{{Template:CH462_Biochemistry_II_2022}}
= Human Neurofibromin - The Tumor Suppressor Gene =

<StructureSection load='' size='340' side='right' caption='Neurofibromin in the Closed Conformation [https://www.rcsb.org/structure/7PGR (7PGR)]. The identical chains that make up the dimer are colored lime and cyan. Two important domains in the function of Neurofibromin are highlighted with the GRD colored red and the Sec14-PH domain colored magenta.' scene='90/904315/Closed_spinning/3'>

== Introduction ==
[[Image:Neurofibromin Surface w Labels.jpg|500 px|right|thumb|Figure 1: Surface Rendering of Neurofibromin in its Open (7PGT) and Closed (7PGR) Conformation.]]
Neurofibromin is encoded by [https://en.wikipedia.org/wiki/Neurofibromin_1 NF1 gene], located on chromosome 17. Neurofibromin functions as a tumor suppressor through its association with the protein [https://proteopedia.org/wiki/index.php/Ras Ras]. The molecular structure of Neurofibromin has been determined by [https://en.wikipedia.org/wiki/Cryogenic_electron_microscopy Cryo-Electron Microscopy]. The structure of neurofibromin isoform 2 revealed different functional states for the Neurofibromin protein.<ref name="Naschberger">PMID:34707296</ref> Mutations in Neurofibromin are associated with diseases such as [https://en.wikipedia.org/wiki/Neurofibroma Plexiform Neurofibromas]. (FLESH OUT INTRODUCTION)

== Function ==
[[Image:Neurofibromin_Cartoon_Domains.jpg|500 px|left|thumb|Figure 2: Neurofibromin Important Domains in one chain of the homodimer]]
Neurofibromin functions as a tumor suppressor protein.<ref name="Trovó-Marqui">PMID:16813595</ref> It prevents cell growth by turning off [https://en.wikipedia.org/wiki/Ras_GTPase Ras] which in its active state, stimulates cell growth and division. Ras is a small, monomeric [https://en.wikipedia.org/wiki/GTPase GTPase]. Ras is membrane-bound and interacts with Neurofibromin, a cytoplasmic protein, in the open conformation of Neurofibromin. (DEFINE RAS) Neurofibromin is brought to the membrane to associate with Ras by [https://medlineplus.gov/genetics/gene/spred1/ SPRED1]. (DEFINE SPRED1) Unlike Ras, Neurofibromin can interact with SPRED1 in both the open and closed conformations. The interaction between Neurofibromin and Ras is activated via an [https://en.wikipedia.org/wiki/Arginine_finger Arginine finger] (Arg 1276) present in the GRD domain of Neurofibromin. Arg 1276 is only accessible for binding when the GRD and Sec14-PH domains are rotated into the open conformation. When Arg 1276 is able to associate with Ras, Neurofibromin downregulates the [https://en.wikipedia.org/wiki/MAPK/ERK_pathway Ras signaling pathway] by speeding up Ras's GTPase activity, hydrolyzing the GTP associated with Ras to GDP. In its GDP bound state, Ras is inactive and cell growth and division are inhibited. (MECHANISTIC EXPLANATION).
[[Image:mechanismofRas.png|340 px|right|thumb|Mechanism of Ras Regulation by Neurofibromin]]

== Structure ==
Neurofibromin is a <scene name='90/904315/Homodimer/5'>homodimer</scene> made up of two identical chains. Neurofibromin has two conformations, open and closed. Shifting between these controls neurofibromin's ability to associate with Ras and perform its function of Ras regulation. The transformation between the overall closed and open conformations transitions it from an active to inactive state. There are <scene name='90/904315/Sec14ph_and_grd_domain/1'>two important domains</scene> involved in the transition between the open and closed conformations, the <scene name='90/904316/Grd_domains/2'>GRD</scene> domain and the <scene name='90/904315/Sec14ph_domain/3'>Sec14-PH</scene> domain. Although neurofibromin is a homodimer with two identical protomers, only one protomer has its GRD and Sec14-PH domains rotated into the open conformation.

<scene name='90/904315/N-heat_arm/1'>N-HEAT/ARM</scene>
<scene name='90/904315/C-heat_arm/1'>C-HEAT/ARM</scene>
== Conformational States ==

=== Closed Conformation (7PGR) ===
In the <scene name='90/904315/Closed/3'>closed, inactive conformation</scene>, the GRD and Sec14-PH domains are rotated so Ras cannot bind. In this conformation, the GRD and Sec14-PH are inaccessible and inactive. Neurofibromin is held in the inactive state by a <scene name='90/904315/Closed_triade/2'>triad</scene> consisting of residues Cys 1032, His 1558, and His 1576 that form a transition metal-binding site with zinc. The rigid organization of the <scene name='90/904315/Catalytic_triade/3'>triad in closed conformation</scene> keeps the GRD domain packed tightly on top of the Heat Arms in the Neurofibromin core. This tight compaction sterically occludes Neurofibromin from associating with Ras. In its active form, Ras and Neurofibromin will associate via an <scene name='90/904316/Arg_finger/2'>Arginine finger</scene> (Arg 1276). However, the steric hindrance from the Neurofibromin core in the closed conformation inhibits this association. Therefore, in the closed conformation, neurofibromin cannot catalyze GTP hydrolysis by Ras and Ras continues to signal for cell growth and proliferation.

