We study the reversible folding/unfolding of short Ala and Gly-based peptides by molecular dynamics simulations of all-atom models in explicit water solvent. A kinetic analysis shows that the formation of a first alpha-helical turn occurs within 0.1-1 ns, in agreement with the analyses of laser temperature jump experiments. The unfolding times exhibit Arrhenius temperature dependence. For a rapidly nucleating all-Ala peptide, the helix nucleation time depends only weakly on temperature. For a peptide with enthalpically competing turn-like structures, helix nucleation exhibits an Arrhenius temperature dependence, corresponding to the unfolding of enthalpic traps in the coil ensemble. An analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occur predominantly through breaking of hydrogen bonds at the helix ends, particularly at the C-terminus. The temperature dependence of the transition-state ensemble and the corresponding folding/unfolding pathways illustrate that folding mechanisms can change with temperature, possibly complicating the interpretation of high-temperature unfolding simulations. The timescale of helix formation is an essential factor in molecular models of protein folding. The rapid helix nucleation observed here suggests that transient helices form early in the folding event.

leads to changes in protein dynamics, followed by binding of the cognate G-protein (transducin) initiating the biological signaling. Present X-ray crystallographic structures do not reveal changes in protein dynamics which are the key for understanding the activation mechanism. Here we compare an energy landscape model (ELM) and spatial motion model (SMM) analysis of both elastic and quasielastic neutron scattering (QENS) data to explain regulation of integral membrane protein mobility by the retinal cofactor of rhodopsin. Mean-square displacements calculated from elastic incoherent neutron scattering (EINS) are consistent with a dynamical transition as observed for globular proteins. In the SMM analysis the quasielastic spectrum is dissected into an elastic peak due to quasistatic atoms, and quasielastic wings due to homogenous line broadening from the mobile atoms in the protein. By contrast, the ELM adopts a wave-mechanical approach and describes the QENS spectrum in terms of inhomogeneous lines due to the various conformational substates of the protein [2]. Application of mode-coupling theory as developed for glass-forming liquids to SMM analysis of the QENS spectra reveals a slowing down of picosecond-nanosecond dynamics in the b-relaxation region for ligand-free opsin versus dark-state rhodopsin. Alternatively, ELM analysis reveals that the ensemble of conformational substates in opsin is smaller versus the dark state. The results are consistent with increased local crowding due to a more collapsed protein structure in ligand-free opsin versus the dark-state rhodopsin. A novel powdered GPCR preparation method together with the QENS technique uncovers changes in structural fluctuations governed by retinal cofactor of rhodopsin.[1] A.V.

We study the dynamical fluctuations of horse heart cytochrome c by molecular dynamics (MD) simulations in aqueous solution, at four temperatures: 300 K, 360 K, 430 K, and 550 K. Each simulation covers a production time of at least 1.5 nanoseconds (ns). The conformational dynamics of the system is analyzed in terms of collective motions that involve the whole protein, and local motions that involve the formation and breaking of intramolecular hydrogen bonds. The character of the MD trajectories can be described within the framework of rugged energy landscape dynamics. The MD trajectories sample multiple conformational minima, with basins in protein conformational space being sampled for a few hundred picoseconds. The trajectories of the system in configurational space can be described in terms of diffusion of a particle in real space with a waiting time distribution due to partial trapping in shallow minima. As a consequence of the hierarchical nature of the dynamics, the mean square displacement autocorrelation function, <|x(t) - x(0)|2>, exhibits a power law dependence on time, with an exponent of around 0.5 for times shorter than 100 ps, and an exponent of 1.75 for longer times. This power law behavior indicates that the system exhibits suppressed diffusion (sub-diffusion) in sampling of configurational space at time scales shorter than 100 ps, and enhanced (super-diffusion) at longer time scales. The multi-basin feature of the trajectories is present at all temperatures simulated. Structural changes associated with inter-basin displacements correspond to collective motions of the Omega loops and coiled regions and relative motions of the alpha-helices as rigid bodies. Similar motions may be involved in experimentally observed amide hydrogen exchange. However, some groups showing large correlated motions do not expose the amino hydrogens to the solvent. We show that large fluctuations are not necessarily correlated to hydrogen exchange. For example, regions of the proteins forming alpha helices and turns show significant fluctuations, but as rigid bodies, and the hydrogen bonds involved in the formation of these structures do not break in proportion to these fluctuations. Proteins 1999;36:175-191. Published 1999 Wiley-Liss, Inc.

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