Neurofibromin

Introduction

Neurofibromin is a cytoplasmic protein located close to the cell membrane that is encoded by the NF1 gene located on chromosome 17 ^[1]. It is a suppressor of the Ras oncogene through its effect on the rate of catalysis from Ras-GTP (active) to Ras-GDP (inactive)^[2]. NF increasing the rate of catalysis of Ras means that Ras spends more time in its inactive state and cannot cause unnecessary cell proliferation linked to cancer^[3].

Structure

Domains

GRD domain

The Gap-related domain, or GRD, is the catalytic domain of neurofibromin. This domain also contains a tubulin-binding domain. Its main catalytic mechanism is the hydrolysis of GTP-bound Ras into GDP-bound Ras, which converts Ras from its active form into its inactive form. The GRD provides an arginine residue, known as the arginine finger, to Ras.

SEC-PH

The Sec-PH domain is the lipid-binding domain of neurofibromin. In the closed conformation of neurofibromin, the hydrophobic core is blocked by the Gap-related domain. The open conformation allows the hydrophobic core in the Sec cavity to be accessible and exposed.

CSRD and CTD

The Cysteine-Serine-rich domain (CSRD) and C-terminal domain (CTD) contain phosphorylation sites. The CSRD is able to be phosphorylated by protein kinases A and C. Phosphorylation by protein kinase C is a positive regulator of neurofibromin activity. The CTD is phosphorylated primarily by protein kinase C. This domain is a negative regulator of neurofibromin activity if particular residues are phosphorylated. It also plays an important role in tubulin binding, as it helps in the transition from metaphase to anaphase. CTD contains a nuclear localization signal as well.

Important Structural Features

Active Site

The active site for GTP hydrolysis of Ras is located in the Gap-related domain of neurofibromin. The catalytic residues include R68, Q61, and Y32, as well as magnesium and water molecules. Arginine is referred to as an “arginine finger” because it points into the binding site of GTP to stabilize and orient the position of glutamine through a network of hydrogen bonds between water molecules. This arginine comes from the Gap-related domain of neurofibromin. When GDP is bound, glutamine is too far away to perform its catalytic action. Glutamine interacts with the gamma phosphate via a hydrogen bond created from an interaction between a water molecule and the gamma phosphate. When GTP is bound, tyrosine moves inward to face it. In the GDP bound form, tyrosine faces outward.

Arginine Finger

Conformations

Neurofibromin is a dimeric protein that is found in the cytoplasm. It exists in two conformations, open and closed. The open conformation has one of the protomers in an auto-inhibited conformation and the other in an open conformation. In the open conformation, Ras is able to bind to neurofibromin. The closed conformation has both protomers in an autoinhibited conformation, which sterically hinders the binding of Ras.

RAS Complex

Mechanism of Ras Coupled with Neurofibromin

The RasGAP interactions that occur when neurofibromin's GAP domain and Ras are bound have two critical catalytic components. The first is the of the NF protein, which stabilizes the catalytic glutamine, as well as stabilizing the transition state of the phosphoryl transfer^[4]. The second component is the catalytic glutamine of the Ras protein, which stabilizes the nucleophilic water as it attacks the third phosphate group in the GTP molecule as shown in Figure 1^[5].

Figure 1: The catalytic glutamine stabilizes the nucleophilic water.

Downstream Effects

Figure X; By cybertory - This file was derived from: Signal transduction v1.png, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=12081090

The NF1 gene that neurofibromin encodes has a high mutation rate, however it is difficult to detect the mutations because of how large the protein is and how randomly the mutations are distributed across the protein. Many of the mutations have been detected in the catalytic Gap-related domain. Misregulated Ras activity can lead to uncontrolled signaling in many different cell signaling pathways. Figure 2 provides an overview of the pathways that are connected to Ras, such as the MEK pathway. Eventually, the pathways relate to gene regulation and cell proliferation. If Ras is hyperactive, cell overgrowth and cancer can result. A focus of drug design is the suppression of Ras and its downstream signaling pathways.

Disease Relevance

Mutations to the neurofibromin protein are implicated in the progression of Neurofibromatosis type 1 (NF1). This condition drives several forms of human cancers by inactivating the Ras suppression effects of NF, allowing Ras to behave as an oncogene. Neurofibromatosis type 1 is an autosomal dominant disorder that affects 1 in 3,000 people, and the NF gene itself has the highest mutation rate of any known human gene, adding to its prevalence^[6]. NF1 primarily causes tumors in the central and peripheral nervous systems, but often has a multisystem expression including tumors in the dermatologic, cardiovascular, gastrointestinal, and orthopedic systems^[7]. The wide range of presentations is consistent with the multiplicity of mutations observed in the causative protein^[8]. This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.