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[[Biomod/2011/MIT/Origami/Process | <font face="courier new" style="color:#ffffff"> '''Process''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/Process | <font face="courier new" style="color:#ffffff"> '''Process''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/Potential | <font face="courier new" style="color:#ffffff"> '''Potential''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/Potential | <font face="courier new" style="color:#ffffff"> '''Potential''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/ScrappedIdeas | <font face="courier new" style="color:#000000"> '''Scrapped Ideas''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/ScrappedIdeas | <font face="courier new" style="color:#000000"> '''Tentative Ideas''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/TeamMembers | <font face="courier new" style="color:#ffffff"> '''Team Members''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/TeamMembers | <font face="courier new" style="color:#ffffff"> '''Team Members''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/Literature | <font face="courier new" style="color:#ffffff"> '''Literature''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Biomod/2011/MIT/Origami/Literature | <font face="courier new" style="color:#ffffff"> '''Literature''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

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For Meeting 8/10/11

What we went over at the last meeting was that the relatively low number of envelope spikes with an uneven distribution on the surface of the virion made it harder for antibodies to simultaneously bind two spikes at once, making it harder to neutralize the virion and mount an effective immune response. The question was why were these spikes so unevenly distributed and as I understood it, if it was possible to find where these were ultimately anchored. Previously, I had mentioned that it was something like GP120(Extracellular)----->GP41(transmembrane)------>Cytoplasmic tail of GP41 Now, I found that there is a protein called Tail Interacting Protein 47(TIP47) that interacts with that cytoplasmic tail of GP41 as well. The same TIP47 interacts with the viral matrix, acting as a linker. So the complete connection between them is something more along the lines of: GP120(Extracellular)-------->GP41(Transmembrane)------>GP41 Cytoplasmic Tail------->TIP47 Linker--------->P17 protein composing HIV matrix Overexpression of TIP47 results in an increase in the number of incorporated envelope spikes, while silencing of it results in impaired infectivity through lack of said spikes. link

For Meeting 8/3/11

The above figure from this paperhighlights one of the main issues that antibodies have with neutralizing HIV antigens. The paper suggests that in addition to being highly mutate-able and the hiding of the conserved regions by carbohydrates and the spatial trimer arrangement, HIV has something else that enables it to evade immune detection.

As the figure shows, there are other viruses that use similar trimer spikes and yet more successful antibodies and or vaccines have been developed against them. The diagram shows that HIV's spikes are not only less orderly distributed but also much farther apart on average than the spikes displayed by other viruses. Although increased number of spikes is associated with increased infectivity, it also appears that a lower number of spikes enables the virus to stick around longer.

With an average of only about 14 spikes per virion, even a neutralization of a handful of spikes would represent a significant decrease in the virion's ability to infect host cells. In part F of the figure we see that the distribution of distances between spikes is such that the mode is at around 15, but the tail brings the actual average to somewhere around 25 to 30 nm. The problem is that these distances are beyond the range that antibodies can bivalently bind to, minimizing their effectiveness.

Where DNA origami can come into play is the flexibility and size advantage it offers. Whereas antibodies can only bivalently bind if the antigens are within about 15 nm, DNA origami structures can be much larger, as demonstrated by the 42 x 36 x 36 nm DNA box. In addition, a certain amount of flexibility can be built in to the strands to account for the variability in inter-spike distances. A spider like DNA structure with flexible legs would appear to be a viable goal.

Structure and Arrangement

One of the major processes in HIV's life cycle is the synthesis of gp160, a precursor to gp120. A protease then cleaves gp160 into the functional sub-components that exist on the surface of HIV as part of the envelope, gp120 and gp41. The amino acid chain of gp120 consists of 5 conserved and 5 variable sequences, alternating among each other. Conserved regions 3 and 4 appear to be particularly important to the efficient binding of the glycoprotein to CD4, and in particular some labeled amino acids that we will discuss later. According to the literature, gp120s are noncovalently associated with gp41(which is anchored in the virus' plasma membrane) and three of these heterodimers associate to form an envelope "spike" on the surface of HIV.

The above diagram gives a better picture on the functional trimer of glycoproteins. The colored portions denote carbohydrates that cover exposed parts of the glycoprotein, enabling the virus to hide from the immune system.

Interactions and Strength

As mentioned previously, the sequential interaction of gp120 with CD4 and then a co-receptor is necessary for the start of new HIV life cycle. GP120 also non covalently interacts with gp41, which I've possibly mentioned as an interaction we can try to displace, since GP120 has been shown to "shed" from the virus after interacting with CD4. The strength of the interactions with the co-receptors and the gp41 continues to elude me, but I have found that the Gibbs free energy for the interaction of gp120 with CD4 is -11 kcal/mol. Apparently the change in entropy is unfavorable, because the reaction causes significant ordering, but this is balanced out by a favorable change in enthalpy.

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