Sandbox Reserved 1767

This Sandbox is Reserved from February 27 through August 31, 2023 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1765 through Sandbox Reserved 1795.

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SHOC2-PP1C-MRASSHOC2-PP1C-MRAS

Introduction (SMP) holophosphatase complex functions as a key regulator of the receptor tyrosine kinase (RTK) signaling pathway by removing an inhibitory phosphate on the RAF family of proteins to allow for MAPK signaling. This interaction of the RTK-Ras pathway and the SMP complex drives cell proliferation. The SMP complex is made of three subunits, SHOC2, PP1C, and MRAS. Each of these subunits has a different shape that corresponds to its different function. uses a crescent shape to enhance substrate interactions and complex stability. contains the the catalytic site of the complex which dephosphorylates the N-terminal phosphoserine (NTpS) of RAF green link here. binds to GTP which triggers assembly of the SMP complex. The C-terminus of the MRAS subunit localizes the complex to the cell membrane. WRITE ABOUT RAF HERE Mutations in one or multiple of these subunits leads to over-activation of the signaling pathway, which may result in cancer and developmental disorders called RASopathies. There are many regulatory mechanisms that serve as a lock on this RAS-MAPK pathway, decreasing the likelihood of unintentional pathway activation. One is a protein dimer called 14-3-3 that keeps inactive RAF localized to the cytoplasm. An N-terminal phosphorylated serine (NTpS) keeps RAF bound to this protein dimer, and when the SMP complex is assembled, the catalytic subunit, PP1C, removes the phosphate group from the serine residue, releasing RAF from the 14-3-3 dimer, and activating the RAS-MAPK cell proliferation pathway. In all images and animations, SHOC2 will be shown as cyan blue, MRAS as lime, and PP1C as violet. Other important components involved in the function of the SMP complex include the 14-3-3 dimer and Raf, which will be shown in salmon and slate-blue, respectively. Structure of Subunits SHOC2 The presence of SHOC2 is essential for complex formation. It a crescent shaped complex that serves as a bridge for PP1C and MRAS, maximizing interaction between the three subunits of the SMP complex. SHOC2 contains a large leucine rich region (LRR) that provides stability and localizes subunit PP1C to the membrane. Houseman SHOC2 only undergoes a when PP1C and MRAS bind, showing SHOC2 is a scaffolding protein that provides a favorable interface for complex formation. SHOC2 depletion is being studied as a therapeutic approach for RAS-driven cancers due to large scale interactions of the subunits being made possible by SHOC2. . SHOC2 and PP1C first engage in binding with each other via an N-terminal RVXF motif on SHOC2 that is complimentary to a sequence on PP1C. SHOC2 residues V64 and F66 GREEN LINK? embed in the complimentary region of PP1C, enhancing SHOC2 affinity for PP1C. SHOC2 bind MRAS-GTP through β strands of a LRR that interacts with a hydrophobic region of MRAS-GTP further stabilizing the complex. KWON PP1C The Protein phosphatase complex 1 (PP1C) subunit contains the catalytic site of the SMP complex. The PP1C subunit is a phosphatase enzyme responsible for the removal of a phosphate group on the N-terminal phosphoserine (NTpS) of RAF (Ser259).. The exact mechanism of dephosphorylation is currently unknown, but there are three catalytic metal ions: 2 Mn2+ and 1 Cl- present that coordinate nucleophilic water molecules in the active site. This dephosphorylation event allows for pathway activation. Although PP1C can dephosphorylate other proteins independently from the SMP complex, it cannot act on Raf unless bound to the complex because it lacks intrinsic substrate selectivity. SHOC2 and MRAS aid in the specificity of the enzymatic activity. Hence, PP1C requires the presence of SHOC2 and MRAS to be function. PP1C binds to SHOC2 and MRAS-GTP in a specific orientation that doesn’t change the conformation of the catalytic site and leaves it accessible for substrate binding. PP1C binds to SHOC2 through a hydrophobic n-terminal disordered region that is complimentary to the RVXF motif on SHOC2. GREEN LINK or picture? Similarly to SHOC2, PP1C does not undergo a significant conformational change when SHOC2 and MRAS-GTP bind. The lack of conformational change shows that the structure of PP1C is not dependent on the SMP complex, but in order to act as a phosphatase it must be bound to the complex.. PP1C