The Proteomic Code: a molecular recognition code for proteins
- PDF / 16,279,521 Bytes
- 44 Pages / 610 x 792 pts Page_size
- 46 Downloads / 273 Views
BioMed Central
Open Access
Review
The Proteomic Code: a molecular recognition code for proteins Jan C Biro Address: Homulus Foundation, 88 Howard, #1205, San Francisco, CA 94105, USA Email: Jan C Biro - [email protected]
Published: 13 November 2007 Theoretical Biology and Medical Modelling 2007, 4:45
doi:10.1186/1742-4682-4-45
Received: 2 September 2007 Accepted: 13 November 2007
This article is available from: http://www.tbiomed.com/content/4/1/45 © 2007 Biro; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract Background: The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code. Review: The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding. Methods and conclusions: A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.
Background Nucleic acids and proteins are the carriers of most (if not all) biological information. This information is complex, well organized in space and time. These two kinds of macromolecules have polymer structures. Nucleic acids are built from four nucleotides and proteins are built from 20 amino acids (as basic units). Both nucleic acids and proteins can interact with each other and in many cases these interactions are extremely strong (Kd ~ 10-9-10-12 M) and extremely specific. The nature and origin of this specificity is well understood in the case of nucleic acid-nucleic acid (NA-NA) interactions (DNA-DNA, DNA-RNA, RNARNA), as is the complementarity of the Watson-Crick (WC) base pairs. The specificity of NA-NA interactions is undoubtedly determined at the basic unit level where the individual bases have a prominent role.
Our most established view on the specificity of proteinprotein (P-P) interactions is completely different [1]. In this case the amino acids in a particular protein together establish a large 3D structure. This structure has protrusions and cavities, charged and uncharged areas, hydrophobic and hydrophilic patches on its surface, which altoge
Data Loading...
