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Computational biology is an emerging field in the study of genomics. It allows researchers to gain a deep understanding of biological products without the need for extensive lab work. It is a power tool as it saves researchers both time and money and allows a more integrative approach to the study of genomics.
=='''Introduction''' ==


Proteins are the final derived state from the central dogma and they are the functional expression of an organisms DNA code. Proteins themselves perform many diverse and often complex functions within the organism that produces them, and knowing what these individual proteins do contributes our understanding of disease states and what can be done to prevent and control them. The knowledge of protein structure function and the evolutionary lineage are all important components when determining what role a protein ultimately plays in an organism and what potential can go wrong.


The advancements provided by bioinformatics has contributed greatly to researches ability to isolate and determine important proteins that have both negative and positive effects on biological systems. These tools have also made it easer to process hypothetical or unknown proteins that would otherwise not be looked at because of there lack of immediate significance and the money that it would cost to work on a protein that may prove to be unimportant to further research.
Nucleotide binding protein 2 is a novel protein defined which represent the eukaryotic nucleotide binding protein family. NUBP2 represent the short form of nucleotide binding protein which  belongs to the partitioning ATPase gene family. The protein from this family function by drawing energy from hydrolysis of ATP, and they share a characteristic sequence motif of “[GA]-X2-(G)-X-G-K-[ST],” called the “phosphate-binding loop (P-loop)” (Walker et al., 1982; Saraste et al., 1990). Although the structure of NUBP2 is not completely solved, but the high similarity of NUBP2 with 2ph1 (MinD homologue, E.coli) make the function analysis possible.
 
E.coli MinD was also included in the Partitioning ATPase gene family, it is a membrane associated ATPase which inhibits the cell division at the poles and consequently induces normal cell division (de Boer et al., 1991), and based on sequence similarity, the E. coli mrp gene (Dardel et al., 1990). The similarity between 2ph1 and NUBP2 is about 39.66% of the sequence, and by using the structure of 2ph1, the function of NUBP2 would be analysed based on the structure searching.
 
The division septum is normally placed at the midpoint of the cell, but potential division sites also exist near each of the cell poles. Restriction of the cell division site at the midpoint is governed by the product of the three genes of the MinB operon, MinC, MinD and MinE. MinC inhibits the division at all of the potential division sites and requires the activity of peripheral membrane ATPase MinD for its function. MinC and MinD act cooperatively to form a non-specific division inhibitor complex. MinE has two functions: it suppresses the MinCD-mediated division inhibition and recognizes the mid-cell point from the cell poles. In order words, MinE promotes mid-cell division by excluding MinCD from the mid-cell site.
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Based on the homology similarity of NUBP2 to E. coli MinD protein, we hypothesed that NUBP2 involves in cell division to determine the position of septum (Z-ring). Another function of this protein is hydrolyse ATP molecules in cell. Further analysis was conducted in structural study on NUBP2 to deduce the function of NUBP2 protein.

Latest revision as of 07:40, 2 June 2009

Introduction

Nucleotide binding protein 2 is a novel protein defined which represent the eukaryotic nucleotide binding protein family. NUBP2 represent the short form of nucleotide binding protein which belongs to the partitioning ATPase gene family. The protein from this family function by drawing energy from hydrolysis of ATP, and they share a characteristic sequence motif of “[GA]-X2-(G)-X-G-K-[ST],” called the “phosphate-binding loop (P-loop)” (Walker et al., 1982; Saraste et al., 1990). Although the structure of NUBP2 is not completely solved, but the high similarity of NUBP2 with 2ph1 (MinD homologue, E.coli) make the function analysis possible. E.coli MinD was also included in the Partitioning ATPase gene family, it is a membrane associated ATPase which inhibits the cell division at the poles and consequently induces normal cell division (de Boer et al., 1991), and based on sequence similarity, the E. coli mrp gene (Dardel et al., 1990). The similarity between 2ph1 and NUBP2 is about 39.66% of the sequence, and by using the structure of 2ph1, the function of NUBP2 would be analysed based on the structure searching. The division septum is normally placed at the midpoint of the cell, but potential division sites also exist near each of the cell poles. Restriction of the cell division site at the midpoint is governed by the product of the three genes of the MinB operon, MinC, MinD and MinE. MinC inhibits the division at all of the potential division sites and requires the activity of peripheral membrane ATPase MinD for its function. MinC and MinD act cooperatively to form a non-specific division inhibitor complex. MinE has two functions: it suppresses the MinCD-mediated division inhibition and recognizes the mid-cell point from the cell poles. In order words, MinE promotes mid-cell division by excluding MinCD from the mid-cell site. Based on the homology similarity of NUBP2 to E. coli MinD protein, we hypothesed that NUBP2 involves in cell division to determine the position of septum (Z-ring). Another function of this protein is hydrolyse ATP molecules in cell. Further analysis was conducted in structural study on NUBP2 to deduce the function of NUBP2 protein.

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