binds to SHOC2 and MRAS-GTP in a specific orientation that doesn’t change the conformation of the catalytic site and leaves it accessible for substrate binding. GREEN LINK or picture? The substrate binds through hydrogen bonds with the main chain and side chain atoms of the catalytic residues **insert residue numbers here**. Mutations in the active site lead to increased activity, causing the Ras/Raf signaling cascade to be triggered more frequently. ***insert what residues are mutated and HOW it leads to more activity. PP1C activity is regulated by short linear interaction motifs or PP1C-binding regulatory proteins. The regulatory proteins bind to small linear motifs in PP1C, like RVXF. The RVXF motif and interaction site is located in PP1C through the N-terminal disordered region, which There is a direct interaction between the RVXF motif of SHOC2 and the hydrophobic RVXF-binding pocket of PP1C. This hydrophobic binding site is adjacent to the catalytic metal ions. In the Ras/Raf signaling cascade, the region of Raf that is C-terminal to the phosphate group binds to this hydrophobic groove, and the remaining residues bind to the hydrophobic region of SHOC2. Raf binding to this region of SHOC2 is what allows PP1C to be specific when in the SMP complex in comparison to PP1C on its own. PP1C also has a singular cysteine (C291) present in the hydrophobic binding site in order to provide further stability to the substrate-protein interaction by forming a covalent bond to the substrate. PP1C is involved in many different cellular signaling pathways including protein synthesis, muscle contraction, and even carbohydrate metabolism. Wolfgang In all these pathways, including the SMP pathway, PP1C does not exist as a monomer, it is present in holoenzyme form complex with one of two regulatory subunits ensuring there is no sporadic pathway activation. Schulman RAS/RAF Figure 1: MRAS binding sites with SHOC2, PP1C, and RAF (PDB 7DSO).. RAF While RAF is not technically part of the SMP protein complex, it is crucial for advancement in the cell signaling pathway SMP helps mediate. RAF plays many different roles in this pathway and has many different domains. RAF has a RAS binding domain (RBD), a N-terminal phosphorylated serine (NTpS), and a kinase domain. Figure ?? shows these domains and mechanistically how RAF is involved in signal advancement or lack thereof. When its N-terminal serine is phosphorylated RAF is bound to a 14-3-3 protein dimer, inactivating the pathway. Whenever the SMP complex is assembled, PP1C dephosphorylates this serine starting the signaling cascade. RAS RAS proteins are GTP-dependent intracellular switches that are anchored to the plasma membrane. . RAS proteins activate RAF kinases through direct binding and membrane recruitment, resulting in RAF dimerization and pathway activation. . The SMP complex has specificity for MRAS. Other RAS proteins may bind to SHOC2, but MRAS induces the complex formation with a significantly lower Kd (dissociation constant). There are no known membrane interacting regions on SHOC2 and PP1C, meaning the hydrophobic fatty acid tail on MRAS is responsible for recruiting the complex to the cell membrane .. A significant amount of steric overlap is seen in MRAS for the binding sites of PP1C, SHOC2, and Raf. In figure 1, MRAS is shown in green, with the SHOC2 binding site colored cyan, the PP1C binding site colored green, and the RAF binding site shown in red on a different RAS protein. Hence, multiple RAS proteins are required for further activation of the receptor tyrosine kinase pathway. Due to the significant overlap in binding domains, one MRAS molecule is needed to recruit SHOC2 and PP1C to the membrane, and another RAS molecule is needed activate RAF. The ability of scene name='95/952694/Cell_membrane/3'>MRAS-GTP to cluster at the cell membrane</scene> is a crucial capability for this protein complex. The presence of this scene name='95/952694/Cell_membrane/3'>palmitoyl tail on RAS </scene>is responsible for this anchoring to the cell membrane, similar to the hydrophobic fatty acid tail on MRAS that is responsible for recruiting SMP to the cell membrane, allowing only for 2D movement and increasing local concentrations of the players needed in this signaling pathway. . MRAS contains two regions called Switch I (SWI) and Switch II (SWII) that undergo conformational changes depending if MRAS is bound to GDP or GTP. . The conformation of these switches determines if the SMP complex can form or not. Mutations