index calculations
- Aminoacyl-tRNA supply and codon use demand models
- transcriptional initiation
- translational initiation, elongation and termination
Figure-2.
Different composite DNA/RNA sequence features are determining the functional
gene products and the yield of small molecules . The specific activity of an
enzyme is the key driver of the product yield and not the general protein yield
achieved. The production yield of small molecule compounds is predominantly
dependent from the balanced activity of all the biosynthetic cascade enzymes
involved. So the iterative improvement of the specific activity of enzymes is
the key for the proper and functional folding of the enzymes involved. It is the
direct function of success for production processes to evolve it towards the aim
to guarantee the highest yield of proper functional working enzymes
possible.
Sincerest regards,
Dr. Hubert S. Bernauer
ATG:biosynthetics GmbH
++49-761-13776959
https://www.atg-biosynthetics.com
Dr. Hubert S. Bernauer
ATG:biosynthetics GmbH
++49-761-13776959
https://www.atg-biosynthetics.com