File:Amyloid plaques.PNG

2020-04-21T06:19:12Z

Daniel Mulawa:

Sandbox Reserved 1619

2020-04-21T06:18:10Z

Daniel Mulawa:

='''Gamma Secretase'''=
<StructureSection load='5FN2' size='350' frame='true' side='right' caption= "Human Gamma Secretase. This protease is made up of 4 subunits: NCT (blue), PS1 (green), APH-1 (pink), and PEN2 (yellow). (PDB code: [https://www.rcsb.org/structure/5FN2 5FN2])" scene=’’>

=Gamma Secretase=

==Introduction==

===Background===
Gamma secretase (GS) is a transmembrane [https://en.wikipedia.org/wiki/Aspartic_protease aspartatic protease] that catalyzes peptide bond hydrolysis of type I integral membrane proteins such as Notch, amyloid precursor protein (APP), and various other substrates. GS recognizes and catalyzes the cleavage of its substrate into 3 residue segments. Products of initial APP cleavage include the 48-residue peptide Aβ48 or the 49-residue peptide Aβ49. GS then cleaves these peptides into a variety of peptide fragments separated by 3 residues; Aβ49 is cleaved into Aβ46, Aβ43, and Aβ40; Aβ48 is cleaved into Aβ45, Aβ42, and Aβ38. These Aβ products are connected to neurological diseases like [https://en.wikipedia.org/wiki/Alzheimer%27s_disease Alzheimer's disease (AD)] with varying length peptide products showing different disease symptoms. The connection between GS and AD has made a popular drug target. Various inhibitors of GS have been identified but no inhibitors have been clinically approved for treating AD, as the important neurological functions of GS has led to dangerous side effects upon inhibition<ref name="Zhou">PMID:30630874</ref>.

===Overall Structure===
GS is composed of 20 transmembrane components (TMs) and has 4 separate protein subunits: Nicastran (NCT), Presenilin (PS1), Anterior Pharynx-defective 1 (APH-1), and Presenilin Enhancer 2 (PEN-2). These subunits are stabilized as functional GS by hydrophobic interactions and 4 [https://en.wikipedia.org/wiki/Phosphatidylcholine phosphatidylcholines].These <scene name='83/832945/Phosphotidylcholines/2'>phosphatidylcholines</scene> have interfaces between: PS1 and PEN-2, APH-1 and PS1, APH-1 and NCT.
<scene name='83/832945/Nct_subunit_shown/1'>NCT</scene> has a large extracellular domain and one TM. NCT is important to substrate recognition and binding.
<scene name='83/832945/Ps1_subunit/1'>PS1</scene> serves as the active site of the protease and contains 9 TMs, each varying in length. The site of autocatalytic [https://en.wikipedia.org/wiki/Bond_cleavage cleavage] is located between <scene name='83/832945/Tm6_and_tm7/1'>TM6 and TM7</scene> of PS1 and a major conformational changes take place in this subunit upon substrate binding.
<scene name='83/832945/Aph-1_subunit/1'>APH-1</scene> serves as a scaffold for anchoring and supporting the flexible conformational changes of PS1.
Activation of the active site is dependent on the binding of <scene name='83/832945/Pen2_subunit/1'>PEN-2</scene>. PEN-2 is also important in maturation of the enzyme.<ref name="Yang">PMID:28628788</ref>

== Structural highlights ==
===Substrate Structure===
[[Image:App.png|250 px|right|thumb|'''Figure 1. APP fragment conformational change in gamma secretase.''' APP bound to GS undergoes a conformational change. The free state consists of 2 helices. Once bound to GS, the N-terminal helix unfolds into a coil and the C-terminal helix unwinds into a β-strand. This β-strand interacts with PS1 and is the site of cleavage by the protease.]]
GS has been structurally characterized in the presence of both [https://en.wikipedia.org/wiki/Amyloid_precursor_protein/ APP] and Notch substrates. In each of these structures, the substrate bound in a similar location and underwent a similar structural transition upon binding to the active site of GS. Each substrate is composed of an N-terminal loop and a TM helix. The peptide substrate enters the enzyme by <scene name='83/832945/App_in_gs_general/1'>lateral diffusion</scene> via the lid complex, and once in place, the TM helix of the substrate is anchored by <scene name='83/832945/Hydrophobic_interactions/2'>van der Waals contacts</scene>. Upon binding to GS, the C-terminal extracellular helix of the substrate unwinds. The substrate's N-terminal end of the TM helix unwinds into a β-strand (Fig. 1). To differentiate substrates, the β-strand is often the main point of identification for the enzyme. Substrate binding induces a structural change in GS, creating two β-strands that form a β-sheet with the one β-strand of the substrate. This β-sheet is in close proximity with the active site, and guides the process of catalysis.<ref name="Zhou">PMID:30630874</ref>

