Origin of the anomalous diffusion observed by MD simulation at the protein-water interface

Bizzarri, Anna Rita; Rocchi, C.; Cannistraro, Salvatore

doi:10.1016/s0009-2614(96)01232-8

Cited by 49 publications

(51 citation statements)

References 30 publications

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“…The values of the calculated water self‐diffusion coefficient range from D = 1.44 × 10 −9 m 2 /s for a fit carried out over all the 520 ps MD simulation to D = 2.21 × 10 −9 m 2 /s for a fit carried out over the first 200 ps of trajectory. A similar behavior has been already reported and could be at the basis for the scattered D values reported in literature for water in hydrated protein systems (40–42). Indeed, a protein can influence the water mobility affecting its diffusion process, which cannot be described by Brownian dynamics.…”

Section: Resultssupporting

confidence: 89%

Molecular dynamics simulation of the antimicrobial salivary peptide histatin‐5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect

Iovino

Falconi

Marcellini

et al. 2001

The Journal of Peptide Research

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The results of 520 ps molecular dynamics simulation of histatin-5, a small peptide present in human saliva and possessing antimicrobial activity, dissolved in water and in 2,2,2-trifluoroethanol, are reported. The simulations indicate that histatin-5 is destabilized in water and begins to unfold after 250 ps, while in organic solvent it maintains a regular secondary structure throughout the trajectory. Analysis of the peptide-solvent hydrogen bonds indicates that 2,2,2-trifluoroethanol is a poorer proton acceptor than water. The fluorine atom of the alcohol is almost never engaged in a hydrogen bond and the organic solvent interacts mainly with the peptide through its hydroxyl group. For some residues analysis of the solvent residence time indicated longer values for 2,2,2-trifluoroethanol than for water. The most striking difference is related to the number of times the solvent enters and leaves the first coordination shell of the peptide. This value was more than one order of magnitude higher for water than for the alcohol, suggesting that this may be the main cause of alpha-helix destabilization perpetrated by water.

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Section: Resultssupporting

confidence: 89%

Molecular dynamics simulation of the antimicrobial salivary peptide histatin‐5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect

Iovino

Falconi

Marcellini

et al. 2001

The Journal of Peptide Research

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“…S6A). In general, after a few picoseconds, the MSD became proportional to t α (29). Linear dependence of the MSD on time (α = 1) is a signature of Brownian diffusive motion as observed for bulk water; α < 1 is a signature of anomalous "subdiffusion," which is characteristic of confined water and protein hydration water.…”

Section: Water Dynamics Within the Hourglass Deviates Dramatically Frommentioning

confidence: 81%

“…For the analysis of the NPT simulations, we stored the system coordinates every 10 ps, but this time interval is too long to reveal the details of water dynamics that occur on the picosecond timescale (29,30). Therefore, we carried out 40 NVE (constant number of particles N, volume V, and energy E) simulations of 50-ps length, saving configurations every 5 fs (Methods).…”

Section: Water Dynamics Within the Hourglass Deviates Dramatically Frommentioning

confidence: 99%

Anomalous behavior of water inside the SecY translocon

Capponi

Heyden

Bondar

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The heterotrimeric SecY translocon complex is required for the cotranslational assembly of membrane proteins in bacteria and archaea. The insertion of transmembrane (TM) segments during nascent-chain passage through the translocon is generally viewed as a simple partitioning process between the water-filled translocon and membrane lipid bilayer, suggesting that partitioning is driven by the hydrophobic effect. Indeed, the apparent free energy of partitioning of unnatural aliphatic amino acids on TM segments is proportional to accessible surface area, which is a hallmark of the hydrophobic effect [Öjemalm K, et al. (2011) Proc Natl Acad Sci USA 108(31):E359-E364]. However, the apparent partitioning solvation parameter is less than one-half the value expected for simple bulk partitioning, suggesting that the water in the translocon departs from bulk behavior. To examine the state of water in a SecY translocon complex embedded in a lipid bilayer, we carried out all-atom molecular-dynamics simulations of the Pyrococcus furiosus SecYE, which was determined to be in a "primed" open state [Egea PF, Stroud RM (2010) Proc Natl Acad Sci USA 107(40):17182-17187]. Remarkably, SecYE remained in this state throughout our 450-ns simulation. Water molecules within SecY exhibited anomalous diffusion, had highly retarded rotational dynamics, and aligned their dipoles along the SecY transmembrane axis. The translocon is therefore not a simple waterfilled pore, which raises the question of how anomalous water behavior affects the mechanism of translocon function and, more generally, the partitioning of hydrophobic molecules. Because large water-filled cavities are found in many membrane proteins, our findings may have broader implications. membrane protein folding | molecular dynamics | protein-conducting channel | protein hydration | confined water T he heterotrimeric SecY translocon complex (SecYEG in bacteria, SecYEβ in archaea, Sec61αβγ in eukaryotes) is required for the cotranslational assembly of membrane proteins and the secretion of soluble proteins (1-3). The SecY subunit (Fig. 1A) has 10 transmembrane helices comprised of two fivehelix domains related by pseudo-twofold symmetry around an axis parallel to the membrane (4-8). These helices form an hourglass-shaped water-filled pore that spans the membrane. The so-called hydrophobic pore ring (HR) comprised of six hydrophobic residues forms the narrowest part of the hourglass, located near the bilayer center. Sitting just above the ring on the extracellular side is a small, distorted helix [transmembrane 2a (TM2a)], called the plug domain that is believed to impede the passage of water and solutes across the membrane. Access to the membrane from the water-filled hourglass-shaped interior of SecY is provided by the so-called lateral gate, formed by helices TM2b and TM7 (Fig. 1A). SecG is not required for function, but SecE is indispensable. Experimental (9-11) and computational studies (12-15) emphasize the importance of interactions of the gate helices with nascent-chain se...

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“…When water molecules are confined to the proximity of the protein surface, anomalous diffusion can take place [41,42]. Both the geometrical complexity and the temporal disorder of the water dynamics, i.e., the residence time distribution of water molecules on different protein residues and the protein surface roughness [42], cause anomalous diffusional behaviour. These results show that the motion of water inside the βLG pores is quite different from that of free water.…”

Section: S525mentioning

confidence: 99%

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

Malek¹,

Odijk²,

Coppens³

2005

Nanotechnology

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The dynamics of water and sodium counter-ions (Na + ) in a C222 1 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm 2 ns −1 , when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

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Origin of the anomalous diffusion observed by MD simulation at the protein-water interface

Cited by 49 publications

References 30 publications

Molecular dynamics simulation of the antimicrobial salivary peptide histatin‐5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect

Molecular dynamics simulation of the antimicrobial salivary peptide histatin‐5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect

Anomalous behavior of water inside the SecY translocon

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

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