Sandbox Reserved 474

From Proteopedia

(Difference between revisions)

Revision as of 02:47, 3 May 2012

This Sandbox is Reserved from 13/03/2012, through 01/06/2012 for use in the course "Proteins and Molecular Mechanisms" taught by Robert B. Rose at the North Carolina State University, Raleigh, NC USA. This reservation includes Sandbox Reserved 451 through Sandbox Reserved 500.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
Click the 3D button (when editing, above the wikitext box) to insert Jmol.
show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

For more help, look at this link: http://www.proteopedia.org/wiki/index.php/Help:Getting_Started_in_Proteopedia

C-Reactive Protein

C-Reactive Protein (CRP) is considered to be a normal plasma protein such that its concentration rises as a cytokine-mediated response resulting from tissue injury, infection or inflammation [1]. CRPs' structure is shown off to the right (PDB entry 1b09) and it does not have a specified active site. It's unique structure puts it in the pentraxin family which includes serum amyloid P component (SAP) and it consists of five identical, non-covalently associated protomers that are arranged in a symmetrical fashion weighing ~ 23kDa [1]. Since it's structure is highly conserved, the calcium dependent binding site allows found within CRP allows for strong binding to phosphocholine (PC) along with other structures and this makes it physiologically relevant. Some recent studies have made a prognostic comparison with increased CRP levels and coronary heart disease, thus reinforcing the idea that CRP also plays a significant role as a future therapeutic target [1].

1 Structure and Function
2 Mechanism
3 Methods Used
4 Regulation of CRP expression
5 Structure of CRP promoter
6 Structure of CRP pentamer
7 Phosphocholine-binding
8 Biological Implications
9 Mediator of Atherosclerosis
10 References

Structure and Function

CRPs five promoter structures are folded into two anti-parallel with flattened jellyroll topologies [2]. Each promoter contains a recognition face with a binding site consisting of two coordinated ions adjacent to a hydrophobic pocket. The co-crystallized structure of CRP with phosphocholine suggest that and are two very crucial residues that mediate binding between phosphocholine and CRP[2]. More specifically, Phe-66 provides specific hydrophobic interactions with the methyl groups of PC. Similarly, Glu-81 is located on the opposite end of the pocket where it interacts well with the positively charged choline nitrogen. Present on the opposite face of the pentamer is the effector face, where the presumed and Fcγ receptors bind, and at this cleft several residues are present ( and Tyr-175) which are both necessary to bind CRP to C1q [2].

Mechanism

Currently Unknown

Methods Used

Some of the methods used to determine the structure included: Crystallization, Data Collection and Processing, Obtaining the phases with molecular replacement and Model Building and refinement [3].

Regulation of CRP expression

Like any other protein, CRP is also regulated at the transcriptional level by cytokine interleukin-6 (IL-6) and by interleukin-1β (IL-1β)[2]. IL-6 and IL-1β are responsible for controlling expression through activation of several transcription factors including STAT3, C/EBP family members and Rel proteins (NF-κB). Due to specific cytokine induced interactions, this unique type of regulation can occur. For instance, STAT3 is considered to be a major factor for serum amyloid A genes, along with NF-κB for the fibrinogen genes [2]. Regarding CRP, the C/EBP (β&δ) are critical for induction [2]. Furthermore, not only do the internal interactions stabilize DNA binding and maximixe induction, but extrahepatic synthesis of CRP has been reported in in other areas such as neurons, atherosclerotic plaques mono- and lymphocytes [2].

Structure of CRP promoter

Based on homology modeling, CRP structure was found to be similar to that of SAP such that the subunits within the structure consisted of a two-layered β sheet with a flattened jelly roll topology [1]. Additionally, there is a presence of two calcium ions that are bound 4 Å apart by protein sidechains, and this is the site of binding, which is referred to as the B side [1]. The other side, designated A hosts a single α helix, and the pentameric disc shows five on one side with ten calcuim ions on the other [1]. The side walls on the A face are constructed from several residues including Asp-112.

Structure of CRP pentamer

In CRP, each subunit in CRP is rotated by 22° towards the five-fold axis in comparison to SAP, where the subunits are planar to each other [1]. Furthermore, an intermoleclar ion pair only forms in CRP from residues and , but this does not occur in SAP. One could deduce that by crystallizing the structure, it causes a shift of the actual ligand-binding sites on the B side of the pentamer which can effect overall binding to other significant structures.

Phosphocholine-binding

It is worthy to note that the major interaction that occurs between CRP and PC is located between the phosphate group of PC and the bound calciums [1]. While the majority of the PC molecule is packed tightly against Phe-66, the rest of the molecule binds thus resulting in a phosphate moiety ester linkage [1]. The overall distance between the the charged nitrogen of PC and the acidic Glu-81 is approximately 3.8 Å and this suggests that this particular interaction is important. Because of this physical phenomenon, future drugs could be developed to potentially block the CRP from binding.

