scholarly journals Role of calcium in the conformational dynamics of factor XIII activation examined by hydrogen–deuterium exchange coupled with MALDI-TOF MS

2011 ◽  
Vol 512 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Ricky T. Woofter ◽  
Muriel C. Maurer
Keyword(s):  
Factor Xiii ◽  
Conformational Dynamics ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Hydrogen Deuterium ◽  
Tof Ms

scholarly journals Detection of Structural and Conformational Changes in ALS-Causing Mutant Profilin1 With Hydrogen/Deuterium Exchange Mass Spectrometry and Bioinformatics Techniques

2021 ◽  
Author(s):  
Ahmad Shahir Sadr ◽  
zahra abdollahpour ◽  
Atousa Aliahmadi ◽  
Changiz Eslahchi ◽  
Mina Nekouei ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Amino Acid ◽  
Conformational Changes ◽  
Docking Simulation ◽  
Hydrogen Deuterium Exchange ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Hydrogen Deuterium ◽  
Tof Ms

Abstract The hydrogen/deuterium exchange (HDX) is a reliable method to survey the dynamic behavior of proteins and epitope mapping. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a quantifying tool to assay for HDX in the protein of interest. We combined HDX-MALDI-TOF MS and molecular docking/MD simulation to identify accessible amino acids and analyze their contribution in the structural changes of profilin1 (PFN1). The molecular docking/MD simulations are computational tools for enabling the analysis of the type of amino acids that may be involved via HDX identified under the lowest binding energy condition. Glycine to Valine amino acid (G117V) substitution mutation is linked to amyotrophic lateral sclerosis (ALS). This mutation is found to be in the actin-binding site of PFN1 and prevents the dimerization/polymerization of actin and invokes a pathologic toxicity that leads to ALS. In this study, we sought to understand the PFN1 protein dynamic behavior using purified wild type and mutant PFN1 proteins. The data obtained from HDX-MALDI-TOF MS for PFN1WT and PFN1G117V at various time intervals, from seconds to hours, revealed multiple peaks corresponding to molecular weights from monomers to multimers. PFN1/Benzaldehyde complexes identified 20 accessible amino acids to HDX that participate in the docking simulation in the surface of WT and mutant PFN1. Consistent results from HDX-MALDI-TOF MS and docking simulation predict candidate amino acid(s) involved in the dimerization/polymerization of PFNG117V. This information may shed critical light on the structural and conformational changes with details of amino acid epitopes for mutant PFN1s’ dimerization, oligomerization, and aggregation.

scholarly journals Load-dependent destabilization of the γ-rotor shaft in FOF1 ATP synthase revealed by hydrogen/deuterium-exchange mass spectrometry

2016 ◽  
Vol 113 (9) ◽  
pp. 2412-2417 ◽  
Author(s):  
Siavash Vahidi ◽  
Yumin Bi ◽  
Stanley D. Dunn ◽  
Lars Konermann
Keyword(s):  
Mass Spectrometry ◽  
Molecular Motor ◽  
Conformational Dynamics ◽  
Bound State ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Membrane Bound ◽  
Deuterium Exchange Mass Spectrometry

FoF1 is a membrane-bound molecular motor that uses proton-motive force (PMF) to drive the synthesis of ATP from ADP and Pi. Reverse operation generates PMF via ATP hydrolysis. Catalysis in either direction involves rotation of the γε shaft that connects the α3β3 head and the membrane-anchored cn ring. X-ray crystallography and other techniques have provided insights into the structure and function of FoF1 subcomplexes. However, interrogating the conformational dynamics of intact membrane-bound FoF1 during rotational catalysis has proven to be difficult. Here, we use hydrogen/deuterium exchange mass spectrometry to probe the inner workings of FoF1 in its natural membrane-bound state. A pronounced destabilization of the γ C-terminal helix during hydrolysis-driven rotation was observed. This behavior is attributed to torsional stress in γ, arising from γ⋅⋅⋅α3β3 interactions that cause resistance during γ rotation within the apical bearing. Intriguingly, we find that destabilization of γ occurs only when FoF1 operates against a PMF-induced torque; the effect disappears when PMF is eliminated by an uncoupler. This behavior resembles the properties of automotive engines, where bearings inflict greater forces on the crankshaft when operated under load than during idling.

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