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Understanding Protein Folding: H-P Lattice Model Overview

Explore the intricate process of protein folding, from its native state to energy landscapes and kinetic traps. Learn about the role of hydrophobic residues, the H-P lattice model, and the systematic approach to finding the native state. Discover how mistakes in folding can impact protein functionality and potential disease development.

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Understanding Protein Folding: H-P Lattice Model Overview

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  1. PROTEIN FOLDING:H-P Lattice Model 1

  2. Outline: • Introduction: What is Protein? • Protein Folding • Native State • Mechanism of Folding • Energy Landscape • Kinetic Trap • Fast Folding • H-P Lattice Model • Our Sample Protein and Its Native State • Summary 2

  3. What Is Protein? • Role of Proteins in Organism: • Catalyzing Biochemical Reactions, • Maintaining Cells Shape, • Cell Signaling, • Immune Responses, • Cell Adhesion, • Cell Cycling, • … • Functional Size of Protein is between 40 to 50 Amino Acid up to a Chain with Several Thousand Residue. • Human Body Makes at least 50,000 Different Type of Proteins with Different Functionality. 3

  4. Structure of Protein 1- Primary Structure: Sequence of Amino Acids Alpha-Helices 2- Secondary Structure: Repeating local structure stabilized by hydrogen bonds 4

  5. Structure of Protein 3- Folded Structure: 5

  6. Protein Folding • Native State: A unique completely determined folded state. • Protein Folding: Process of collapsing of protein to the folded structure. • Folding to the correct state is essential for function correctly. • Mis-folding, usually results in inactive proteins, might cuase several diseases like Alzheimer, etc. 6

  7. Protein Folding • Protein Folding is Dominated by Hydrophobic Residues. • Hydrophobic: Non-polar, Make Cluster in Polar Solvents. • Hydrophilic: Polar, Dissolve More Readily in Polar Solvents. Protein Tries to Maximize the Contacts Between Its Hydrophobic Residues. 7

  8. Protein Folding At Native State: CONTACT BETWEEN HYDROPHOBIC MOLECULES IS MAXIMIZED. 8

  9. Energy Landscape Protein Folding How can Protein Find Its Native State Correctly? How Does It Fold to Its Native State? 9

  10. Protein Folding What is the Systematic Way of Finding Native State? Kinetic Traps!!! 10

  11. Protein Folding Mistakes are mainly because of: • Kinetic Traps, • Thermal Motions, • Retrying the Earlier Conformation, • Etc. These effects could either misfold the protein or delay the protein folding process significantly. 11

  12. Protein Folding Unfolded Protein Fast Collapse to a Compact Form with Hydrophobic Core. Internal Reformations Native State 12

  13. HP Lattice Model 13

  14. Our Problem We Develop a Code to Find the Native State of Protein in HP Lattice Model. 14

  15. Method A Start Sequence Find the Conformation with the Greatest Number of HH Contacts. Using Self Avoiding Random Walk Generate Many Conformations. Native State Count Number of HH Contacts in Each Conformation. End A 15

  16. Results H P 16

  17. Summary • Protein folding is a complex process. • The folding process is dominated by Hydrophobic interactions. • At Native state, Hydrophobic contacts are maximized. • Toward Native state, a protein makes many mistakes. • HP Lattice model could describe general behavior of folding process and Native state. 17

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