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One step beyond: Simulation of peptide aggregation

One step beyond: Simulation of peptide aggregation. 12-residue N-terminal region of SIV-gp32 (SIVwt): NH 2 -G V F V L G F L G F L A. Surface glycoprotein gp120. Simian Immunodeficiency Virus (SIV) envelope glycoprotein precursor gp160. Proteolytic cleavage.

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One step beyond: Simulation of peptide aggregation

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  1. One step beyond: Simulation of peptide aggregation 12-residue N-terminal region of SIV-gp32 (SIVwt): NH2-G V F V L G F L G F L A Surface glycoprotein gp120 Simian Immunodeficiency Virus (SIV) envelope glycoprotein precursor gp160 Proteolytic cleavage Transmembrane glycoprotein gp32 Viral fusogenic activity ATR-IR1 and ThioflavinT fluorescence2 b-sheet aggregates depending on peptide concentration. 1. Martin, I. et al. Journal of Virology, 1994, 68, 1139 2. Cladera, J. et al. Journal of Biological Chemistry 1999, 274, 29951. Patrica Soto

  2. Is it possible to simulate the b-sheet aggregate? Molecular Dynamics simulations to investigate stability of suprastructures of SIVwt peptide aggregates in DMSO Simulation box with 30 parallel chains of SIVwt peptide in DMSO. Amount of particles: ~ 30000 Frame at Tinitial Distance between chain #1 and #30: ~12 nm The simulations show the spontaneous helical twisting of the protofibril Patrica Soto

  3. Spontaneous twisting… t = 0 ns t = 10 ns t = 20 ns t = 35 ns • Parallel or antiparallel? • Chirality • Twisted ribbon as energetically more favorable geometry t = 50 ns Patrica Soto

  4. Is it possible to simulate the spontaneous aggregation into ordered b-sheet aggregates? Solvent: hexane t = 20ns t = 50ns t = 0ns t = 2 ns t = 75ns t = 90ns SIVwt peptide spontaneously aggregates into stable clusters that exhibit high population of b-sheet secondary structure Patrica Soto

  5. Is it possible to simulate the spontaneous aggregation into ordered b-sheet aggregates? Solvent: water t = 2ns t = 0ns t = 35ns t = 50ns SIVwt peptide spontaneously aggregates into stable clusters that exhibit high population of b-sheet secondary structure Patrica Soto

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