Simulation of Proteins at Constant pH

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Rahmani, Parisa | 2013

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Type of Document: M.Sc. Thesis
Language: Farsi
Document No: 44420 (04)
University: Sharif University of Technology
Department: Physics
Advisor(s): Ejtehadi, Mohammad Reza
Abstract:
Proteins are of fundamental importance for life on Earth and participate in virtually every process within cells. The function of a protein depends on its three dimensional structure. If this is disrupted, the protein loses its biological activity. In addition to temperature, pressure and ionic strength, pH is also an important factor that affects the configuration of proteins. Proteins contain acidic and basic residues. Variations in pH lead to changes in distribution of atomic charge, which in turn affect the stability and function of proteins. Protein folding occurs in a specific pH range, a deviation from which may facilitate misfolding or Amyloid aggregation. It is therefore necessary to study pH-dependent conformational phenomena of proteins. In this dissertation, we become familiar to lambda dynamics method for molecular dynamics simulation at constant pH. We use this method for simulation of Beta Amyloid protein at two pH values (2, 4.25). We show that Beta Amyloid which has an ordered secondary structure at pH= 7, loses most of its secondary structure at low pH values
Keywords:
Molecular Dynamic Simulation ; PH ; Landa Dynamics Method ; Beta-Amyloid Protein

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