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elNémo examples



Application of NMA to molecular replacement


On the potential of normal mode analysis for solving difficult molecular replacement problems

Here we show how normal mode analysis can be used to phase X-ray crystallographic data by molecular replacement when the original templates fail to give a solution. Note the gain of 6 percent points and more in the free r-factor, bringing it down well below the noise threshold of about 50!
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Maltodextrin binding protein HIV-1 protease Glutamine binding protein

These examples constitute the supplementary on-line material for: Suhre, K. & Sanejouand, Y.H., On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004
Copyright © International Union of Crystallography



Prediction of membrane channel opening and closure


E. coli membrane channel protein TolC (1ek9)

Here we model the putative TolC opening/closing of the outer-membrane part of TolC (beta-barrel). TolC is a homo-trimer. Each monomer is indicated by a separate color (blue, white, red:-) The animation follows the fifth lowest frequency mode (11) with an equal perturbation in both directions from the crystallographic state. See how the channel exit opens and closes!
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TolC from the side TolC viewed inside-out View into TolC


E. coli membrane associated protein TolB (1crz)

This eample shows how the periplasmic domain of TolB (red) might act as a lid on the membrane bound beta-barrel (blue). Watch the channel in the middle of the blue domain being covered by the red lid! This movement follows the second lowest frequency normal mode (mode 8). Note that the protein distortion may appear somewhat "unrealistic" since the movement applied here "overstresses" the linear perturbation that is assumed in any harmonic oscillator.
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TolB viewed from outside the cell TolB from the side TolB seen from a periplasmic position


All images were produced with VMD using the Tachyon ray tracer. Surface plots were made using MSMS via the VMD interface.



If you find results from this site helpful for your research, please cite one of our papers:

elNémo is maintained by Yves-Henri Sanejouand.
It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: 20 June 2014.