Student Projects for UMass Chemistry 423 Spring 2012-4

From Proteopedia

1 Bone Morphogenetic Protein 7 (BMP-7)

Bone Morphogenetic Protein 7 (BMP-7)

Introduction

(BMP-7) is a protein that is involved in a variety of aspects of embryonic and adult development. Some of the areas it is involved in are neural tissue induction, the formation of bones and joints in the skeletal system, and neurogenesis in the adult brain. It regulated through the binding of different antagonists, such as Noggin, forming that shows the two separate components of the complex. Neural induction is the process by which the undifferentiated ectoderm layer of the embryo are signaled to form neuro-ectoderm cells by the mesoderm. These differentiated cells will become neural cells. Only some of the cells are signaled to differentiate in this way, and the rest become the epidermis. In bone formation, first a flexible membrane is formed in the embryo that develops into cartilage. As the embryo develops, signaling through proteins in the BMP family including BMP-7 causing ossification to occur, which is the process of forming bone, replacing the cartilage membranes. This can be seen in the development of the skull. BMP can also signal for cartilage to transform to bone, which is how much of the rest of the skeleton develops. One of the most important aspects of BMP-7 is its role in neurogenesis in the adult brain. Neurogenesis is the process by which new neurons are created in the adult brain. Initially it was thought that proteins in the BMP family would inhibit neurogenesis unless deactivated by the antagonist, Noggin. But when the levels of neurogenesis were examined with the over expression and signalling of BMP, there was no inhibition of the creation of neurons. In fact further research has shown that BMP-mediated signalling is required to allow neurogenesis in adults.[i]

Because BMP’s are crucial in much of the development and upkeep of many organs and systems, there are many disease that can arise or be affected by dysfunctional BMP genes and proteins. The incorrect implementation of BMP-7 during development can result in issues with skeletal and neural development. BMP-7 can also have impacts after the initial fetal development. Research has linked a lack of BMP-7 signalling to the progression of gastrointestinal cancers, particularly colon and esophageal cancer.[ii]

There have also been developments in using BMP’s as therapeutics. Because the main role of BMP’s is bone formation, one of the most promising areas is in bone reformation after injury. BMP-7 and BMP-2 have been successfully adapted and used in combination with bone grafts during surgery, and have been extremely useful in spinal cervical fusion. [iii]

While these therapeutics are great developments, there is still much more potential because of the effects of BMP on the whole body. Currently, research is being conducted to understand how BMP-7 can be used in treating chronic kidney disease. And because of the ability to regulate neurogenesis, it is possible that BMP proteins can be used in the treatment or cure of neurodegenerative diseases such as Alzheimer's. [ii]

Overall Structure

BMP-7 has a variety of structural characteristics. First and foremost are the two different proteins which make up the Bone Formation complex. We can see BMP-7 and the Noggin in the scene to the right (). The secondary structures in BMP-7 are vital to the proteins function (specifically the binding). The alpha helicies and beta sheets in the green screen to the right (). The anti parallel beta sheets in the BMP-7 portion of the complex (the smaller domain) are vital for the binding interactions of the molecule. It is these anti-parrallel sheets which bind Noggin (the aforementioned red protein). These are pointed towards in the previous depiction.

BMP-7 is the most functionally important to the molecule. It contains the regions for cytokine binding, protein complex binding, and protein homodimerization ^[1]. These functions are discussed in the following binding section.

In addition to these pieces there are two important sites AC1 and AC2. The AC1 site is pictured as follows, the active site is in between the red colored faces of the beta sheets. . Lastly there is a site for a ligand to bind. The location of these anti parallel binding sheets is seen .

Binding Interactions

BMP-7 uses two pairs of antiparallel referred as Finger 1 and Finger 2 for binding activities. The curvature of the fingers creates a site in which the α3 of the other subunit binds to stabilize the . Free BMP-7 shows conformational changes in the "wrist " and "knuckles" areas upon complexing with receptors and antagonist proteins.^[2] has Finger 1 and Finger 2 have a flat shape, however upon with noggin or another BMP-7 the protein adopts an arc shape.

by BMP-7 occurs by the binding of the protein to high affinity type II receptor (at the knuckles epitope) follow by the recruitment of the low affinity type I receptor (at the "wrist " epitope). The binding causes the trans-phosphorylation of the Type I receptor at a a glycine- and serine- rich region (GS-Box) by the type II receptor kinase.^[3] Afterwards the type I receptor Ser/Thr-kinase activates leading to intracellular signaling.

