Comparing Bound and Unbound Protein Structures for Investigating Flexibility
نویسندگان
چکیده
Fast methods for volume based Protein-Protein docking exist (eg. [1] or [4]). However, they employ the rigid-body assumption, and often miss the correct solution. To enhance todays docking algorithms the "induced fit" (comformational changes of a protein during the docking process) must be handled. Flexibility studies can help improving docking algorithms. Flexibility can be considered by enumerating possible conformations starting with the unbound protein using information about preferred movements. A different approach[8] assigns weights to the residues and thus decreases the penalizing influence of some residue which is likely to have a different conformation in the complexed form.
منابع مشابه
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder
Most of the proteins in a cell assemble into complexes to carry out their function. In this work, we have created a new database (named ComSin) of protein structures in bound (complex) and unbound (single) states to provide a researcher with exhaustive information on structures of the same or homologous proteins in bound and unbound states. From the complete Protein Data Bank (PDB), we selected...
متن کاملThe relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking.
We investigate the extent to which the conformational fluctuations of proteins in solution reflect the conformational changes that they undergo when they form binary protein-protein complexes. To do this, we study a set of 41 proteins that form such complexes and whose three-dimensional structures are known, both bound in the complex and unbound. We carry out molecular dynamics simulations of e...
متن کاملSimulation of conformational changes occurring when a protein interacts with its receptor
In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subject...
متن کاملPredicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures
DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions. Accurate prediction of such target sequences, often represented by position weight matrices (PWMs), is an important step to understand many biological processes. Recent studies have shown that knowledge-based potential fun...
متن کاملEnsemble-based characterization of unbound and bound states on protein energy landscape.
Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping p...
متن کامل