Conformational substates and motions in myoglobin. External influences on structure and dynamics

Abstract

Myoglobin, a simppe dioxygen-storage protein, is a good laboratory for the investigation of the connection between protein structure, dynamics, and function. Fourier-transform infrared spectroscopy on carbon-monoxymyoglobin (MbCO) shows three major CO bands. These bands are excellent probes for the investigation of the structure-function relationship. They have different CO binding kinetics and their CO dipoles form different angles with respect to the heme normal, implying that MbCO exists in three major conformational substates, A0, A1, and A3. The entropies and enthalpies of these substates depend on temperature above approximately 180 K and are influenced by pH, solvent, and pressure. These results suggest that even a protein as simple as Mb can assume a small number of clearly different structures that perform the same function, but with different rates. Moreover, protein structure and dynamics depend strongly on the interaction of the protein with its environment.

Ultrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

“…5,26,27 The A 0 peak, the smallest of the three features at room temperature and neutral pH, is believed to arise from configurations in which the ligand interacts most weakly with H64 because the distal histidine is swung out of the pocket. [36][37][38][39]56 As has been discussed in detail previously 5,8,[57][58][59] Figure 1 suggests that the substitution of the distal histidine (H64) by a valine spectroscopically mimics the A 0 state of wtMbCO.…”

Cytochrome c552Mutants: Structure and Dynamics at the Active Site Probed by Multidimensional NMR and Vibration Echo Spectroscopy

“…The red shifting of the CO stretching frequency of Ht-M61A/Q64N relative to Ht-M61A is reminiscent of the IR spectrum of aqueous MbCO, which exhibits three primary CO stretching peaks corresponding to three structurally distinct conformational substates. 39,51,56,[62][63][64][65][66] The A 0 band (1965 cm -1 ) is attributed to a conformation in which the distal histidine (His64) is positioned out of the heme pocket, 51,[67][68][69][70][71] while the A 1 (1944 cm -1 ) and A 3 (1938 cm -1 ) bands arise from the distal histidine being localized in the heme pocket in two distinct orientational geometries. 39,72 In the case of MbCO, the inclusion of a polar, hydrogen-bond-donating residue inside the heme pocket results in a spectral shift of the CO stretch to lower frequencies.…”

Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates

“…The most dramatic of these evidences is that below Ϸ200 K the reactions that follow photodissociation of the CO-myoglobin complex cannot be described by conventional kinetics that would arise from a single barrier. Instead, the time course follows a nonexponential path that suggests an ensemble of barriers, and from its analysis it was concluded (6)(7)(8)(9) that the protein, like glasses and spin glasses, assumes a large number of slightly differing conformational substates. At ambient temperature, these substates rapidly equilibrate to produce a thermally averaged homogeneous state, but at cryogenic temperatures they are distinct and noninterconvertible.…”