Sandbox 122

3-Dimensional Model of Karyopherin-β23-Dimensional Model of Karyopherin-β2

Students: Mary Acheampong, Rosieva Ashong-Katai, Kavita Bhikhi, Daviana Dueño, Bobby Glover, Lachoy Harris, Alafia Henry, Randol Mata, Hillary Ramirez and Marisa VanBrakle, Hostos-Lincoln Academy.

Teacher: Allison Granberry, Hostos-Lincoln Academy

Mentors: Michael Rout, Natalia Ketaren

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IntroductionIntroduction

Karyopherin beta 2 (Kapβ2) is an importin that transports various cargo proteins into the nucleus through interactions with nucleoporins, which are proteins of the nuclear pore complex (NPC). One might overlook the significance of this protein but it actually plays a crucial role in the human body by mediating transport of RNA-binding proteins involved in transcription, RNA processing, RNA transport and translation. The structure of Kapβ2 is composed of 20 antiparallel helices called HEAT repeats. These HEAT repeats contribute to Kapβ2’s large superhelical shape. The protein is shown to form two arches: one at the N-terminal and the other at the C-terminal. Through recognition of a nuclear localization signal (NLS) located on its cargo, Kapβ2 binds to its cargo via its C-terminal arch. Release of the cargo is mediated by RanGTP, which once bound, modifies the shape of Kapβ2. This slight conformational change results in the dissociation of the cargo from its binding site. The Hostos-Lincoln Academy SMART (Students Modeling a Research Topic) Team and MSOE have designed and made a physical model by three-dimensional (3-D) printing technology, revealing the cargo and RanGTP binding domains. Supported by grants from the HHMI Pre-College Program and the Camille and Henry Dreyfus Foundation.

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Background InformationBackground Information

In eukaryotes, proteins must be transported in and out of the nucleus. This nucleocytoplasmic transport of proteins across the nuclear envelope must occur through the gateway of the NPC. The NPC is a large structure consisting of 456 constituent binding proteins called nucleoporins (Nups).1 Movement through the NPC is facilitated transport that relies on interaction with specific Nups. Importins and exportins are proteins that aid this facilitated transport by both binding to a specific cargo to be transported and interacting with specific Nups located in the central channel of the NPC.2

Karyopherinβ is a group of proteins that is composed of both importins and exportins. Importins are proteins that carry cargos into the nucleus while exportins serve the opposite function. As of today, twenty different Kapβs have been identified. Each of these Kapβs is capable of recognizing and transporting a specific group of cargos. In order to bind to its cargo a Kapβ has to recognize a Nuclear Localizaton or Export Signal (NLS or NES) is located in the polypeptide chain of the cargo. These signals can vary from 7 amino acids to longer than 100 amino acids in length.

An importin, such as Kapβ2, binds to a specific cargo by recognition of an NLS and carries the cargo through the NPC by interacting with intrinsically disordered Nups called FG-Nups. FG-Nups line the passageway of the NPC and contain repeats of phenylalanine and glycine. These unstructured FG-Nups form a low-density cloud within the central channel extending from the cytoplasm to the nucleoplasm. The cloud acts as an effective exclusion filter for those particles that do not contain FG repeat binding sites. This is referred to as the zone of selectivity.

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How does Kapβ2 identify its cargo?How does Kapβ2 identify its cargo?

Structure of Kapβ2

Kapβ2 is a superhelix comprised of 20 HEAT repeats, each of which consists of two anti-parallel helices.

HEAT repeats 9-13 and 14-18 form the binding site of the cargo while repeats 1-8 constitute the Ran binding site.

Kapβ2 Cargo Binding and Conformational Change

The NLS, located on the cargo, binds to the C-terminal arch of Kapβ2.

Recognition of the NLS by Kapβ2 follows certain guidelines:

(i) NLS, when not bound to Kapβ2, lacks a secondary structure.

(ii) NLS has an overall positive charge allowing for electrostatic compatibility with Kapβ2.

(iii) General sequence for the NLS is either hydrophobic with a central basic motif or rich with basic residues and lacking hydrophobic residues. The NLS of 2H4M follows the former motif as opposed to the latter.

Upon binding conformational change occurs in which the NLS gains structure and conforms to the shape of the C-terminal arch of Kapβ2.

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How does Kapβ2 release its cargo?How does Kapβ2 release its cargo?

Passage of Kapβ2 Through the NPC4

Once the cargo binds to Kapβ2, the complex travels through the NPC by hydrophobic interactions with the FG-Nups.

These interactions occur at two binding sites: one located between HEAT repeat 5 and 6, and the other between HEAT 6 and 7.

Dissociation of NLS5

Ran is a GTP binding protein that is found in greater concentrations in the nucleus than in the cytoplasm.

RanGTP has an overall positive charge allowing it to bind to the core of the N-terminal arch of the highly negative Kapβ2.  

Alt text

Figure#. Chart showing polar interactions between residues of Kapβ2 and Ran3. Negatively charged residues are highlighted in red and positively charged residues are highlighted in blue.

RanGTP binds to Kapβ2 at its N-terminal arch, beginning at HEAT repeat 1 through 7. This results in conformational changes not only within the N-terminal arch but also within a long (61 residue) loop of HEAT repeat 8, which is thought to be the cause of the dissociation of the cargo.