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#5138 01/21/05 11:55 PM
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Jason Offline OP
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Hello All,

I am rather new to Charmm and have a question about which neutral histidine residue is better, HSE or HSD. I imagine the answer is something like, it depends on the situation. I am trying to model human fibrinogen. I would appreciate any answer, even if it is it depends.

Thanks,

Jason Hower
U of Washington Chemical Engineering
Charmm user since Jan. 2005


Jason Hower University of Washington Dept. of Chemical Engineering
Jason #5139 01/22/05 05:41 AM
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Hi,
HSD and HSE, though both represents the neutral histidine but still they differ in the positioning of the H atom i.e. either delta or epsilon! So,my suggestion is to go back to the references and find out from the structure reported there for the fibrinogen model as to wheather histidine has a H on the delta or on the epsilon position! I am sure the 3D structure of the fibrinogen or related molecules must be known!
Pri...

mzzt #5140 01/22/05 08:39 PM
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rmv Online Content
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It's not so easy to answer that question, and the last I knew it's only been done unambiguously via NMR for a few enzyme systems. Most crystal structures are fits to e- density and refinement with a program like X-PLOR, and the His sidechain rotation can be subject to both the forcefield and uncertainities in the e- density. Still, it's not unreasonable to assume the crystal structure is correct, and then determine the protonation states by inspection. If either NE or ND of the His ring are suitably positioned to make a good hydrogen bond if protonated, then place the proton on that N atom.


Rick Venable
computational chemist

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rmv #5141 01/23/05 07:00 AM
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Thanks for your help! I will move forward again next week.


Jason Hower University of Washington Dept. of Chemical Engineering

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