Β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water Xiongwu Wu, Bernard R. Brooks Biophysical.

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Presentation transcript:

β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water Xiongwu Wu, Bernard R. Brooks Biophysical Journal Volume 86, Issue 4, Pages 1946-1958 (April 2004) DOI: 10.1016/S0006-3495(04)74258-7 Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 1 The chemical structure of the synthetic peptide. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 2 The simulation system in a periodic cubic boundary. The peptide is shown as thick sticks, the sodium ion is shown as a sphere, and the water molecules are shown as thin sticks. Carbon, oxygen, nitrogen, hydrogen, and sodium atoms are colored as green, red, blue, white, and yellow, respectively. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 3 The number of interstrand hydrogen bonds during the three SGMD simulations. Interstrand hydrogen bonds are hydrogen bonds between the backbone atoms of Tyr-1–Gln-2–Asn-3 and backbone atoms of Gly-6–Ser-7–Gln-8–Ala-9. Each peak in the plot represents a β-hairpin folding-unfolding event. Thirteen folding-unfolding events are identified as labeled and are analyzed in this article. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 4 Representative conformations of each folded structure. Only backbone atoms are shown. Atoms are colored as described in the legend of Fig. 2 except for the structures of cluster I and cluster II. Hydrogen bonds are marked by dotted lines. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 5 Comparison of the side-chain packing in cluster I and cluster II structures. Only heavy atoms are shown. The side chains of Gln-2, Asp-5, and Gln-8 are colored purple. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 6 Comparison of the experimental NOEs and the average distances of corresponding atom pairs of cluster I and cluster II (in parentheses). The distances violating the NOEs are shown in bold numbers. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 7 The ϕ–ψ distributions of Gln-2, Asn-3, Ser-7, and Gln-8 observed in our simulations. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 8 The populations and average energies of the peptide at a different number of intrapeptide hydrogen bonds during each SGMD simulation. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 9 The numbers of hydrogen bonds from 10,000ps to 30,000ps in simulation A. The shadowed areas mark the folded periods of Fold 1 and Fold 2. HBMM, HBSP, HBPP, HBPW, and HBP are numbers of hydrogen bonds between backbone atoms, between side chains and any peptide atoms, between any two peptide atoms, between the peptide and water, and between the peptide and any atoms, respectively. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 10 Typical conformational changes during a β-hairpin folding. The conformation at 17,000ps represents an unfolded structure with some intrapeptide interactions. At 184,000ps the peptide becomes fully hydrated. Side-chain interactions bring the two strands together at 19,700ps. At 20,700ps the peptide reaches a β-hairpin structure. Only heavy atoms are shown. Backbone atoms are shown as thick sticks. Atoms are colored as described in the legend of Fig. 2. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 11 Distances of the backbone hydrogen bonding atoms during simulations starting from the folded state. The dashed lines mark the standard distance (2Å) to form a hydrogen bond. (a) SGMD simulation; (b) MD simulation. Biophysical Journal 2004 86, 1946-1958DOI: (10.1016/S0006-3495(04)74258-7) Copyright © 2004 The Biophysical Society Terms and Conditions