Normal mode analysis TSD

The journal for this task can be found here.

Introduction

For this task 2gk1 is chosen as reference structure since it contains a ligand similar to the native one and therefore allows to easily observe the effect the presence of the ligand exerts on the normal modes.

Elastic network models

elNemo

elNemo is available only as a webserver and employs elastic network models <ref name="elnemo">Suhre,K. and Sanejouand,Y.-H. (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic acids research, 32, W610-4.</ref>. Atoms considered are limitied to only C-alpha atoms and using a technique termed 'rotation-translation-block', which groups residues into so-called super-residues, there are hardly any restrictions on the input protein's size. The latter approximation is reported to have only little effect on low frequency modes, and the number of residues grouped together is chosen depending on the protein's size. Therefore, small proteins may only contain one residue per super-residue.

Various measurements are reported as results. For each mode, a collectivity can be calculated that expresses how many atoms are affect by the motion of the mode. The larger the value the more atoms are significantly affected.
Additionally, B-factors are calculated from the normal mode and scaled to the observed values, reported in the PDB file. From this a global correlation value is calculated which describes how well the current mode approximates the general global flexibility of the input structure.
For any given mode there is also a map of distance fluctuations created that shows the movement of each residue during the movement of the mode. For this calculation the two most extreme conformations in the mode are used.
Furthermore, the mean square displacement, describing the distance travelled by an atom, is calculated for every C-alpha atom in a mode. This different from the distance fluctuations before, since here, for every time step, the absolute distances are summed up, resulting in the actual distance travelled, which is a different type of information <ref name="msd1"> Weisstein, Eric W. "Mean Square Displacement." From MathWorld--A Wolfram Web Resource. http://mathworld.wolfram.com/MeanSquareDisplacement.html </ref><ref name="msd2">http://isaacs.sourceforge.net/phys/msd.html</ref>.

What information do the different servers provide?

Normal Modes

   How are the normal modes calculated, that is from which part of the structure? How many normal modes could in principle be calculated for your protein without any cutoff.
   Visualize the modes (provided by server or using for example PyMol or VMD) and describe what movements you observe: hinge-movement, “breathing”…
   Which regions of your protein are most flexible, most stable?
   Can you identify domains for your protein? Compare to the CATH, SCOP and Pfam domains of your protein.
   For WEBnm@ try the amplitude scaling and vectors option.
   Try the comparison/upload of second structure option, if: (i) you have PDB structures in different conformations or (ii) your protein has a bound ligand. Then either upload a structure with and one without the ligand, or delete the ligand in your structure. Note: Due to the force field that considers only C_alpha atoms, only changes in the backbone will give results. The model does not resolve changes in side-chain positions or SNPs.

Comparison

   Can you observe notable differences between the normal modes calculated by the different servers?

Comparison to Molecular Dynamics

   When your MD simulations are finished, compare the lowest-frequency normal modes with your MD simulation using visualization software, e.g. PyMol or VMD. Can you observe different movements or similar dynamics? If possible, compare an overlay of the lowest-frequency modes to your MD simulation. You can superimpose the normal modes for example in VMD.
   What are the advantages and disadvantages of NMA compared to MD?