Protein Folding Mechanism

Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.

1. Protein folding mechanism Presented by SABAHAT ALI(16-ARID-2569) BAKHTAWAR AMJAD(16-ARID-2542) RASHID IQBAL(16-ARID-256

2. Introduction and protein structure Proteins have several layers of structure each of which is important in the process of protein folding.  The first most basic level of this structure is the sequence of amino acids themselves.( primary structure) The next layer in protein structure is the secondary structure . Secondary structure includes α-Helixes and β-sheets.  The tertiary structure is the next layer in protein structure. This takes the α-Helixes and β-sheets and allows them to fold into a three dimensional structure.

3. Protein folding Proteins are folded and held together by several forms of molecular interactions . The molecular interactions include the thermodynamic stability of the complex, the hydrophobic interactions and the disulfide bonds formed in the proteins.

4. Protein folding Protein folding considers the question of how the process of protein folding occurs,i.e . How the unfolded protein adopts the native state? It has been aptly been described as the second half of the genetic code Predict 3D structure from primary sequence Avoid misfolding related to human disease Design protein with novel function

5. protein folding depends upon The process depends upon; the solvent (water or lipid bilayer) The concentration of salt The PH The temperature The possible presence of cofactor Molecular chaperones

6. Process of protein folding Primary structure The primary structure of a protein its linear amino-acid sequence, determines its native conformation .The specific amino acid residues and their position in the polypeptide chain are the determining factors for which portions of the protein fold closely together and form its three-dimensional conformation. The amino acid composition is not as important as the sequence .

7. Secondary stucture Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. Characteristic of secondary structure are the structures known as alpha helices and beta sheets that fold rapidly because they are stabilized by  intramolecular hydrogen bonds , as was first characterized by Linus Pauling. 

8. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability. Protein secondary structure takes on the three forms Alpha helix beta sheet Turn , coil or loop

9. Hydrogen bonding scheme for alpha helix Main chain oxygen of ith residue (written as O( i ) Amide of N ( i+4) th residue(written as N(i+4) O( i )-----N(i+4)e.g.1---5,2-----6----

10. Beta sheets ma

11. Tertiary structure The alpha helices and beta pleated sheets can be  amphipathic  in nature, or contain a hydrophilic portion and a hydrophobic portion. This property of secondary structures aids in the tertiary structure of a protein in which the folding occurs so that the hydrophilic sides are facing the aqueous environment surrounding the protein and the hydrophobic sides are facing the hydrophobic core of the protein.

12. Quaternary structure Tertiary structure may give way to the formation of quaternary structure in some proteins, which usually involves the "assembly" or "co assembly" of subunits that have already folded; in other words, multiple polypeptide chains could interact to form a fully functional quaternary protein.

13. Driving force of protein folding Folding is a  spontaneous process that is mainly guided by hydrophobic interactions , formation of intramolecular  hydrogen bonds ,  van der Waals forces, and it is opposed by conformational entropy .The process of folding often begins  co- translationally , so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still being synthesized by the ribosome; however, a protein molecule may fold spontaneously during or after biosynthesis .

14. Hydrophobic effect Protein folding must be thermodynamically favorable within a cell in order for it to be a spontaneous reaction. Since it is known that protein folding is a spontaneous reaction, then it must assume a negative Gibbs free energy value .  Minimizing the number of hydrophobic side-chains exposed to water is an important driving force behind the folding process.

15. The hydrophobic effect is the phenomenon in which the hydrophobic chains of a protein collapse into the core of the protein (away from the hydrophilic environment). The multitude of hydrophobic groups interacting within the core of the globular folded protein contributes a significant amount to protein stability after folding, because of the vastly accumulated vander Waals forces (specifically London Dispersion forces).

16. chaperones a class of proteins that aid in the correct folding of other proteins  in vivo . Chaperones exist in all cellular compartments and interact with the polypeptide chain in order to allow the native three-dimensional conformation of the protein to form; however, chaperones themselves are not included in the final structure of the protein they are assisting in .