Bone morphogenetic proteins (BMPs)are regulated by the binding of three classes of antagonist inhibitory proteins: Noggin; the DAN family; and verterbrate Chordin and Drosophila SOG. Noggin is a homologous BMP-specific anatagonist protein found to regulate the dorsal structures in ventralized Xenopus embryos. The structure of the of the Noggin resembles the BMPs in that it have two pairs of antiparallel β-strands extending out from a core containing disulphides bonds. In contrast to BMP-7, binding of the monomer consists of between the α4 of each monomer. When noggin binds to BMP-7, the tip of finger 1 and 2 in BMP-7 curls around the N-terminal segment of the noggin.^[4]

BMP ligands have two prominent for receptor binding interfaces: convex type II and concave type I. Superposition of the noggin-BMP-7 structure show the masking of both pairs of binding epitopes. The obstruction of the type I receptor-binding occurs due to hydrophobic interactions. The of Pro 35 of the noggin inserts into the hydrophobic pocket on BMP-7 formed by Trp 52, Trp 55, Val 87, Tyr 128, and Met 131.^[5] In contrast, the type II receptor-binding is obstructed by the C-terminal half of the clip segment by the distal tip of finger 1 and by finger 2. In summary, the binding of noggin to BMP-7 consists of a hydrophobic side chain from the backbone insetred into the hydrophobic pocket of BMP followed by complementary interactions between two curved hydrophobic surfaces.

Follistatin is a proposed BMP antagonist which is present in embryonic muscle cells. The BMP antagonist enhances the BMP-7 action for muscle grwoth but it prevents the induction of apoptosis and muscle loss. The antagonist protein interacts directly with BMP but does not prevent the ligan from binding to its receptors resulting in a trimeric complex.^[6]

Additional Features

BMPs and their antagonists such as Noggin can affect developing chick limbs. Through experimentation, it was found that wild type – Noggin and "Cys232 variant" (formation of cartilage of developing limbs) but Pro35Arg weakly inhibits chondrogenesis. Glu48Lys, Ile218Glu, Leu46Asp Noggin . These variants also inhibits interdigital apoptosis in the same way. In this process, purified noggins was added to beads and exposed to developing chick limbs. Mutations in human Noggin gene (NOG) cause changes in joint formation. If there are changes in positions of Pro35Arg, Cys184Tyr, Gly189Cys, Ile220Asn, Tyr222Cys/Tyr222Asn, or Pro223Leu, it is . Changes in positions of Pro35Arg, Arg204Leu, and Tyr222Cys is associated with tarsal/carpal coalition syndrome (TCC) and changes with Trp217Gly with multiple synostoses (SYNS1). Most of these changes can cause problem with joint formation and folding and stability. One particular mutation of interest is which is similar to Noggin Pro35Arg because it decreased binding affinities and lower inhibition of chrondogenesis. It is due to the structure of the polar hydroxyl group of serine that it is unable to bind to the hydrophobic pocket on the BMP. ^[7]

Credits

Introduction - Alec

Overall Structure - William

Drug Binding Site - Felix

Additional Features - Paula

References

↑ Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature. 2002 Dec 12;420(6916):636-42. PMID:12478285 doi:10.1038/nature01245
↑ Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature. 2002 Dec 12;420(6916):636-42. PMID:12478285 doi:10.1038/nature01245
↑ Sebald W, Mueller TD. The interaction of BMP-7 and ActRII implicates a new mode of receptor assembly. Trends Biochem Sci. 2003 Oct;28(10):518-21. PMID:14559178
↑ Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature. 2002 Dec 12;420(6916):636-42. PMID:12478285 doi:10.1038/nature01245
↑ Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature. 2002 Dec 12;420(6916):636-42. PMID:12478285 doi:10.1038/nature01245
↑ Amthor H, Christ B, Rashid-Doubell F, Kemp CF, Lang E, Patel K. Follistatin regulates bone morphogenetic protein-7 (BMP-7) activity to stimulate embryonic muscle growth. Dev Biol. 2002 Mar 1;243(1):115-27. PMID:11846481 doi:10.1006/dbio.2001.0555
↑ Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature. 2002 Dec 12;420(6916):636-42. PMID:12478285 doi:10.1038/nature01245