Biological Implications

It is known that CRP belongs to a highly conserved pentraxin class that is responsible for innate immunity and it aids in the prevention of developing an autoimmunity [1]. For instance, a direct correlation has been made between increased levels of CRP to complications of atherosslerosis which may include a mycardial infarction. In addition, CRP has the ability to predict future outcomes as a result of the infarction. Furthermore, it was discovered that CRP deposits itself within the infarcted tissues and it activates complement [1]. This effect was presumed to promote both pro and anti effects of CRP, which leaves it open as a future drug target [1]. One other biological effect/function of CRP includes CRP's unique ability to identify pathogens to server as the hosts' first line of defense.

Mediator of Atherosclerosis

It has been shown that at known concentrations, CRP elicits effects which result in either proinflammatory or proatherosclerotic phenotype [4]. Several in vitro experiments have shown CRP to downregulate eNOS transcription, thus destabilizing its mRNA, resulting in in a decreased release of basel and stimulated NO, key endothelial factors [4]. By inhibiting NO production, CRP effectively facilitates apoptosis and blocks angiogenesis. Furthermore, it has been proposed that it is responsible for promoting the upregulation of nuclear factor-κB, which is a key promotor of several proatherosclerotic genes [4]. In addition, recent evidence has shown that it also has proatherogenic effects within smooth vascular muscle as well [4].

References

1. Darren Thompson, Mark B Pepys, Steve P Wood, The physiological structure of human C-reactive protein and its complex with phosphocholine, Structure, Volume 7, Issue 2, 15 February 1999, Pages 169-177, ISSN 0969-2126, 10.1016/S0969-2126(99)80023-9.

2. Steven Black, Irving Kushner, David Samols, C-reactive Protein*, Journal of Biological Chemistry, Volume 279,No. 47, Issue 19, 19 November 2004, Pages 48487-48490, DOI 10.1074/jbc.R400025200

3. PDB of CRP

4. Subodh Verma, Paul E. Szmitko, Edward T.H. Yeh, C-reactive Protein: Structure Affects Function, Journal of the American Heart Association, Volume 109, 2004, Pages 1914-1917, ISSN: 1524-4539, DOI: 10.1161/01.CIR.0000127085.32999.64

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_474"

@@ Line 10: / Line 10: @@
 == Structure and Function ==
 CRPs five promoter structures are folded into two anti-parallel <scene name='Sandbox_Reserved_474/Beta-sheet/1'>β-Sheets</scene> with flattened jellyroll topologies [2].  Each promoter contains a recognition face with a <scene name='Sandbox_Reserved_474/Phosphocholine/1'>phosphocholine</scene> binding site consisting of two coordinated <scene name='Sandbox_Reserved_474/Calcium_ion/1'>calcium </scene> ions adjacent to a hydrophobic pocket.
-The co-crystallized structure of CRP with phosphocholine suggest that <scene name='Sandbox_Reserved_474/Phe-66/2'>Phe-66</scene> and <scene name='Sandbox_Reserved_474/Glu-81/1'>Glu-81</scene> are two very crucial residues that mediate binding between phosphocholine and CRP[2].  More specifically, Phe-66 provides specific hydrophobic interactions with the methyl groups of PC.  Similarly, Glu-81 is located on the opposite end of the pocket where it interacts well with the positively charged choline nitrogen.  Present on the opposite face of the pentamer is the effector face, where the presumed <scene name='Sandbox_Reserved_474/C1q/1'>C1q</scene> and Fcγ receptors bind, and at this cleft are several residues present (<scene name='Sandbox_Reserved_474/Asp-112/1'>Asp-112</scene> and Tyr-175) which are both necessary to bind CRP to C1q [2].
+The co-crystallized structure of CRP with phosphocholine suggest that <scene name='Sandbox_Reserved_474/Phe-66/2'>Phe-66</scene> and <scene name='Sandbox_Reserved_474/Glu-81/1'>Glu-81</scene> are two very crucial residues that mediate binding between phosphocholine and CRP[2].  More specifically, Phe-66 provides specific hydrophobic interactions with the methyl groups of PC.  Similarly, Glu-81 is located on the opposite end of the pocket where it interacts well with the positively charged choline nitrogen.  Present on the opposite face of the pentamer is the effector face, where the presumed <scene name='Sandbox_Reserved_474/C1q/1'>C1q</scene> and Fcγ receptors bind, and at this cleft several residues are present (<scene name='Sandbox_Reserved_474/Asp-112/1'>Asp-112</scene> and Tyr-175) which are both necessary to bind CRP to C1q [2].
 == Mechanism ==