17. Molecular Chaperones In molecular biology, molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures. Chaperones are present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly.

18.  Chaperones may assist in folding even when the nascent polypeptide is being synthesized by the ribosome. Molecular chaperones operate by binding to stabilize an otherwise unstable structure of a protein in its folding pathway, they assist the de novo folding of proteins or they form repair machines for misfolded or even aggregated proteins, and they are therefore especially important for the survival of cells during stress situations .

19. A well studied example is the bacterial GroEL system, assists in the folding of globular proteins. In eukaryotic organisms chaperones are known as heat shock proteins .

20. These are basically proteins that are involved in the folding and unfolding of other proteins. Various approaches have been applied to study the structure, dynamics and functioning of chaperones.

21. Chaperone-assisted folding is required in the crowded intracellular environment to prevent aggregation. Used to prevent misfolding and aggregation which may occur as a consequence of exposure to heat or other changes in the cellular environment .

22. Experimental techniques for studying protein folding: X-ray crystallography Fluorescence spectroscopy Circular Dichroism

23. X Ray crystallography crystallography is one of the more efficient and important methods for attempting to decipher the three dimensional configuration of a folded protein. To be able to conduct X-ray crystallography, the protein under investigation must be located inside a crystal lattice .

24. Only by relating the electron density clouds with the amplitude of the x-rays can this pattern be read and lead to assumptions of the phases or phase angles involved that complicate this method.

25. Fluorescence spectroscopy Fluorescence spectroscopy is a highly sensitive method for studying the folding state of proteins. Three amino acids, phenylalanine ( Phe ), tyrosine (Tyr) and tryptophan ( Trp ), have intrinsic fluorescence properties, but only Tyr and Trp are used experimentally because their quantum yields are high enough to give good fluorescence signals.

26. Models of protein folding

27. Protein folding mechanism nascent protein nonfunctional linear Native functional Nonlinear 3D

28. Protein folding is either by; co translational process( N terminus is folded while the C terminus is synthesizing) or after translation

29. Incorrect protein folding A protein is considered to be misfolded if it cannot achieve its normal native state. This can be due to mutations in the amino acid sequence or a disruption of the normal folding process by external factors .   misfolded protein typically contains β-sheets that are organized in a supramolecular arrangement known as a cross-β structure . These β-sheet-rich assemblies are very stable, very insoluble , and generally resistant to proteolysis .

30. The misfolding of proteins can trigger the further misfolding and accumulation of other proteins into aggregates or oligomers. The increased levels of aggregated proteins in the cell leads to formation of  amyloid -like structures which can cause degenerative disorders and cell death.

31. Disease caused by misfolding Alzheimer’s disease Cystic fibrosis Parkinson’s disease Huntington's disease Gaucher’s disease

32. Unfolding Of proteins Denaturation Introduction: Denaturation is a process in which a protein loses its native shape due to the disruption of weak chemical bonds and interaction, thereby becoming biologically inactive

33. For Example Changing pH denatures proteins. Certain reagents such as urea and guanidine hydrochloride denature proteins . Detergents such as sodium dodecyl sulphate denature proteins by associating with non- polar group of proteins.

34. When protein is denatured it loses its function. Examples A denatured enzyme ceases/stops its function. A denatured antibody do not binds to its antigen.

35. The denatured state of protein does not necessarily mean that complete unfolding or denaturation of protein . Under some of conditions these proteins exhibit both properties denaturation and renaturation.

36. Mechanism of protein unfolding Unfolding of native proteins occur at both temperatures higher temperature and lower temperature. Types of denaturation Heat denaturation/thermal denaturation. Cold denaturation.

37. How denaturation occurs at the level of protein structure Denaturation occurs at the secondary ,tertiary and quaternary structure but not at the primary structure level . When the shape is compromised and the molecule can no longer function in its desired capacity.