Dataset Information

Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations.

ABSTRACT: In the present work, the kinetic intermediates of holo- and apo-myoglobin were studied by correlating the ion-neutral collision cross section and time resolved H/D back exchange rate simultaneously in a trapped ion mobility spectrometer coupled to a mass spectrometer (HDX-TIMS-MS). The high mobility resolution of the TIMS cell permitted the observation of multiple IMS bands and complementary molecular dynamics simulations resulted in the assignment of candidate structures for each experimental condition studied (e.g., holo [M?+?8H](+8)-[M?+?9H](+9) and apo [M?+?9H](+9)-[M?+?19H](+19)). Inspection of the kinetic intermediates suggests that the tertiary structure of apomyoglobin unfolds quickly upon the loss of the Fe protoporphyrin IX that stabilizes the interactions between the A, G, and H helices. In the absence of the porphyrin heme, the apomyoglobin unfolds to Xn kinetic intermediates that vary in the extent of unfolding as a result of the observed charge state.

SUBMITTER: Schenk ER

PROVIDER: S-EPMC4402236 | biostudies-other | 2015 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations.

Schenk Emily R ER Almeida Raybel R Miksovska Jaroslava J Ridgeway Mark E ME Park Melvin A MA Fernandez-Lima Francisco F

Journal of the American Society for Mass Spectrometry 20150218 4

In the present work, the kinetic intermediates of holo- and apo-myoglobin were studied by correlating the ion-neutral collision cross section and time resolved H/D back exchange rate simultaneously in a trapped ion mobility spectrometer coupled to a mass spectrometer (HDX-TIMS-MS). The high mobility resolution of the TIMS cell permitted the observation of multiple IMS bands and complementary molecular dynamics simulations resulted in the assignment of candidate structures for each experimental c ...[more]

PMID: 25690175

Similar Datasets

Project description:The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 ?s. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex.

Dataset Information

Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations.

Publications

Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets