Mechanism of the unfolding of transmembrane alpha-helical segment (1-36)-bacteriorhodopsin studied by molecular dynamics simulations

Article Abstract:

A study investigated the mechanism of the unfolding of the first transmembral segment 1-26 bacteriorhodopsin using molecular dynamics simulations with an explicit representation of a chloroform/methanol mixture and several Langevin dynamics simulations. Analysis revealed that the unfolding of alpha-helix proceeds through the formation of local disturbed regions and is stabilized by pi-helical hydrogen bonds (pi-bulges) in the central part of the peptide. Other results are discussed.

Case studies, Membrane proteins, Proteins, Protein folding, Molecular dynamics, Bacterial proteins, Protein denaturation

---

Proton transfer and associated molecular rearrangements in the photocycle of photoactive yellow protein: Role of water molecular migration on the proton transfer reaction

Article Abstract:

The quantum mechanical/ molecular mechanical (QM/MM) calculations are used to study the mechanism of the proton transfer and the molecular rearrangements after the photoisomerization of the chromophore in the photocycle of the photoactive yellow protein. The analysis shows that the water molecular migration plays an important role in the reaction, as it propagates the proton transfer by the hydrogen bond rearrangement.

Quantum theory, Quantum mechanics, Protein research, Rearrangements (Chemistry)

---

Analysis of the bacteriorhodopsin photocycle by singular value decomposition with self-modeling: a critical evaluation using realistic simulated data

Article Abstract:

Through experimental investigations, it is shown that data matrices consisting of sample optical absorption as a function of wavelength and another variable, such as time, are decomposable using known matrix algebraic methods. The connection of the two decompositions is explored with reference to the problem of the bacteriorhodopsin photocycle.

Chemistry, Analytic, Analytical chemistry, Chemical properties

Similar abstracts:

• Abstracts: Structural disorder of the CD3[zeta] transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations
• Abstracts: Binding of calcium and other metal ions to the EF-hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations
• Abstracts: Dynamics of water in the hydration shells of [C.sub.60]: molecular dynamics simulation using a coarse-grained model
• Abstracts: Influence of the percolation network geometry on electron transport in dye-sensitized titanium dioxide solar cells
• Abstracts: A systematic study of the structure and bonding of halogens on low-index transition metal surfaces. Density-dependent equations of state for metal, nonmetal, and transition states for compressed mercury fluid

This website is not affiliated with document authors or copyright owners. This page is provided for informational purposes only. Unintentional errors are possible.