=== Open Conformation (7PGT) ===
In the <scene name='90/904315/Open_conformation/4'>open, active conformation</scene>, (REWRITE ABOUT RAS REGULATION)

This transition is initiated by movement of the transition metal-binding site. The Cys 1032, His 1558, and His 1576 Residues become separated and zinc is not able to bond. In the active form, one protomer has its GRD and Sec14-PH domains oriented oppositely from the inactive form. The GRD rotates -130° and the Sec14-PH domain rotates -90° (TOWARDS WHAT?) Due to this rotation, Cys 1032 is now located too far away, approximately 30 Å, from His 1558 and His 1576 which results in the loss of the metal-binding site and no formation of the <scene name='90/904315/Open_conformation_triade/5'>triad</scene>. The lack of the transition metal-binding site allows the GRD to orient itself to associate with <scene name='90/904315/Ras_open_conformation/3'>Ras</scene>. This association positions the <scene name='90/904315/Open_conformation_arginine_fin/2'>Arginine Finger</scene> (TO DO WHAT?). When Neurofibromin is in the open, active conformation, Arg 1276 is able to <scene name='90/904315/Ras_open_conformation_with_arg/2'>bind to Ras</scene> because there is no steric hindrance from the Neurofibromin core.

[[Image:Domain Rotation.jpg|500 px|left|thumb|Figure 3: Rotation of the GRD and Sec14-PH domains from the closed conformation (7PGR) of neurofibromin to the open conformation (7PGT) of neurofibromin to allow Ras binding. The GRD rotates -130° and the Sec14-PH domain rotates -90°]]

== Disease and Medical Relevance ==
Currently over 1485 mutations of Neurofibromin have been identified that lead to life-threatening illnesses or conditions such as Neurofibromatosis Type I.<ref name="Lupton">PMID: 34887559 </ref> Mutations to the NF1 gene that prevent the interaction of Neurofibromin with Ras, remove this check on Ras dependent cell proliferation and uncontrolled cell growth can lead to tumors and a higher risk of cancer. [https://en.wikipedia.org/wiki/Neurofibromatosis_type_I Neurofibromatosis Type 1], the most well-known disease resulting from mutations in Neurofibromin, is characterized by cognitive impairment, soft, non-cancerous tumors on or under the skin known as neurofibromas, birthmarks called [https://en.wikipedia.org/wiki/Caf%C3%A9_au_lait_spot cafe-au-lait macules], clusters of freckles in unusual places, and problems with the bones, eyes and nervous system.

Neurofibromin is also involved in the differentiation of [https://en.wikipedia.org/wiki/Neural_crest neural crest-derived cells], [https://en.wikipedia.org/wiki/Mesenchymal_stem_cell mesenchymal cells], [https://en.wikipedia.org/wiki/Neural_stem_cell neural cells], [https://en.wikipedia.org/wiki/Melanocyte melanocytes], and [https://en.wikipedia.org/wiki/Osteocyte bone cells]. As Neurofibromin is essential for embryonic development, mutations to the NF1 gene can result in psychological retardation resulting from Type I neurofibromatosis. Most of the 1485 point mutations identified lead to a synthesis of truncated, non-functional protein an. Type I Neurofibromatosis is inherited in an autosomal dominant manner but about 50% of cases result from de novo mutations. <ref name="Abramowicz">PMID:25182393</ref>

Mutations in the NF1 gene have been found in sporadic cancers such as [https://en.wikipedia.org/wiki/Glioblastoma glioblastoma], [https://en.wikipedia.org/wiki/Neuroblastoma neuroblastoma], [https://en.wikipedia.org/wiki/Lung_cancer lung cancer], [https://en.wikipedia.org/wiki/Ovarian_cancer ovarian cancer], and [https://en.wikipedia.org/wiki/Breast_cancer breast cancer]. Researchers are still unsure as to whether biallelic loss of NF1 is common or if it is only a hemizygous loss of the gene that contributes to the growth progression of certain sporadic tumors.<ref name="Ratner">PMID:25877329</ref>

== Student Contributors ==
*Hannah Luchinski
*Sophie Mullinix

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1710

2022-04-12T14:42:22Z

Hannah Luchinski:

