I agree with Herman, and would like to add to his list of explanations why density may not be observed. It is possible that the compound binding to your protein simply doesn't contain those bits without density. I have known cases where the compound in the vial does not match the label on the vial. In addition I've had cases where bits were cleaved from the compound at some point before binding. Sometimes you can't see it because it simply isn't there.
Dale Tronrud On 08/24/11 01:02, herman.schreu...@sanofi-aventis.com wrote: > Dear Francis, > > Although I am a member of the "never truncate a disordered side chain" > camp, I think for ligands it is quite a different story. > > For me a random disordered lysine on the protein surface is completely > uninteresting, except if one wants to examine the electrostatic surface. > A non-expert end-user is either not aware of truncations and ends up > with wrong results, or has to laboriously put back the side chains the > crystallographer laboriously had removed before. > > However, a bound ligand is very different. Determining its binding mode > is usually THE goal of the study and every hydrogen bond with the > protein is discussed in great detail. Chemists and modelers use these > structures to design more potent ligands and theoreticians use these > structures to improve their force fields. Also biochemists and > biologists may be tempted to draw all kind of conclusions about > important interactions where in fact there may be none. > > Especially when the ligand has designed to make a certain interaction > and in absence of experimental data you model the same interaction, the > chemist and modeler will be very happy and immediately jump on it to > design more of the same. I have seen many cases where theoretically, the > ligand would be able to make a wonderful interaction with the protein, > but that flexible side chains on the protein or ligand just did not want > to give up their freedom (entropy) to become locked in such an > interaction. Not seeing flexible parts of a ligand is not resolution > dependent. At higher resolution you see even less of the flexible parts > since there is less model bias possible. > > So my approach: If there is weak or even very weak but real density for > the flexible parts of the ligands (I usually scroll down to 0.6 sigma), > I build the part, or build 2 or 3 conformations in case of discrete > disorder. Here I think I take more liberties then most of my colleagues. > > > However, if no convincing (weak) density is present above the noise > level I remove the undefined parts and do not even consider to leave > them in with occupancy zero. They will appear on the display of the end > user and give the impression that an interaction is present where there > is none. If the ligand would make the interaction, it would be visible > in the electron density maps. > > My choice is definitively [1], but before rushing to get more > experimental data I would first put some brain power in it: maybe it is > better for binding not to fix certain flexible side chains (less entropy > loss), flexibility may endow the protein with broader substrate/ligand > specificity, there may be crystal contacts which prevent the correct > binding mode, components of the crystallization buffer may interfere > with proper ligand binding etc. > > Best, > Herman > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Francis E Reyes > Sent: Tuesday, August 23, 2011 8:37 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Modeling ligands in binding pockets when the density > is weak. > > Seems to be a quiet day on the BB, so I propose this question: > > > Suppose you have a ligand in the binding pocket and some mediocre data > (3 A or so), the 'core' of the ligand is well defined in 2Fo-Fc map > using the model phases of your protein, however there are 'chains/tails' > of the ligand which are not. Composite omit or simulated annealing omit > maps do not produce density for these 'chains' > > The question here is how the chains/tails should be modeled (if at all). > > > > [1] Model in the core, but remove the atoms for the chains (and > conclude the diffraction data do not support interactions with the > protein and subsequent experiments are needed (higher resolution data, > biochemical data, etc)). > > or > > [2] Model in the chains/tails noting that potential hydrogen bond > donors/acceptors on the protein are within hydrogen bonding distance to > the chains/tails. You do this and subsequent refinement still does not > produce the expected density for the chains. > > > or > > [3] Your solution here. > > > > If this situation has been discussed before, please let me know . > > F > > --------------------------------------------- > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder
