Proteins and folding

Transcription

1 Proteins and folding October 8th, Kinga Futó Biopolymers Mitotic spindle of a dividing cell Actin filament network in the epidermal cell of Tobacco leaf. DNA strand released from bacteriophage 1

2 Structure of proteins Primary structure: amino acid sequence Frederick Sanger 1958 Nobel prize Peptide bond Determining the sequence of insuline 1955 Secondary structure of proteins Secondary structural elements are stabilized by hydrogen bonds. β-sheet α-helix 2

3 Tertiary and quaternary structure of proteins Spatial relationship of secondary structural elements relative to each other. Spatial assembley of subunits Hemoglobin α-subunit Hemoglobin A (2α- and 2β- subunit) Driving force of the folding Hydrophobic core Hydrophil amino acids on the surface 3

4 Protein folding Folding: self-assembly of proteins. Unfolded protein Native state of protein Anfinsen experiment, RNase A (1961) Native structure Wrong conformation -mercapto ethanol -mercapto ethanol slow oxidation Denaturated structure Native structure Conclusions: The 3D structure of proteins is determinated by their amino acid sequence. The native structure is thermodynamically the most stabilized state. 4

5 Energy Levinthal paradox Cyrius Levinthal Every peptid unit has ~ 10 conformational states In the case of an 100 aa.-long polipeptide chain variations 1 conformational state: s s, ~ years are needed for reaching the native state Cyrius Levinthal Conformation In the reality the folding occurs within 1 second! Conclusion: Protein folding is not random, must have pathways. Energy landscape for protein folding Two-state system General case There are more than one transitions. Single domains or small proteins usually have two-state folding behavior. The depth of the well symbolizes the energetic stabilization of the native state versus the denaturated state. All paths lead to the native state (energetic minimum). 5

6 The Folding Funnel The unfolded state is an ensemble of a large number of molecules with different conformations. 6

7 Molten Globule State (MG) it is an intermediate of the folding transition U MG F it is a compact globule, yet expanded over a native radius native-like secondary structure it has a slowly fluctuating tertiary structure non-specific assembly of secondary structure and hydrophobic interactions MG is about a 10 % increase in size than the native state The Folding Funnel A new view of protein folding suggested that there is no single route, but a large ensemble of structures follow a many dimensional funnel to its native structure. Progress from the top to the bottom of the funnel is accompanied by an increase in the native-like structure as folding proceeds. 7

8 Misfolded proteins Prion: propageted, misfolded proteins, infectious agents - Transmissible spongiform encephalopaty (Kuru or laughing sickness) Daniel Carleton Gajdusek 1976 Nobel prize -Creutzfeldt-Jakob disease -bovine spongiform encephalopaty (mad cow disease) Accumulation of β-amyloid Alzheimer s disease Amiloyd plaques in mice brain Members of Fore tribe of New Guinea suffering in Kuru 8

9 Molecular chaperones Nascent polypeptides come off the ribosome and fold spontaneously, molecular chaperones are involved in their folding in vivo, and are related to heat shock proteins (hsp). Function of Heat Shock Proteins Minimize heat and stress damage to proteins (renaturation/degradation) Facilitate correct folding of proteins by minimizing aggregation and other misfolding Bind to nascent polypeptides to prevent premature folding Facilitate membrane translocation/import by preventing folding prior to membrane translocation Facilitate assembly/disassembly of multiprotein complexes ATP hydrolysis. 9

10 To fold or not to fold? Intrinsically Disordered Protein (IDPs): Some proteins must be unfolded or disordered in order to perform their functions, and others fold only in complex with target structures. IDPs play roles in processes such as: Cell signaling and cell cycle regulation Oncogene, e.g. P53 contains large unstructured regions in its native state Assembly of cytoskeletal proteins, e.g. Tau protein Membrane fusion and membrane transport DNA recognition molecules, e.g. the basic DNA-binding region of the leucine zipper protein Protein-RNA recognition, e.g. ribosomal proteins Transcriptional activation domains Amyloid formation, e.g. prion protein Summary 10

11 The End! 11