{{Template:CH462_Biochemistry_II_2022}}
= Human Neurofibromin - The Tumor Suppressor Gene =

<StructureSection load='' size='340' side='right' caption='Neurofibromin in the Closed Conformation [https://www.rcsb.org/structure/7PGR (7PGR)]. The identical chains that make up the dimer are colored lime and cyan. Two important domains in the function of Neurofibromin are highlighted with the GRD colored red and the Sec14-PH domain colored magenta.' scene='90/904315/Closed_spinning/3'>

== Introduction ==
[[Image:Neurofibromin Surface w Labels.jpg|500 px|right|thumb|Figure 1: Surface Rendering of Neurofibromin in its Open (7PGT) and Closed (7PGR) Conformation.]]
Neurofibromin is encoded by [https://en.wikipedia.org/wiki/Neurofibromin_1 NF1 gene], located on chromosome 17. Neurofibromin functions as a tumor suppressor through its association with the protein [https://proteopedia.org/wiki/index.php/Ras Ras]. The molecular structure of Neurofibromin has been determined by [https://en.wikipedia.org/wiki/Cryogenic_electron_microscopy Cryo-Electron Microscopy]. The structure of neurofibromin isoform 2 revealed different functional states for the Neurofibromin protein.<ref name="Naschberger">PMID:34707296</ref> Mutations in Neurofibromin are associated with diseases such as [https://en.wikipedia.org/wiki/Neurofibroma Plexiform Neurofibromas]. (FLESH OUT INTRODUCTION)

== Function ==
[[Image:Neurofibromin_Cartoon_Domains.jpg|500 px|left|thumb|Figure 2: Neurofibromin Important Domains]]
Neurofibromin functions as a tumor suppressor protein.<ref name="Trovó-Marqui">PMID:16813595</ref> It prevents cell growth by turning off [https://en.wikipedia.org/wiki/Ras_GTPase Ras] which in its active state, stimulates cell growth and division. Ras is a small, monomeric [https://en.wikipedia.org/wiki/GTPase GTPase]. Ras is membrane-bound and interacts with Neurofibromin, a cytoplasmic protein, in the open conformation of Neurofibromin. (DEFINE RAS) Neurofibromin is brought to the membrane to associate with Ras by [https://medlineplus.gov/genetics/gene/spred1/ SPRED1]. (DEFINE SPRED1) Unlike Ras, Neurofibromin can interact with SPRED1 in both the open and closed conformations. The interaction between Neurofibromin and Ras is activated via an [https://en.wikipedia.org/wiki/Arginine_finger Arginine finger] (Arg 1276) present in the GRD domain of Neurofibromin. Arg 1276 is only accessible for binding when the GRD and Sec14-PH domains are rotated into the open conformation. When Arg 1276 is able to associate with Ras, Neurofibromin downregulates the [https://en.wikipedia.org/wiki/MAPK/ERK_pathway Ras signaling pathway] by speeding up Ras's GTPase activity, hydrolyzing the GTP associated with Ras to GDP. In its GDP bound state, Ras is inactive and cell growth and division are inhibited. (MECHANISTIC EXPLANATION).
[[Image:mechanismofRas.png|340 px|right|thumb|Mechanism of Ras Regulation by Neurofibromin]]

== Structure ==
Neurofibromin is a <scene name='90/904315/Homodimer/5'>homodimer</scene> made up of two identical chains. Neurofibromin has two conformations, open and closed. Shifting between these controls neurofibromin's ability to associate with Ras and perform its function of Ras regulation. The transformation between the overall closed and open conformations transitions it from an active to inactive state. There are <scene name='90/904315/Sec14ph_and_grd_domain/1'>two important domains</scene> involved in the transition between the open and closed conformations, the <scene name='90/904316/Grd_domains/2'>GRD</scene> domain and the <scene name='90/904315/Sec14ph_domain/3'>Sec14-PH</scene> domain. Although neurofibromin is a homodimer with two identical protomers, only one protomer has its GRD and Sec14-PH domains rotated into the open conformation.

<scene name='90/904315/N-heat_arm/1'>N-HEAT/ARM</scene>
<scene name='90/904315/C-heat_arm/1'>C-HEAT/ARM</scene>
== Conformational States ==

=== Closed Conformation (7PGR) ===
In the <scene name='90/904315/Closed/3'>closed, inactive conformation</scene>, the GRD and Sec14-PH domains are rotated so Ras cannot bind. In this conformation, the GRD and Sec14-PH are inaccessible and inactive. Neurofibromin is held in the inactive state by a <scene name='90/904315/Closed_triade/2'>triad</scene> consisting of residues Cys 1032, His 1558, and His 1576 that form a transition metal-binding site with zinc. The rigid organization of the <scene name='90/904315/Catalytic_triade/3'>triad in closed conformation</scene> keeps the GRD domain packed tightly on top of the Heat Arms in the Neurofibromin core. This tight compaction sterically occludes Neurofibromin from associating with Ras. In its active form, Ras and Neurofibromin will associate via an <scene name='90/904316/Arg_finger/2'>Arginine finger</scene> (Arg 1276). However, the steric hindrance from the Neurofibromin core in the closed conformation inhibits this association. Therefore, in the closed conformation, neurofibromin cannot catalyze GTP hydrolysis by Ras and Ras continues to signal for cell growth and proliferation.

