Pymol analysis shows the formation of multiple h-bond with donor nitrogen atom (in figure). Similarly, there have been instances where polar oxygen participates in multiple h-bonds. Kindly explain chemistry behind this phenomenon? How does one interpret this using the donor-acceptor concept of h-bonding ? Can the two h-bond occur simultaneously (as in figure) ?
note: the donor -H-acceptor concept is understood already for single acceptor and donors.
No, these two hydrogen bonds cannot exist simultaneously, each hydrogen can only participate in one hydrogen bond at any moment. However, experimental structures show a time-average over the conformational space of a protein accessible at the temperature of the experiment. Your image shows two hydrogen bonds with not quite ideal geometry -You can well imagine that by a slight change of the chi1 torsion angle of Asp33, you can either achieve a more ideal hydrogen bond to either one or the other of the side chain oxygens. However, since both conformations are probably populated fairly equally, you see an averaged positioning of the COO- and two potential hydrogen bonds.
All you never wanted to know about hydrogen bonds:
http://evans.rc.fas.harvard.edu/pdf/smnr_2009_Kwan_Eugene.pdf
No, these two hydrogen bonds cannot exist simultaneously, each hydrogen can only participate in one hydrogen bond at any moment. However, experimental structures show a time-average over the conformational space of a protein accessible at the temperature of the experiment. Your image shows two hydrogen bonds with not quite ideal geometry -You can well imagine that by a slight change of the chi1 torsion angle of Asp33, you can either achieve a more ideal hydrogen bond to either one or the other of the side chain oxygens. However, since both conformations are probably populated fairly equally, you see an averaged positioning of the COO- and two potential hydrogen bonds.
All you never wanted to know about hydrogen bonds:
http://evans.rc.fas.harvard.edu/pdf/smnr_2009_Kwan_Eugene.pdf
Professor Annemarie Honegger
Does the terms "hydrogen bonds" and "polar contacts" mentioned in PyMOL are same?
Can you please explain me this?
"Polar contacts" is a simple approximation to identify potential hydrogen bonds that also works reasonably well with objects that do not contain explicit hydrogen atoms. Experimental PDB files usually do contain hydrogen atom coordinates, since hydrogens are not visible in electron density at the typical resolutions you get in protein crystallography. There are better ways to identify H-bonds in PyMOL, by using predicted hydrogen positions. See https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts. You may alter the stringency of detection by altering the distance cut-offs.
Where it is really critical (discussing the role of HBonds in active sites, involving His side chains, non-neutral pH, ligands) you may want to look at a more detailed analysis of the pH dependent protonation states and the influence of the environment on the pKa pf protonizable groups, e.g in APBS (pdbpqr) or even more sophisticated external programs, and also do some analysis and optimization e.g. checking whether Asn and Gln side chain rotamers are correct (You cannot determine from electron density alone which is the oxygen and which the hydrogen atom in their side chain). In your example, a careful energy minimization of your system in a suitable program would probably have resolved the ambiguous hydrogen bond into one of the two conformations averaged in the experimental structure.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Atomic, Molecular and Optical Physics
- Atoms