Abstract
BackgroundIt has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins.ResultsIn an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a) It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b) It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c) It can take as input an uploaded PDB file and a results file (obtained from functionality (b)) and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA) distributions.ConclusionWe believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological determinants of protein folding by analyzing the topological changes in proteins over the unfolding/folding pathways.
Highlights
It has long been known that small regions of proteins tend to fold independently and are stabilized by interactions between these distinct subunits or modules
GANDivAWeb The GANDivAWeb webserver is based on the GANDivA (Genetic Algorithm-based Network modularity DetectIVe Algorithm) algorithm which is an implementation of the Guimera algorithm [10] that uses a genetic algorithm (GA) to optimize the modularity score, instead of simulated annealing which was used in the original algorithm
The algorithm has been written in C and was developed using the parallel genetic algorithm PGAPACK [13], the GNU Scientific Library [14] and the OpenMPI [15] and MPICH [16] MPI [17] implementations
Summary
It has long been known that small regions of proteins tend to fold independently and are stabilized by interactions between these distinct subunits or modules. Such units, known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process Such AFUs can be used as model systems in order to study the structural organization of proteins. It is recognized that small regions of proteins tend to fold independently and are stabilized by interactions between these distinct subunits or modules. In the belief that an unequivocal definition of a module must be based on the most fundamental property of protein 3D structure, namely, the adjacency matrix of inter-residues contact, we adopted a network representation of the protein
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