=== Open Conformation (7PGT) ===
In the <scene name='90/904315/Open_conformation/4'>open, active conformation</scene>, (REWRITE ABOUT RAS REGULATION)

This transition is initiated by movement of the transition metal-binding site. The Cys 1032, His 1558, and His 1576 Residues become separated and zinc is not able to bond. In the active form, one protomer has its GRD and Sec14-PH domains oriented oppositely from the inactive form. The GRD rotates -130° and the Sec14-PH domain rotates -90° (TOWARDS WHAT?) Due to this rotation, Cys 1032 is now located too far away, approximately 30 Å, from His 1558 and His 1576 which results in the loss of the metal-binding site and no formation of the <scene name='90/904315/Open_conformation_triade/5'>triad</scene>. The lack of the transition metal-binding site allows the GRD to orient itself to associate with <scene name='90/904315/Ras_open_conformation/3'>Ras</scene>. This association positions the <scene name='90/904315/Open_conformation_arginine_fin/2'>Arginine Finger</scene> (TO DO WHAT?). When Neurofibromin is in the open, active conformation, Arg 1276 is able to <scene name='90/904315/Ras_open_conformation_with_arg/2'>bind to Ras</scene> because there is no steric hindrance from the Neurofibromin core.

[[Image:Domain Rotation.jpg|500 px|left|thumb|Figure 3: Rotation of the GRD and Sec14-PH domains from the closed conformation (7PGR) of neurofibromin to the open conformation (7PGT) of neurofibromin to allow Ras binding. The GRD rotates -130° and the Sec14-PH domain rotates -90°]]

== Disease and Medical Relevance ==
Currently over 1485 mutations of Neurofibromin have been identified that lead to life-threatening illnesses or conditions such as Neurofibromatosis Type I.<ref name="Lupton">PMID: 34887559 </ref> Mutations to the NF1 gene that prevent the interaction of Neurofibromin with Ras, remove this check on Ras dependent cell proliferation and uncontrolled cell growth can lead to tumors and a higher risk of cancer. [https://en.wikipedia.org/wiki/Neurofibromatosis_type_I Neurofibromatosis Type 1], the most well-known disease resulting from mutations in Neurofibromin, is characterized by cognitive impairment, soft, non-cancerous tumors on or under the skin known as neurofibromas, birthmarks called [https://en.wikipedia.org/wiki/Caf%C3%A9_au_lait_spot cafe-au-lait macules], clusters of freckles in unusual places, and problems with the bones, eyes and nervous system.

Neurofibromin is also involved in the differentiation of [https://en.wikipedia.org/wiki/Neural_crest neural crest-derived cells], [https://en.wikipedia.org/wiki/Mesenchymal_stem_cell mesenchymal cells], [https://en.wikipedia.org/wiki/Neural_stem_cell neural cells], [https://en.wikipedia.org/wiki/Melanocyte melanocytes], and [https://en.wikipedia.org/wiki/Osteocyte bone cells]. As Neurofibromin is essential for embryonic development, mutations to the NF1 gene can result in psychological retardation resulting from Type I neurofibromatosis. Most of the 1485 point mutations identified lead to a synthesis of truncated, non-functional protein an. Type I Neurofibromatosis is inherited in an autosomal dominant manner but about 50% of cases result from de novo mutations. <ref name="Abramowicz">PMID:25182393</ref>

Mutations in the NF1 gene have been found in sporadic cancers such as [https://en.wikipedia.org/wiki/Glioblastoma glioblastoma], [https://en.wikipedia.org/wiki/Neuroblastoma neuroblastoma], [https://en.wikipedia.org/wiki/Lung_cancer lung cancer], [https://en.wikipedia.org/wiki/Ovarian_cancer ovarian cancer], and [https://en.wikipedia.org/wiki/Breast_cancer breast cancer]. Researchers are still unsure as to whether biallelic loss of NF1 is common or if it is only a hemizygous loss of the gene that contributes to the growth progression of certain sporadic tumors.<ref name="Ratner">PMID:25877329</ref>

== Student Contributors ==
*Hannah Luchinski
*Sophie Mullinix

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1710

2022-04-12T14:39:54Z

Hannah Luchinski: