Limits...
Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

D'Atri V, Porrini M, Rosu F, Gabelica V - J Mass Spectrom (2015)

Bottom Line: The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data.Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)?Which one(s) can I apply to my systems?

View Article: PubMed Central - PubMed

Affiliation: Univ. Bordeaux, IECB, ARNA laboratory, Pessac, F-33600, France.

No MeSH data available.


Related in: MedlinePlus

Monitoring of ΩCALC of [(dTGGGGT)4 + 3 NH4]5- for four gas phase 500 ns MD replicas started from different time points of the solution molecular dynamics (MD): after (A) 1 ns, (B) 5 ns, (C) 10 ns, and (D) 50 ns of MD in solution. Red and grey line are to ΩCALC obtained by using EHSSrot-Siu and mobcal-He25, respectively. The black horizontal line indicates the average experimental value. The starting structures taken from the solution MD and the final structures of the MD simulations in gas phase are shown on the left and on the right, respectively. Furthermore, the ΩCALC of the starting structures and the final structures of the MD simulations in gas phase are indicated below each structure. (G4)4 refers to the ΩCALC calculated for the sole G-core (in orange on the molecular models), while (TG4T)4 refers to the ΩCALC calculated for the whole structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4440389&req=5

fig05: Monitoring of ΩCALC of [(dTGGGGT)4 + 3 NH4]5- for four gas phase 500 ns MD replicas started from different time points of the solution molecular dynamics (MD): after (A) 1 ns, (B) 5 ns, (C) 10 ns, and (D) 50 ns of MD in solution. Red and grey line are to ΩCALC obtained by using EHSSrot-Siu and mobcal-He25, respectively. The black horizontal line indicates the average experimental value. The starting structures taken from the solution MD and the final structures of the MD simulations in gas phase are shown on the left and on the right, respectively. Furthermore, the ΩCALC of the starting structures and the final structures of the MD simulations in gas phase are indicated below each structure. (G4)4 refers to the ΩCALC calculated for the sole G-core (in orange on the molecular models), while (TG4T)4 refers to the ΩCALC calculated for the whole structure.

Mentions: In helium, we measured ΩEXP,He = 787 ± 3 Å2 (average value ± standard deviation on 10 measurements) without the alternate gas option, and ΩEXP,He = 789.1 ± 1.6 Å2 (7) with the alternate gas option. Overall average is 788.0 ± 2.5 Å2, and a typical CCS distribution is shown in Fig.5D. The CCS peak resolution in helium is ∼55. For the same nucleic acid complex, Gidden et al. had reported an experimental CCS of 775 ± 15 Å2, [20] measured with a home-made, 5-cm-long drift tube.[34] The average helium experimental values differ by 1.5%. In nitrogen, we obtain ΩEXP,N2 = 1010 ± 2 Å2 (six experiments, see Fig.5E for a typical distribution) on both instrument configurations, and the CCS peak resolution is ∼90.


Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

D'Atri V, Porrini M, Rosu F, Gabelica V - J Mass Spectrom (2015)

Monitoring of ΩCALC of [(dTGGGGT)4 + 3 NH4]5- for four gas phase 500 ns MD replicas started from different time points of the solution molecular dynamics (MD): after (A) 1 ns, (B) 5 ns, (C) 10 ns, and (D) 50 ns of MD in solution. Red and grey line are to ΩCALC obtained by using EHSSrot-Siu and mobcal-He25, respectively. The black horizontal line indicates the average experimental value. The starting structures taken from the solution MD and the final structures of the MD simulations in gas phase are shown on the left and on the right, respectively. Furthermore, the ΩCALC of the starting structures and the final structures of the MD simulations in gas phase are indicated below each structure. (G4)4 refers to the ΩCALC calculated for the sole G-core (in orange on the molecular models), while (TG4T)4 refers to the ΩCALC calculated for the whole structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440389&req=5

fig05: Monitoring of ΩCALC of [(dTGGGGT)4 + 3 NH4]5- for four gas phase 500 ns MD replicas started from different time points of the solution molecular dynamics (MD): after (A) 1 ns, (B) 5 ns, (C) 10 ns, and (D) 50 ns of MD in solution. Red and grey line are to ΩCALC obtained by using EHSSrot-Siu and mobcal-He25, respectively. The black horizontal line indicates the average experimental value. The starting structures taken from the solution MD and the final structures of the MD simulations in gas phase are shown on the left and on the right, respectively. Furthermore, the ΩCALC of the starting structures and the final structures of the MD simulations in gas phase are indicated below each structure. (G4)4 refers to the ΩCALC calculated for the sole G-core (in orange on the molecular models), while (TG4T)4 refers to the ΩCALC calculated for the whole structure.
Mentions: In helium, we measured ΩEXP,He = 787 ± 3 Å2 (average value ± standard deviation on 10 measurements) without the alternate gas option, and ΩEXP,He = 789.1 ± 1.6 Å2 (7) with the alternate gas option. Overall average is 788.0 ± 2.5 Å2, and a typical CCS distribution is shown in Fig.5D. The CCS peak resolution in helium is ∼55. For the same nucleic acid complex, Gidden et al. had reported an experimental CCS of 775 ± 15 Å2, [20] measured with a home-made, 5-cm-long drift tube.[34] The average helium experimental values differ by 1.5%. In nitrogen, we obtain ΩEXP,N2 = 1010 ± 2 Å2 (six experiments, see Fig.5E for a typical distribution) on both instrument configurations, and the CCS peak resolution is ∼90.

Bottom Line: The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data.Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)?Which one(s) can I apply to my systems?

View Article: PubMed Central - PubMed

Affiliation: Univ. Bordeaux, IECB, ARNA laboratory, Pessac, F-33600, France.

No MeSH data available.


Related in: MedlinePlus