===Lid Complex===
The <scene name='83/832945/Lidremake/1'>lid complex</scene> is the first point of entry and recognition for the substrate. This lid is located within the NCT subunit between Asn55 and Asn435. This lobe of NCT is divided into two separate subunits; the large and small lobes with Phe287 from the large lobe acting as a pivot between them. This <scene name='83/832945/Pivot/1'>Phe is further surrounded by Phe103, Leu171, Phe176, and Ile180</scene> of the small subunit. This congregation of hydrophobic residues composes a greasy pocket that provides an environment for easy structural movement. The lid consists of 5 aromatic residues which are highly involved with stabilizing the closed conformation. In particular, this conformation is stabilized by <scene name='83/832945/Trp164scene/1'>Trp164, which interacts with Pro424, Phe448, and the aliphatic side chain of Gln420</scene>. Once the substrate binds and the lid is opened, a charged, hydrophilic binding pocket is revealed. This pocket contains <scene name='83/832945/Gluandtyr_remake/1'>Glu333 and Tyr337 surrounded by several charged residues</scene>, and is further involved with substrate binding and recognition once the lid is removed. However, this lid complex is relatively far away from the catalytic site of the enzyme in PS1. Once the substrate binds, the enzyme undergoes a conformational change to shorten this distance, and the rotation of the large lobe in relation to the small lobe reorients the substrate for cleavage by aligning the pocket in NCT to the active site in PS1. <ref name="Bai">PMID:26280335</ref>

===Active Site===
The <scene name='83/832945/Asp_257_and_asp_385/12'>active site</scene> is located between TM6 and TM7 of the PS1 subunit, which is mainly hydrophilic and disordered. Both TM6 and TM7 contribute an aspartate residue to the active site. These two aspartates, <scene name='83/832945/Asp_257_and_asp_385/10'>Asp257 and Asp385</scene> are located approximately 10.6 A˚ apart when inactive.<ref name="Bai">PMID:26280335</ref> Substrate recognition is controlled by the closely spaced PAL sequence of <scene name='83/832945/Asp_257_and_asp_385/11'>Pro433, Ala434, and Leu435</scene>. GS becomes active upon substrate binding, when TM2 and TM6 each rotate about 15 degrees to more closely associate. Two β-strands are induced in PS1, creating an <scene name='83/832945/Beta_sheet_complex/1'>antiparallel β-sheet</scene> with the β-strand of the substrate.<ref name="Zhou" /> The β-strand of the substrate interacts via main chain H-bonds with the PAL sequence, stabilizing the active site. Asp257 and Asp385 hydrogen bond to each other and are located 6–7 Å away from the scissile peptide bond of the substrate, allowing catalysis to occur.<ref name="Yang" /> GS cleaves in 3 residue segments which is driven by the presence of three amino acid binding pockets in the active site. <ref name="Bolduc" />
In APP, the cleavage site is between the helix and the N-terminal β-strand. GS can cleave via different pathways, depending on its starting point, but the 2 most commonly used pathways produce Aβ48 and Aβ49.<ref name="Bolduc">PMID:27580372</ref>. Tripeptide cleavage starting between <scene name='83/832945/3_residues_for_cleavage/2'>Thr719 and Leu720</scene> results in Aβ48. Cleavage between <scene name='83/832945/3_residues_for_cleavage/3'>Leu720 and Val721</scene> yields Aβ49. The accumulation of these Aβ peptides has strong implications in Alzheimer's disease.<ref name="Zhou">PMID:30630874</ref>

==Relevance==

GS is connected with the development of AD. In this, Aβ fragment build up leads to [https://en.wikipedia.org/wiki/Amyloid amyloid]plaques in brain.<ref name="Devendra">PMID:29477076</ref> These plaques then go on to cause severe neural dysfunction over time.

Mutations in GS are also connected with AD. Over 200 of GS mutations have been linked to causing AD. These mutations target "hot spots" on the enzyme and are aggregated at the interface between PS1 and APP.The vast majority of these mutations are clustered in regions surrounding the C-terminal half of the APP TM helix and the β-strand. Mutations at these locations affect the integrity of APP recruitment and catalysis, implicating a role in the development of Aβ plaques that impair neural function.

Inhibition of GS could be a potential AD treatment, but this would require targeting only APP cleavage over other GS substrates. APP cleavage leads to products such as Aβ42 and Aβ43<ref name="Yang">PMID:28628788</ref>, which are prone to aggregation and formation of Aβ plaques. Increased peptide length is thought to cause aggregations, and many of the mutations within PS1 result in elevated ratios of Aβ42 to the shorter Aβ40<ref name="Bai">PMID:26280335</ref>. The differential binding of APP and Notch to GS provides a starting point for this differentiation but will require further follow-up studies to confirm that the structural differences observed are biologically relevant. Currently, in order to combat this complex situation, differences in binding between different substrates are being utilized to create drugs that selectively inhibit APP binding with GS, and possibly create a more ideal target for AD treatment<ref name="Zhou">PMID:30630874</ref>.

