1. GroEL and GroES By: Jim, Alan, John

2. Background Proteins fold spontaneously to their native states, based on information in their amino acid sequence Proteins fold spontaneously to their native states, based on information in their amino acid sequence Sometimes proteins fail to fold and need help Sometimes proteins fail to fold and need help Cells have developed molecules that catalyse protein folding called chaperones. Cells have developed molecules that catalyse protein folding called chaperones. Molecular chaperones supervise the state of newly formed proteins, hold them to the proper pathway of folding, and keep them from improper influences that might lead to incorrect assembly. Molecular chaperones supervise the state of newly formed proteins, hold them to the proper pathway of folding, and keep them from improper influences that might lead to incorrect assembly.

3. Background Chaperones act catalytically to speed up the process of protein folding by lowering the activation barrier between misfolded and native states (Lesk 297) Chaperones act catalytically to speed up the process of protein folding by lowering the activation barrier between misfolded and native states (Lesk 297) Chaperones themselves contain no information about particular folding patterns, rather they anneal misfolded proteins and allow them to find their native state. Chaperones themselves contain no information about particular folding patterns, rather they anneal misfolded proteins and allow them to find their native state.

4. GroEL-GroES GroEL-GroES contains 2 products of the GroE operon GroEL-GroES contains 2 products of the GroE operon GroELL for large GroELL for large GroESS for small GroESS for small The active complex contains 14 copies of GroEL and 7 copies of GroES The active complex contains 14 copies of GroEL and 7 copies of GroES In the presence of a nucleotide, GroEL and GroES form a symmetrical GroES 7 -GroEL 14 -GroES 7 complex In the presence of a nucleotide, GroEL and GroES form a symmetrical GroES 7 -GroEL 14 -GroES 7 complex

5. GroEL Structure 14 GroEL form 2 seven-fold rings, packed back to back 14 GroEL form 2 seven-fold rings, packed back to back Each ring surrounds an open cavity to receive unfolded proteins Each ring surrounds an open cavity to receive unfolded proteins The cavity is closed at the bottom (with a wall between the two rings) so the protein cannot pass internally between cavities The cavity is closed at the bottom (with a wall between the two rings) so the protein cannot pass internally between cavities The 2 rings communicate with allosteric structural changes The 2 rings communicate with allosteric structural changes

6. GroES Structure GroES subunits form another 7-membered ring that caps one of the GroEL rings GroES subunits form another 7-membered ring that caps one of the GroEL rings The GroEL ring capped by GroES is called the cis ring and the non-capped ring is the trans ring The GroEL ring capped by GroES is called the cis ring and the non-capped ring is the trans ring

7. GroEL-GroES Complex Formation of the GroEL- GroES complex requires a large and remarkable conformational change in the cis GroEL ring, changing the interior surface of the cavity from hydrophobic to hydrophilic, and breaking the symmetry between the two GroEL rings. Formation of the GroEL- GroES complex requires a large and remarkable conformational change in the cis GroEL ring, changing the interior surface of the cavity from hydrophobic to hydrophilic, and breaking the symmetry between the two GroEL rings. ATP is bound and broken down to ADP+P for the energy to make this change ATP is bound and broken down to ADP+P for the energy to make this change

8. GroEL-GroES Complex The enclosed cavity is the site of protein folding The enclosed cavity is the site of protein folding Misfolded proteins in the cavity are given about 20 seconds to refold. After 20 seconds, they are expelled either refolded successfully, or given another chance to enter the same or a different chaperon complex to try again Misfolded proteins in the cavity are given about 20 seconds to refold. After 20 seconds, they are expelled either refolded successfully, or given another chance to enter the same or a different chaperon complex to try again A misfolded protein will be kept in solitary confinement until it has reformed correctly. A misfolded protein will be kept in solitary confinement until it has reformed correctly.

9. Swinging or Hinging Motion In order to do its work, GroEL undergoes conformation changes to its domains: twisting and bending along multiple axes In order to do its work, GroEL undergoes conformation changes to its domains: twisting and bending along multiple axes The apical domain swings about 60º in a hinge motion, hiding hydrophobic residues inside the cavity. The apical domain swings about 60º in a hinge motion, hiding hydrophobic residues inside the cavity. A second hinge in the equatorial domain swings to lock in ATP and expose a critical residue for hydrolysis. A second hinge in the equatorial domain swings to lock in ATP and expose a critical residue for hydrolysis.

