Search results for "Elastic network"
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On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
2012
Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a…
Terahertz Absorption change in Photosynthetic Reaction Center upon photoactivation
2012
Photosynthetic reaction center is a membrane protein which plays an important role in converting solar energy into chemical energy. Upon continuous illumination a charge separation occurs within the protein which is stable for several seconds [1]. The stability of this state is very important to protect the protein against the release of excess heat and an instable radical due to charge recombination. Absorption of terahertz radiation corresponds to the excitation of large vibrations in the protein and is thus suitable for studying its different dynamical states. Here we recorded terahertz absorption spectra of the dark and illuminated state of reaction centre from the purple membrane bacte…