Myoglobin dynamics

The myoglobin dynamics near 200 K have been the subject of considerable investigation. There have been many experiments show a... 

To provide an understanding of the importance of solvent mobility and the intrinsic protein energy surface, an MDS of proteins and surrounding solvent molecules at different temperatures has been performed. The simulation of myoglobin dynamics showed that solvent mobility is the dominant factor in determining protein atomic fluctuations above 180 K (Vitkup et ah, 2000). The drastic effects of water molecule dynamics on the intramolecular motion of RNase and xylase was demonstrated in recent computer simulation studies (Reat et al., 2000 Tarek et al, 2000). Extensive simulations were carried out to identify the time-scale of water attachment to lysozyme (Steprone et... 

Lim, M. Jackson, T. A. Anfinrud, P. A., Femtosecond near-lR ahsorhance study of photoexcited myoglobin Dynamics of electronic and thermal relaxation. J. Phys. Chem. 1996, 100, 12043-12051. 

Picosecond TR of carbonmonoxy Coo A (a CO-sensing transcriptor activator) shows vFe-His at 211 cm" immediately after photolytic CO-loss. vFe-N(His) is at 231 cm" in cytochrome d from Alcaligentes xylosoxidansP Ultrafast time-resolved IR was used to probe myoglobin dynamics via vFe-His This mode was seen at 244 cm" in the resonance Raman spectrum of the ferrous form of flavohaemoglobin from E. coli and at 211 cm" for the SoxB-type cytochrome c oxidase from Bacillus stearothermophilusP ... 

Rector K D, Rella C W, Hill J R, Kwok A S, Sligar S G, Chien E Y T, DIott D D and Fayer M D 1997 Mutant and wild-type myoglobin-CO protein dynamics vibrational echo experiments J. Phys. Chem. 

Hermans, J., Subramaniam, S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr. J. Chem. 27 (1986) 225-227... 

Fiber R and M Karplus 1990. Enhanced Sampling in Molecular Dynamics Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon Monoxide Diffusion through Myoglobin. Journal of the American Chemical Society 112 9161-9175. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

A typical TIC chromatogram from an analysis of peptides resulting from enzymatic digest of myoglobin. The peaks represent individual peptides eluting from an LC column and being mass measured by a spectrometer coupled to it through a dynamic-FAB inlet/ion source. 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Quasielastic (Rayleigh) scattering of the 46.5 keV Mossbauer radiation was used to examine the liquid dynamics of glycerol [245, 246] and the harmonic vibrations of the nonhydrogen atoms in polycrystalline myoglobin [247] as a function of temperature. The y-quanta emitted by the Mossbauer source are... 

Li TP, Hassanali AA, Singer SJ (2008) Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer. J Phys Chem B 112(50) 16121-16134... 

Elber, R. Karplus, M., Enhanced sampling in molecular-dynamics - use of the time-dependent Hartree approximation for a simulation of carbon-monoxide diffusion through myoglobin, J. Am. Chem. Soc. 1990,112, 9161-9175... 

H. Frauenfelder, B.H. McMahon, R.H. Austin, K. Chu, and J.T. Groves, The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl. Acad. Sci. 98, 2370(2001). 

Applications of Car-Parrinello Molecular Dynamics in Biochemistry - Binding of Ligands in Myoglobin... 

Finally, we note that low-temperature crystallographic studies have been carried out on one nucleic acid, the 5-DNA dodecamer whose room-temperature structure was solved in Dickerson s laboratory (Dickerson, 1981). Refinement at 16 K revealed a large overall drop in B, but some of the atoms in the molecule still had very large B-factors even at this very low temperature. These large residual mean-square displacements were interpreted as demonstrating the presence of static disorder however, by analogy with the results on myoglobin, a disorder which is dynamic at room temperature but becomes frozen into a static distribution at low temperature is also consistent with the observations. It is also possible that the disorder in these atoms is dynamic even at 16 K this point has been considered by Hartmann et al. (1982). 

The first electrochemical studies of Mb were reported for the horse heart protein in 1942 (94) and subsequently for sperm whale Mb (e.g., 95) through use of potentiometric titrations employing a mediator to achieve efficient equilibriation of the protein with the electrode (96). More recently, spectroelectrochemical measurements have also been employed (97, 98). The alternative methods of direct electrochemistry (99-102) that are used widely for other heme proteins (e.g., cytochrome c, cytochrome bs) have not been as readily applied to the study of myoglobin because coupling the oxidation-reduction eqiulibrium of this protein to a modified working electrode surface has been more difficult to achieve. As a result, most published electrochemical studies of wild-type and variant myoglobins have involved measurements at eqiulibrium rather than dynamic techniques. 

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