10. Rotational Motion The most important motion of GroEL is the rotational motion of the apical domain in order to expose a different bounded surface to the inner GroEL tube. The most important motion of GroEL is the rotational motion of the apical domain in order to expose a different bounded surface to the inner GroEL tube. In its unbound form, the residues that line the interior of the GroEL tube are hydrophobic, or not willing to combine with water molecules. In the bounded form, they readily accept water molecules. In its unbound form, the residues that line the interior of the GroEL tube are hydrophobic, or not willing to combine with water molecules. In the bounded form, they readily accept water molecules. The hydrophobic residues that formed the lining become part of the inter- subunit contacts, while the hydrophilic residue surfaces are exposed. The hydrophobic residues that formed the lining become part of the inter- subunit contacts, while the hydrophilic residue surfaces are exposed.

11. Why is the Apical Domain Rotation Important? As stated previously, GroEL attempts to allow misfolded proteins to refold themselves. As stated previously, GroEL attempts to allow misfolded proteins to refold themselves. The characteristic of misfolded proteins, that renders them subject to non-specific aggregation, is the surface exposure of hydrophobic residues that are buried in the native state. (Lesk, 299) The characteristic of misfolded proteins, that renders them subject to non-specific aggregation, is the surface exposure of hydrophobic residues that are buried in the native state. (Lesk, 299)

12. No, Really, Why is that Rotation So Great? Proteins with this negative property bind to the open form of GroEL. (Recall that in the open, unbounded form, GroELs cavity is also hydrophobic.) Then once the misfolded protein is within GroELs inner tube, GroELs inner residues become hydrophilic (having water affinity), coaxing the protein to refold itself correctly. Proteins with this negative property bind to the open form of GroEL. (Recall that in the open, unbounded form, GroELs cavity is also hydrophobic.) Then once the misfolded protein is within GroELs inner tube, GroELs inner residues become hydrophilic (having water affinity), coaxing the protein to refold itself correctly.

13. The GroEL-GroES Operational Cycle The operational cycle of the complex GroEL-GroES can best be described through individual points. When capped by GroES, the GroEL rings have two different states. The first is open, where the ring is available for the reception of misfolded proteins. The second is closed, and actually contains a misfolded protein. When seen separate from GroES, the GroEL ring is in an open state, allowing for the entry of proteins. The inside of the Gro-EL ring has a flexible hydrophobic lining. This allows for the binding of misfolded proteins, through hydrophobic and van der Waals interactions. Throughout these processes, however, it is possible for the protein to become unfolded partially, when in an incorrect state.

14. With the binding of ATP and GroES, the cap (GroES) is ready for the ring (GroEL), however, there must first be a conformational change in the cis ring. The ending result is a closed cavity where the substrate protein can refold, once it is released from the apical domains. It must also be taken away from potential aggregation partners. When the cis ring undergoes the conformational change, it more than doubles the available volume of the cavity. This allows for larger unfolding/refolding transition states to exist. The inside of the GroEL cavity also changes from hydrophobic to hydrophilic. This peels the bound misfolded protein off of the surface and unfolds it even further. The burial of the original interior GroEL surface in intersubunit contacts within the GroEL-GroES complex itself breaks the binding of the protein to the original hydrophobic internal surface, leaving a macroclathrate complex. This new complex (cavity) is composed of a crystal lattice, housing the protein in the cavity.

15. Finally, hydrolysis of ATP in the cis ring allows for the weakening of the structure. Binding of the ATP in the trans ring causes the disassembly of the cis assembly, allowing for the release of the GroES and substrate protein. In the end, the ring is left in original state. It needs to be noted that through the process, there is a necessity of seven or fourteen ATP molecules. In the end, the cost is much larger than the energy required to unfold a protein. However, it needs to be stated that it this cost is infinitely smaller than the death of a cell, and is also quite smaller than the synthesis of the polypeptide chain.

16. GroEL-GroES The interaction between GroEL and GroES is necessary for certain proteins to fold under otherwise non-permissive conditions (Lorimer 720). The interaction between GroEL and GroES is necessary for certain proteins to fold under otherwise non-permissive conditions (Lorimer 720).