to MRAS lead to consistent GTP-loading, causing an increase in the formation of the SMP complex and there is consistent activation of the cell-proliferation pathway in the absence of external growth factors. Auto-inhibition Figure 3: Mechanism of SMP complex formation and activation of RAF.. The Ras-Raf signaling cascade will be inhibited without the dephosphorylation of Raf at Ser259. There is a dimer present in the cytoplasm that interacts with Raf through hydrogen bonds between R129 of 14-3-3 and Ser259 of Raf when Ser259 is phosphorylated. This interaction causes an as 14-3-3 restricts Raf to the cytoplasm and sterically inhibits Raf from binding with activated Ras. This interaction is crucial in regulating cell proliferation, as it prevents cell growth in the absence of a signal. Extracellular growth factors trigger GTP to bind to MRAS, which triggers SMP formation. Upon SMP complex formation, PP1C is brought into close proximity of Ras, leading to the dephosphorylation of Ser259 of Raf by the active site of PP1C. Once dephosphorylated, Raf is in the , allowing for the interaction of Ras and Raf, and the initiation of the signaling cascade. Switch I and Switch II Figure 2: MRAS SWI and SWII open and closed conformations.. SHOC2-PP1C-MRAS is a central gatekeeper in receptor tyrosine kinase signaling 1. Figure 1 shows the specific pathways SHOC2-PP1C-MRAS mediates. When MRAS is bound to GDP, shown in the left of figure 1, Raf is bound to a 14-3-3 protein dimer restricting it to the cytoplasm. When MRAS-GDP is exchanged for GTP via a nucleotide exchange factor GEF, a conformational change occurs. This change, shown in figure 2, causes a shift from the to of Switch I. fThe Switch I (SWI) region is made up of residues 42-48 of the MRAS domain. 1 These residues are crucial for the binding of MRAS, SHOC2, and PP1C because MRAS undergoes a conformational change that allows for SMP complex assembly upon GTP binding. When GTP is bound to MRAS, it is in the “closed conformation” because hydrogen bond interactions between the γ phosphate of GTP and residues in the SWI region of MRAS cause SWI to adopt a closed conformation, as seen in figure 2. The closed conformation allows for the binding of SHOC2 and PP1C because there is no steric clash between the scene name='95/952693/Switch_i_gtp_bound/11'>SWI region of MRAS</scene> and the surface of SHOC2 when GTP is bound. The only large-scale conformational change occurs in the MRAS subunit. When GDP is bound to the MRAS domain, it is in the “open” conformation. Since the γ-phosphate is not bound to GDP, there are no hydrogen bond interactions with the oxygens of the γ-phosphate group and the MRAS SWI region, causing MRAS to adpot an "open" conformation. Since SHOC2 and PP1C do not undergo much conformational change, they are in a slow equilibrium of binding and unbinding until MRAS binds to GTP allowing MRAS to bind to SHOC2 and PP1C. ===Cancer and Rasopathies=== should we intersperse this? Common mutations in SHOC2 and PP1C lead to amino acid changes on the interaction surfaces, that can lead to higher binding affinity.The interface of SHOC2-PP1C is stabilized by the Q249K mutation because this creates a salt bridge with E116 of PP1C. This enhances the binding energy by -22.7 kcal/mol. The G63R mutation on SHOC2 creates two additional hydrogen bonds with D242 on PP1C, released an additional 18.88kcal/mol of interaction energy. Mutations to MRAS can result in consistent GTP-loading, increasing the formation of the SMP complex in the absence of external growth factors that are necessary for activation of the pathway in a healthy organism. The majority of wild type MRAS in cells were in the GDP state, whereas the MRAS with the Q71R mutation locked in GTP-induced RAS conformational changes. MRAS G23V (equivalent to the oncogenic G13V in RAS), like MRAS Q71L (Q61L in RAS), also shows increased interaction with other effectors such as BRAF, CRAF, and AF6 (Fig. 6C), consistent with activating mutations leading to GTP-loading of MRAS (13). (THIS WILL BE A GREEN LINK) Mutations in PP1C can trigger increased active site activity, increasing the RAF proteins that are active and available to bind to RAS. In patients with Noonan Syndrome, a disease in the rasopathy family, point mutations G23V and T68I in MRAS were identified, however, the outcome of these is unknown.​​ Universally, when this MAPK cascade is unregulated, cells are able to proliferate regardless of external signals, leading to cancer and/or RASopathies.