</StructureSection>

== References ==
<references/>

==Student Contributors==
Layla Wisser

Daniel Mulawa

2020-04-07T04:20:22Z

Daniel Mulawa:

File:App.png

2020-04-07T04:17:43Z

Daniel Mulawa:

2020-03-30T22:27:06Z

Daniel Mulawa:

='''Gamma Secretase'''=
<StructureSection load='5FN2' size='350' frame='true' side='right' caption='Human Gamma Secretase Basic Structure.' scene=’’>

=Gamma Secretase=

==Introduction==

===Background===
Gamma Secretase is a transmembrane aspartate protease. It catalyzes peptide bond hydrolysis of type I integral membrane proteins such as Notch, APP, and various other substrates. It recognizes and catalyzes the reaction with its substrate using 3 residue segments. These substrates generate amyloid-β (Aβ). This product is important for various neural processes, and it is well known for its Implications with Alzheimer’s disease (AD). This has made gamma secretase a popular drug target, specifically using gamma secretase (GS) inhibitors. However, due to the nature of gamma secretase having various neural functions, there are dangerous side effects when it is inhibited.

===Overall Structure===
Γ-secretase is composed of 20 transmembrane components (TMs) and has 4 subunits: Nicastran, Anterior Pharynx-defective 1, Presenilin, and Presenilin Enhancer 2. These subunits are stabilized by hydrophobic interactions and 4 phosphatidylcholines.These phosphatidylcholines have interfaces between: PS1 and PEN-2, APH-1 and PS1, APH-1 and NCT.
Nicastrin (NCT) has a large extracellular domain and 1 TM. It is important to substrate recognition and binding.
Presenilin (PS1) serves as the active site of the protease and contains 9 TMs, each varying in length. The site of autocatalytic cleavage is located between TM6 and TM7 in PS1 and major conformational changes take place in this subunit upon substrate binding.
Anterior pharynx-defective 1 (APH-1) serves as a scaffold for anchoring and supporting the flexible conformational changes of PS1
Activation of the active site is dependent on the binding of Presenilin enhancer 2 (PEN-2). PEN-2 is also important in maturation of the enzyme.

== Structural highlights ==
===Substrate Structure===
Though gamma secretase has multiple substrates, the substrate of main concern is called Amyloid Precursor Protein (APP). APP is composed of an N-terminal loop, a transmembrane (TM) helix, and a C-terminal β-strand. The uses lateral diffusion as a mechanism of entry into the enzyme, and once in place, the TM helix is anchored by hydrogen bonds. In order to differentiate substrates, the β-strand is often the main point of identification for the enzyme. After this, the helix undergoes unwinding and the process of catalysis can begin.

===Lid Complex===
[[Image:777.png|300 px|right|thumb|Lid Complex of Gamma Secretase]]
Lid is the first point of entry and recognition for the substrate. This lid complex is located within the NCT subunit between Asn55 and Asn435. This lobe is divided into two separate subunits, and Phe287 from large lobe acts as pivot between them. This Phe is further surrounded by Phe103, Leu171, Phe176, and Ile180 of the small subunit, and these residues compose a greasy pocket for that provides an environment for easy movement. The lid consists of 5 aromatic residues which are highly involved with stabilizing the closed conformation. In particular, this conformation is stabilized by Trp164, which has interacts with Pro424, Phe448, and the aliphatic side chain of Gln420. Once the substrate binds and the lid is opened, a charged, hydrophilic pocket is revealed. This pocket contains Glu333 and Tyr337 surrounded by several charged residues, and is involved with further substrate binding and recognition.

===Active Site===
[[Image:Asp with Pal labeled.png|300 px|right|thumb|Active Site of Gamma Secretase]]
The <scene name='83/832945/Active_site/1'>active site</scene> is located between TM6 and TM7 of the PS1 subunit, which is mainly hydrophilic and disordered. Each of these transmembrane helices has an aspartate residue, <scene name='83/832945/Asp_257_and_asp_385/1'>Asp 257 and Asp 385</scene>, which are located approximately 10.6 A˚ apart when inactive.<ref name="Bai">PMID:26280335</ref> The PAL sequence of <scene name='83/832945/Pal_sequence/1'>Pro433, Ala434, and Leu435</scene> is in close proximity with the catalytic aspartates and is important to substrate recognition. Gamma secretase becomes active upon substrate binding, when TM2 and TM6 each rotate about 15 degrees to more closely associate and the two Asp residues hydrogen bond to each other during catalysis. Asp257 and Asp385 are located 6–7 Å away from the scissile peptide bond of the substrate.

==Relevance==
APP build up leads to Amyloid plaques in brain
Inhibition of γ-secretase could be potential AD treatment
Location of majority of mutations
Over 200 mutations that cause AD
AD mutations heavily target interface between PS1 and APP
Important to look at differences between substrates

</StructureSection>

== References ==
<references/>

==Student Contributors==
Layla Wisser

Daniel Mulawa