Figure 3 - available via license: Creative Commons Attribution 3.0 Unported
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Overlaps of the first five principal components and normal modes. 1.0 indicates a perfect directional agreement while 0.0 denotes that the vectors are perpendicular or unrelated. Please check online version for colour figure.
Source publication
Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular...
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Background:
One key step in the development of inhibitors for an enzyme is the application of computational methodologies to predict protein-ligand interactions. The abundance of structural and ligand-binding information for HIV-1 protease opens up the possibility to apply computational methods to develop scoring functions targeted to this enzyme....
Citations
... Comparative analyses between the apo form of the enzyme and these ternary complexes clearly indicate that NS5B structure undergoes significant structural rearrangements to accommodate the template, both at the global and local levels (Fig. 7). The dynamic behavior of NS5B has been corroborated by very recent MD simulation data [132]. ...
Background:
HCV-linked pathologies represent worldwide health threats. Over the years, an enormous number of independent studies have been devoted to the understanding of the molecular bases of HCV infection. A significant amount of these investigations has been focused on the structural characterization of the virus proteins with the aim of developing structure-based innovative therapeutic approaches. An analysis of the current Protein Data Bank content unravels that the structural biology of the virus has hitherto covered a large fraction of the HCV proteins (75%).
Objective:
The present review recapitulates the state-of-the-art of structural characterizations of HCV individual proteins with a specific focus on their structural versatility/flexibility.
Results:
This survey indicates there is accumulating evidence that structural flexibility is a common feature among HCV proteins. This versatility can be detected at different structural level i.e. occurrence of alternative oligomeric states and/or of local and global flexibility. Somewhat surprisingly, some disordered or highly flexible regions of HCV proteins, such as the core and the antigenic fragment 412-423 of E2, present highly conserved sequences among the virus genotypes. The overall versatility of HCV proteins plays an important role in host protein recognition, drug resistance mechanisms, and virus escape from the host immunogenic system. Of particular relevance is the emerging idea that HCV uses local structural flexibility as an alternative tool to sequence variability to evade the immune response of the host organism.
Conclusion:
We believe that concepts emerged from this survey will be important for the development of anti-HCV vaccines that are eagerly needed.
