Molecular Biology. Practical Guide - Velikov V.A. 2013

Calculations in Protein Work
Translation of Nucleotide Sequences

Having information on the Introduction/19.html">Primary Structure of DNA makes it possible to gain considerable insight into the protein it encodes. Conversely, the DNA sequence can be reconstructed from the protein data, although this is more challenging due to the degeneracy of METABOLISM/28.html">The Genetic Code. Computational and molecular modeling Methods often yield faster and more accurate results than direct experiments. Naturally, this does not diminish The Importance of direct experimentation, especially when studied homolog Proteins and validated computational algorithms are lacking.

The works listed below introduce internet resources that host software for various calculations involving proteins and Nucleic Acids. The content of these Assignments may vary or be entirely flexible, as their primary objective is to provide practical experience in utilizing specialized web portals.

One of the most prominent specialized websites in the Russian-language internet segment is MOLBIOL.RU – Classical and Molecular Biology. Founded in 2000, the site operates stably and continues to develop intensively, featuring an active forum. When working with the programs, it is essential to follow the provided instructions, which are clear and straightforward.

For a more detailed molecular analysis of a specific protein and for multiple protein sequence alignment, information should be retrieved from Amino Acid Sequence Databases such as Swiss-Prot, the NCBI Protein Database, and other resources in bioinformatics, Genomics, and Proteomics. It should be noted that the majority of proteins present in biomedical databases are obtained via "in silico Translation", meaning the proteins are annotated based on nucleotide sequences.

The program hosted on MOLBIOL.RU translates a nucleotide sequence in selected reading frames. Multiple frames can be chosen simultaneously, and both single-letter and three-letter amino acid codes can be used. Various specialized manipulations of The nucleotide sequence, such as generating the complementary strand or searching for rare codons, can be performed using a dedicated form.

Procedure

1. Open the home page of the MOLBIOL.RU website (http://www.molbiol.ru). Explore the sections available on this page.

2. On the main page, locate the "Calculations" section.

3. Select the "Nucleotide Sequence Translation" tab.

4. As an example, "translate" the NADH dehydrogenase Gene of Nikolsky's viper. Fig. 2 shows a partial sequence of this gene obtained at the Laboratory of Molecular Biology of Saratov State University named after N.G. Chernyshevsky (Velikov et al., Bulletin of Saratov State Agrarian University, 2006, No. 3; Efimov et al., Genetics, 2008, No. 2). Comparing the obtained result with The amino acid sequence of the common viper's NADH dehydrogenase reveals differences in 6 Amino Acids (see App. 16).

Class="center">Fig. 2. NADH dehydrogenase gene of Nikolsky's viper, subunit 2 (GenBank: EU625372.1)

5. Translate several other proposed genes. Nucleotide sequences for all currently known genes are accessible in the GenBank database hosted by the National Center for Biotechnology Information (US National Library of Medicine - http://www.pubmed.com or http://www.ncbi.nlm.nih.gov/pubmed).

6. When entering any gene sequence, please note that all characters other than standard nucleotide designations (agctuswrymkhbdvn) are ignored. Memorize the designations for NUCLEOTIDES other than agct (App. 8). Lowercase letters are generally easier to distinguish in writing.