Bearing Proteins Research Articles

GenNBPSeq: Online Web Server to Generate Never Born Protein Sequences Using Toeplitz Matrix Approach with Structure Analysis

Background: In biology, the translation of genetic information to its corresponding protein sequences is carried out by using the Universal Genetic Code. Out of all the possible combinations of 20 amino acids, proteins are formed by the possible combinations that occur naturally. This leaves a large number of unknown combinations of protein sequences that includes the Never Born Proteins. A Never Born Protein is a theoretically possible protein that does not occur in nature or may be selected by evolution in future. Objective: In this study, the "GenNBPSeq" online web server is developed to generate Never Born Protein Sequences and to analyze their sequence and structural stability. Methods: The “GenNBPSeq” server is developed based on the Gray Code and Partitioned Gray Code representations of the Universal Genetic Code combined with the novel Toeplitz matrix approach. The sequence and structure analysis is done by various Bioinformatics tools for the sample Never Born Protein sequences. Results: The “GenNBPSeq” server is available at http://bioinfo.bdu.ac.in/nbps and the users can generate Never Born Protein sequences and download them in FASTA formats. The Never Born Protein sequences obtained by the above Toeplitz matrix approach contain same amino acid composition. They also form protein secondary and 3-Dimensional structures with intrinsic stability. Conclusion: This study conjectures that the Never Born Protein Sequences generated by “GenNBPSeq” server using Toeplitz matrix approach may exhibit intrinsic structural stability. Synthesizing these Never Born Proteins and analyzing their biological applications are major research areas in Systems and Synthetic Biology.

Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach

In this paper, we identify all possible Gray Code and Partitioned Gray Code representations of the Universal Genetic Code for n = 2-bit and 3-bit binary numbers. We analyse the Hamming Distance matrices of all these Gray code and Partitioned Gray Code possibilities for which we obtain the Toeplitz and Partitioned Toeplitz Matrices, respectively. We use this Gray Code and Partitioned Gray Code representations of the Universal Genetic Code combined with the novel Toeplitz matrix approach to generate many Never Born Protein (NBP) Sequences, which exhibit intrinsic structural stability. In general, Never Born Protein sequences may have many potential applications in synthetic biology and opens a new vista in understanding this new subset of proteins for better applications in drug discovery, synthesis of fine chemicals, etc.

Entropy of never born protein sequences

BackgroundA Never Born protein is a theoretical protein which does not occur in nature. The reason why some proteins were selected and some were not during evolution is not known. We applied information theory to find similarities and differences in information content in Never Born and natural proteins.FindingsBoth block and relative entropies are similar what means that both protein kinds contain strongly random sequences.An artificially generated Never Born protein sequence is closely as random as a natural one.ConclusionsInformation theory approach suggests that protein selection during evolution was rather random/non-deterministic.Natural proteins have no noticeable unique features in information theory sense.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-200) contains supplementary material, which is available to authorized users.