Special Issue "Hypothetical Proteins"
Deadline for manuscript submissions: closed (29 February 2012)
Prof. Dr. Annalisa Santucci
Dipartimento di Biotecnologie, Universita' degli Studi di Siena, via Fiorentina 1, 53100 Siena, Italy
The development of automated genome sequencing provided researchers with a tremendous wealth of biological information, whose potential has still to be fully realized. Although often conserved among different organisms, Open Reading Frames (ORFs) encode also for ‘hypothethical proteins’ (HPs), which are defined as proteins predicted from nucleic acid sequences but whose existence has not been proved by any experimental chemical evidence. Often, HPs cannot be related to other proteins with known structure or function; such a lack of sequence similarity is one of the main constraints to any genome functional annotation strategy.
Advances in a broad spectrum of genetic and biochemical tools speeded up the genome annotation process via structural approaches. In this context, high throughput crystallization techniques, NMR spectroscopy, X-ray diffraction and structural analyses combined with “omics” technologies such as structural genomics, transcriptomics and proteomics contributed to determine the tertiary structures and the number of isoforms or molecular species of many HPs, as wells as their intracellular/extracellular location also in relation to their function. Furthermore, a great effort to understand the geometrical location of functional site and the biochemical/biological functions of proteins lay in the development of bioinformatic tools and databases. However, much effort still needs to be dedicated to the optimization of technological platforms and bioinformatic tools for the functional analysis of HPs, in order to contribute substantially to the piecing together of the structure-function puzzle.
Prof. Dr. Annalisa Santucci
- data mining
- functional analysis
- genome sequencing
- structural genomics
Article: Structural Modeling and Biochemical Characterization of Recombinant KPN_02809, a Zinc-Dependent Metalloprotease from Klebsiella pneumoniae MGH 78578
Int. J. Mol. Sci. 2012, 13(1), 901-917; doi:10.3390/ijms13010901
Received: 27 October 2011; in revised form: 29 December 2011 / Accepted: 9 January 2012 / Published: 16 January 2012| Download PDF Full-text (3917 KB) | Download XML Full-text
Article: Structural and Functional Characterization of Two Alternative Splicing Variants of Mouse Endothelial Cell-Specific Chemotaxis Regulator (ECSCR)
Int. J. Mol. Sci. 2012, 13(4), 4920-4936; doi:10.3390/ijms13044920
Received: 8 February 2012; in revised form: 19 March 2012 / Accepted: 20 March 2012 / Published: 19 April 2012| Download PDF Full-text (760 KB) | Download XML Full-text | Supplementary Files
Review: Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins
Int. J. Mol. Sci. 2012, 13(6), 7109-7137; doi:10.3390/ijms13067109
Received: 9 March 2012; in revised form: 29 May 2012 / Accepted: 1 June 2012 / Published: 8 June 2012| Download PDF Full-text (2870 KB) | Download XML Full-text | Supplementary Files
Article: Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum
Int. J. Mol. Sci. 2012, 13(6), 7354-7364; doi:10.3390/ijms13067354
Received: 20 April 2012; in revised form: 25 May 2012 / Accepted: 4 June 2012 / Published: 14 June 2012| Download PDF Full-text (1213 KB) | Download XML Full-text
Last update: 26 February 2014