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We use molecular dynamics simulations to study anomalous internal protein dynamics observed for the backbone atoms of hydrated elastin and hydrated myoglobin in the picoseconds and nanoseconds regimes. The anomalous dynamics manifests itself in a sublinear increase of the atomic mean square displacements and in a power-law or logarithmic-like decay of correlation functions. We find that several, but not all, observations can be described in the frameworks of rugged potential-energy landscape and fractional Fokker-Planck approaches, in particular, a fractional Ornstein-Uhlenbeck process. Furthermore, mode-coupling theory allows us to rationalize findings at ambient temperatures, but there are deviations between theoretical predictions and simulation results related to the anomalous dynamics at cryogenic temperatures. We argue that the observations are consistent with a scenario where a broad β-relaxation peak shifts through the picoseconds and nanoseconds regimes when cooling from 300 to 200 K, say. Inspection of trajectories of consecutive nitrogen atoms along the protein backbone reveals that correlated forward-backward jumps, which exhibit a substantial degree of cooperativity, are a key feature of the anomalous dynamics.

Backbone ( 15 N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives 15 N relaxation in such systems, i.e., how different forms of motion contribute to the measurable relaxation rates. To address this problem, we have investigated, both experimentally and via molecular dynamics simulations, the dynamics of a 26-residue peptide imitating the N-terminal portion of the histone protein H4. One part of the peptide was found to be fully flexible, whereas the other part features some transient structure (a hairpin stabilized by hydrogen bonds). The following motional modes proved relevant for 15 N relaxation. 1) Sub-picosecond librations attenuate relaxation rates according to S 2 $0.85-0.90. 2) Axial peptide-plane fluctuations along a stretch of the peptide chain contribute to relaxation-active dynamics on a fast timescale (from tens to hundreds of picoseconds). 3) 4/j backbone jumps contribute to relaxation-active dynamics on both fast (from tens to hundreds of picoseconds) and slow (from hundreds of picoseconds to a nanosecond) timescales. The major contribution is from polyproline II (PPII) 4 b transitions in the Ramachandran space; in the case of glycine residues, the major contribution is from PPII 4 (b) 4 rPPII transitions, in which rPPII is the mirror-image (right-handed) version of the PPII geometry, whereas b geometry plays the role of an intermediate state. 4) Reorientational motion of certain (sufficiently long-lived) elements of transient structure, i.e., rotational tumbling, contributes to slow relaxation-active dynamics on $1-ns timescale (however, it is difficult to isolate this contribution). In conclusion, recent advances in the area of force-field development have made it possible to obtain viable Molecular Dynamics models of protein disorder. After careful validation against the experimental relaxation data, these models can provide a valuable insight into mechanistic origins of spin relaxation in disordered peptides and proteins.

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

The transfer matrix method is used to simulate the magneto-optic surface plasmon resonance (MOSPR) of Au/Co/Au trilayer systems focused on the magneto-optic activity in transverse configuration. The results show a strong thickness dependence of the normalized difference of reflectivity at opposite directions of the magnetization (d-signal) and a strong change of the d-signal with the refractive index n of the biologically active layer. Within a range of the refractive index typically covered by a commercial SPR biosensor (n ¼ 1:33À1:40), the magnitude of the d-signal of an Au(10:75 nm)/Co(6 nm)/Au(20:25 nm) trilayer decreases from small to large n by a factor > 63. This finding demonstrates that the enhanced sensitivity of an MOSPR biosensor can be exploited only by defined thicknesses of the metal layers for distinct refractive index regions.