spinqualitylabelsall models SHOC2-MRAS-PP1C Holophosphatase Complex Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

ReferencesReferences

1. Hauseman ZJ, Fodor M, Dhembi A, Viscomi J, Egli D, Bleu M, Katz S, Park E, Jang DM, Porter KA, Meili F, Guo H, Kerr G, Mollé S, Velez-Vega C, Beyer KS, Galli GG, Maira SM, Stams T, Clark K, Eck MJ, Tordella L, Thoma CR, King DA. Structure of the MRAS-SHOC2-PP1C phosphatase complex. Nature. 2022 Sep;609(7926):416-423. doi: 10.1038/s41586-022-05086-1. Epub 2022 Jul 13. PMID: 35830882; PMCID: PMC9452295..

2. Hurley TD, Yang J, Zhang L, Goodwin KD, Zou Q, Cortese M, Dunker AK, DePaoli-Roach AA. Structural basis for regulation of protein phosphatase 1 by inhibitor-2. J Biol Chem. 2007 Sep 28;282(39):28874-28883. doi: 10.1074/jbc.M703472200. Epub 2007 Jul 18. PMID: 17636256..

3. Kwon JJ, Hajian B, Bian Y, Young LC, Amor AJ, Fuller JR, Fraley CV, Sykes AM, So J, Pan J, Baker L, Lee SJ, Wheeler DB, Mayhew DL, Persky NS, Yang X, Root DE, Barsotti AM, Stamford AW, Perry CK, Burgin A, McCormick F, Lemke CT, Hahn WC, Aguirre AJ. Structure-function analysis of the SHOC2-MRAS-PP1C holophosphatase complex. Nature. 2022 Sep;609(7926):408-415. doi: 10.1038/s41586-022-04928-2. Epub 2022 Jul 13. PMID: 35831509; PMCID: PMC9694338..

4. ​Liau NPD, Johnson MC, Izadi S, Gerosa L, Hammel M, Bruning JM, Wendorff TJ, Phung W, Hymowitz SG, Sudhamsu J. Structural basis for SHOC2 modulation of RAS signalling. Nature. 2022 Sep;609(7926):400-407. doi: 10.1038/s41586-022-04838-3. Epub 2022 Jun 29. PMID: 35768504; PMCID: PMC9452301..

5. Lavoie H, Therrien M. Structural keys unlock RAS-MAPK cellular signalling pathway. Nature. 2022 Sep;609(7926):248-249. doi: 10.1038/d41586-022-02189-7. PMID: 35970881.​.

6. Young LC, Hartig N, Boned Del Río I, Sari S, Ringham-Terry B, Wainwright JR, Jones GG, McCormick F, Rodriguez-Viciana P. SHOC2-MRAS-PP1 complex positively regulates RAF activity and contributes to Noonan syndrome pathogenesis. Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10576-E10585. doi: 10.1073/pnas.1720352115. Epub 2018 Oct 22. PMID: 30348783; PMCID: PMC6233131.​​.

Student ContributorsStudent Contributors

- Sloan August

- Rosa Trippel

- Kayla Wilhoite