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Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins
College of Pharmacy, Gachon University, 534-2 Yeonsu 3-dong, Yeonsu-gu, Incheon 406-799, Korea
College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 487-010, Korea
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742, Korea
These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 9 March 2012; in revised form: 29 May 2012 / Accepted: 1 June 2012 / Published: 8 June 2012
Abstract: Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.
Keywords: Helicobacter pylori; structural genomics; NMR; X-ray; unknown protein; hypothetical protein; structural homology
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Park, S.J.; Son, W.S.; Lee, B.-J. Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins. Int. J. Mol. Sci. 2012, 13, 7109-7137.
Park SJ, Son WS, Lee B-J. Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins. International Journal of Molecular Sciences. 2012; 13(6):7109-7137.
Park, Sung Jean; Son, Woo Sung; Lee, Bong-Jin. 2012. "Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins." Int. J. Mol. Sci. 13, no. 6: 7109-7137.