Computational biology: Protein predictions

Dodson, Eleanor J.
November 2007
Nature;11/8/2007, Vol. 450 Issue 7167, p176
Academic Journal
The article discusses the study that assesses the three-dimensional structure of proteins from its amino-acid sequence through X-ray diffraction and nuclear magnetic resonance (NMR). The peptide sequence is mapped against the existing information, and energy profile of each atom is incorporated into the low-energy models. Findings reveal that the shape of the protein matches with the lowest-energy conformation of the molecule that reflects the combined properties of amino acids. It also indicates an achievement of amino acid hydrogen-bonding as well as side-chain interactions in certain structures.


Related Articles

  • MÄ°OMODULÄ°N F MOLEKULUNUN FƏZA QURULUÅžU. Əhmǝdov, N. A.; Abbasli, R. M.; İsmayilova, L. İ. // Journal of Qafqaz University;2011, Issue 31, p44 

    Myomodulin molecules belonging to the family of neuropeptides influence the flow of neurotransmitters in neurons and mebranes. Using the method of theoretical conformational analysis the spatial structure of the heptapeptide molecule myomodulin F with the amino acid sequence...

  • Evolutionary Pareto-optimization of stably folding peptides. Gronwald, Wolfram; Hohm, Tim; Hoffmann, Daniel // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These...

  • The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles. Gendoo, Deena M. A.; Harrison, Paul M. // PLoS Computational Biology;Aug2012, Vol. 8 Issue 8, p1 

    Prion Proteins (PrP) are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species. Here, we perform a comprehensive principle components analysis (PCA) on the tertiary structures of PrP globular proteins to discern PrP...

  • MobiDB: a comprehensive database of intrinsic protein disorder annotations. Di Domenico, Tomás; Walsh, Ian; Martin, Alberto J.M.; Tosatto, Silvio C.E. // Bioinformatics;8/1/2012, Vol. 28 Issue 15, p2080 

    Motivation: Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences. Alternatively, the...

  • ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Tamiola, Kamil; Mulder, Frans A. A. // Bioinformatics;Apr2011, Vol. 27 Issue 7, p1039 

    Summary: We describe here the ncIDP-assign extension for the popular NMR assignment program SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of connected...

  • Enhanced Amphiphilic Profile of a Short β-Stranded Peptide Improves Its Antimicrobial Activity. Manzo, Giorgia; Scorciapino, Mariano A.; Wadhwani, Parvesh; Bürck, Jochen; Montaldo, Nicola Pietro; Pintus, Manuela; Sanna, Roberta; Casu, Mariano; Giuliani, Andrea; Pirri, Giovanna; Luca, Vincenzo; Ulrich, Anne S.; Rinaldi, Andrea C. // PLoS ONE;Jan2015, Vol. 10 Issue 1, p1 

    SB056 is a novel semi-synthetic antimicrobial peptide with a dimeric dendrimer scaffold. Active against both Gram-negative and -positive bacteria, its mechanism has been attributed to a disruption of bacterial membranes. The branched peptide was shown to assume a β-stranded conformation in a...

  • Solution state structures of human pancreatic amylin and pramlintide. Cort, John R.; Zhihong Liu; Lee, Gregory M.; Huggins, K.N.L.; Janes, Susan; Prickett, Kathryn; Andersen, Niels H. // PEDS: Protein Engineering, Design & Selection;Aug2009, Vol. 22 Issue 8, p497 

    We have employed pramlintide (prAM) as a surrogate for hAM in CD and NMR studies of the conformational preferences of the N-terminal portion of the structure in media which do not provide long-lived monomeric solutions of hAM due to its rapid conversion to preamyloid β aggregate states....

  • Pressure-induced local unfolding of the Ras binding domain of RalGDS. Inoue, Kyoko; Yamada, Hiroaki; Akasaka, Kazuyuki; Herrmann, Christian; Kremer, Werner; Maurer, Till; Döker, Rolf; Kalbitzer, Hans Robert // Nature Structural Biology;Jul2000, Vol. 7 Issue 7, p547 

    The reliable prediction of the precise three-dimensional structure of proteins from their amino acid sequence is a major, still unresolved problem in biochemistry. Pressure is a parameter that controls folding/unfolding transitions of proteins through the volume change ΔV of the...

  • A COMPARATIVE STUDY OF PROTEIN STRUCTURE VISUALIZATION TOOLS FOR VARIOUS DISPLAY CAPABILITIES. Ansari, Shaheda N.; Iliyas, Sayyed // Bioscience Discovery: An International Journal of Life Sciences;Jun2011, Vol. 2 Issue 2, p222 

    A molecular graphics visualization tool is required to view the structure that is encoded by atomic coordinate PDB files and to be able to manipulate the images to view the molecule from various perspectives. Without a proper tool, the PDB file will be read as a text file that lists each atom...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics