Acquisition and Interpretation of Hydrogen Exchange Data from Peptides, Polymers, and Proteins

Calcium-induced changes in calmodulin structural dynamics and thermodynamics

“…The fraction of un-exchanged amide proton, F, was calculated at various time intervals using Eq. (1) [24].…”

Structural dynamic and thermodynamic analysis of calcineurin B subunit induced by calcium/magnesium binding

“…One minute after the addition of D 2 O, single-beam spectra were recorded using kinetic scanning mode. The spectra were recorded at 1, 2, 3, 4, 5, 6,7,8,9,10,15,20,30,40,50, 60, 90, 120, 150, and 180 min. An 8-scan interferogram was collected at each time interval between 1 and 10 min, whereas a 64-or 128-scan interferogram was recorded at each time interval between 15 and 90 min and longer.…”

Perturbations in protein dynamics associated with ligand binding to the blood coagulation enzymes thrombin and Factor XIII.

“…The method exploits differences in the rate of chemical exchange for backbone amide protons in proteins. Half-lives ranging from milliseconds to years is possible for amide protons in proteins due to secondary and tertiary structure, protein flexibility, and protein mobility (220)(221)(222)(223). Equation 4 relates the rate of chemical exchange to the concentration The rate of chemical exchange is highly dependent on pH and temperature.…”

“…At a pH of 2.5, the rate of proton exchange is at a minimum. More acidic conditions (pH < 2.5) lead to catalysis occurring through proton addition and a more basic environment (pH > 2.5) promotes proton abstraction (220). In addition, exchange is much slower at 0 °C than at 25 °C.…”

“…A few factors influence the rate of backbone amide proton exchange that are intrinsic to the protein (220)(221)(222)(223). First, the degree of solvent accessibility for the proton is an important consideration.…”