TY - JOUR
T1 - An atomistic structure of ubiquitin +13 relevant in mass spectrometry
T2 - Theoretical prediction and comparison with experimental cross sections
AU - Goldstein, Moshe
AU - Zmiri, Liron
AU - Segev, Elad
AU - Wyttenbach, Thomas
AU - Gerber, R. Benny
PY - 2014/6/15
Y1 - 2014/6/15
N2 - The 3D structure of protein ions in the gas phase is presently not obtainable from experiment in atomic detail. Here we use a theoretical approach to determine the 3D structure of ubiquitin +13 (UBQ +13) in the absence of solvent. Global minimization of the UBQ +13 force field within the recently developed DEEPSAM algorithm yields a nearly linear overall geometry. Four helical segments are found in this full atomistic structure - three of them are 310-helices and one is an α-helix. The protein cross section computed for the predicted structure is in excellent accord with ion mobility experimental results of UBQ +13. This suggests that computational structure predictions together with (theoretical and experimental) cross section values can serve as a useful tool for determining the atomistic structures of charged proteins in the gas phase.
AB - The 3D structure of protein ions in the gas phase is presently not obtainable from experiment in atomic detail. Here we use a theoretical approach to determine the 3D structure of ubiquitin +13 (UBQ +13) in the absence of solvent. Global minimization of the UBQ +13 force field within the recently developed DEEPSAM algorithm yields a nearly linear overall geometry. Four helical segments are found in this full atomistic structure - three of them are 310-helices and one is an α-helix. The protein cross section computed for the predicted structure is in excellent accord with ion mobility experimental results of UBQ +13. This suggests that computational structure predictions together with (theoretical and experimental) cross section values can serve as a useful tool for determining the atomistic structures of charged proteins in the gas phase.
KW - Highly charged protein
KW - Mass spectrometry
KW - Theoretical prediction
UR - http://www.scopus.com/inward/record.url?scp=84901276494&partnerID=8YFLogxK
U2 - 10.1016/j.ijms.2014.04.013
DO - 10.1016/j.ijms.2014.04.013
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AN - SCOPUS:84901276494
SN - 1387-3806
VL - 367
SP - 10
EP - 15
JO - International Journal of Mass Spectrometry
JF - International Journal of Mass Spectrometry
ER -