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Water plays an important role in osmolyte-induced hairpin structure change: A molecular dynamics simulation study
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10.1063/1.4757419
/content/aip/journal/jcp/137/14/10.1063/1.4757419
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/14/10.1063/1.4757419

Figures

Image of FIG. 1.
FIG. 1.

The root-mean-square deviation (RMSD) of GB1p peptide corresponding to the NMR structure in the simulation trajectories of (a) native (F) structure of GB1p peptide in GdmSCN/water, (b) native structure of GB1p peptide in TFE/water, and (c) unfolded (U) structure of GB1p peptide in TFE/water compared to that in pure water, respectively.

Image of FIG. 2.
FIG. 2.

The breaking of backbone hydrogen bonds (HBs 1–6) in three trajectories of native structure of GB1p peptide in GdmSCN/water.

Image of FIG. 3.
FIG. 3.

The total number of backbone hydrogen bonds formed as a function of simulation time in three trajectories of unfolded structure of GB1p peptide in TFE/water and in pure water. The initial (unfolded) and final (folded) structures of GB1p peptide in the simulations are shown with new carton mode. The carbonyl and amide groups of the residues involved in the backbone hydrogen bonds (dash lines) are shown with licorice mode.

Image of FIG. 4.
FIG. 4.

The number of individual backbone hydrogen bond formed as a function of simulation time in three trajectories of unfolded structure of GB1p peptide in TFE/water.

Image of FIG. 5.
FIG. 5.

The breaking and formation of hydrogen bonds for residues involved in backbone hydrogen bonds of GB1p peptide in a typical trajectory of native structure of GB1p peptide in GdmSCN/water solution (black line: the number of backbone hydrogen bonds; red line: the number of hydrogen bonds formed between carbonyl group and water as hydrogen bonding donor; green line: the number of hydrogen bonds formed between carbonyl group and Gdm+ as hydrogen bonding donor).

Image of FIG. 6.
FIG. 6.

The average number of local TFE concentration around individual residues in the simulation of unfolded structure of GB1p peptide in TFE/water. The hollow bars indicate the position of hydrophobic residues.

Image of FIG. 7.
FIG. 7.

The breaking and formation of hydrogen bonds for residues involved in backbone hydrogen bonds of GB1p peptide in a typical trajectory of unfolded structure of GB1p peptide in TFE/water solution (black line: the number of backbone hydrogen bonds; red line: the number of hydrogen bonds formed between carbonyl group and water as hydrogen bonding donor; green line: the number of hydrogen bonds formed between carbonyl group and TFE as hydrogen bonding donor).

Image of FIG. 8.
FIG. 8.

(a) The total number of TFE and water molecules in the first shell of GB1p peptide as a function of simulation time in the same trajectory of unfolded structure of GB1p peptide in TFE/water solution as Fig. 7 . (b) The breaking and formation of hydrogen bonds for residues involved in all backbone hydrogen bonds of GB1p peptide in TFE/water solution (black line: the number of backbone hydrogen bonds; red line: the number of hydrogen bonds formed between carbonyl groups and water as hydrogen bonding donor; green line: the number of hydrogen bonds formed between carbonyl groups and TFE as hydrogen bonding donor).

Image of FIG. 9.
FIG. 9.

The distribution of the hydrogen bond number formed per water molecule (including hydrogen bonds among water and water, water and Gdm+, and water and TFE) in three simulation systems: (a) GdmSCN/water, (b) TFE/water, and (c) pure water.

Tables

Generic image for table
Table I.

The average number of hydrogen bonds on the backbone and within the turn region of GB1p peptide formed in the simulation of native structure of GB1p peptide in TFE/water and pure water, respectively. The average is over the last 50 ns of the simulations.

Generic image for table
Table II.

Average number of cosolvent (Gdm+ and SCN ions) and solvent (water) molecules within 6 Å of each individual residue of GB1p in GdmSCN/water solution. The average is over the last 50 ns of the simulation.

Generic image for table
Table III.

The average number of hydrogen bonds of the carbonyl groups of the residues involved in intra-protein hydrogen bonds and solvent molecules (water and/or TFE) formed in the simulation of native structure of GB1p peptide in TFE/water and pure water, respectively. The average is over the last 50 ns of the simulations.

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/content/aip/journal/jcp/137/14/10.1063/1.4757419
2012-10-08
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Water plays an important role in osmolyte-induced hairpin structure change: A molecular dynamics simulation study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/14/10.1063/1.4757419
10.1063/1.4757419
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