UTF-8Modeling hydrophobic effectBGSU CHEM 4450/5450 General Biochemistry I Final Project
Over the past two weeks you've explored properties that affect miscibility of two liquids and considered the difference between properties that affect individual particles vs. those that arise from collections of particles. The Final Project of this semester for our evening sessions is focused on investigating what gives rise to the tendency for soluble proteins to fold with their hydrophobic amino acids on the interior and 'hidden' from the aqueous solvent. You can work towards a better understanding of this phenomenon by modifying the following model to recapitulate a similar behavior ('understanding' in this case means knowing what is required to cause the behavior).
Below, there are two compartments with the following characteristics:
- each has a polymer of 24 linked, green particles (all of the same particle type, 'Pl'). Note: any change you make to the particles of one polymer will by definition affect the other polymer too!
- each polymer is 'pinned' to the center of the compartments (small white 'x' symbol)
- the radius of gyration (Rg) for each polymer is plotted on the graph at the right as a measure of how compact or folded each polymer is. Rg is a calculated value that essentially measures the average distance between all monomers in a polymer. Extended polymers have larger Rg values, whereas folded polymers have smaller Rg values.
The Challenge: Make changes to the compartments (adding solvent particles, changing particle properties, etc.) to control how folded the polymers are.
First: we will work in groups the first night (Dec. 2). There will be 4 groups trying to get their polymer to fold or unfold with either weak or relatively strong monomer:monomer interactions.
Second (for next week): Make the polymer in the left compartment as compact/folded as possible and the other as extended as possible. In other words, create conditions in the two compartments that maximize the difference between their radii of gyration.
Note:
- to select an individual particle in the polymer, hold down the <Shift> key and left-click with your mouse (double-left-click to modify the polymer particle properties).
- you are asked to output the radius of gyration data to Excel for questions below. To do this, click the "List data sets" button (leftmost button) above the graph and double click on one of the channels. Channel 0 corresponds to the left polymer, channel 1 to the right (see pink labels on polymers). Paste into MS Excel. There are three columns:
- column 1: 'i' (the index of the data point measured)
- column 2: the time point (i.e. measured in thousands of femtoseconds)
- column 3: the radius of gyration for the given polymer at that index/time point
Questions (to be answered directly in the page below and uploaded):
1.)Please type your name here:Jon Mase
2.) Describe your assigned challenge: 0.2eV, folded, high temperature
3.) What were the initial conditions for your challenge in terms of:
- monomer:monomer interactions
- presence of solvent (yes/no)
- solvent:solvent interactions
- solvent:polymer interactions
4.) What were the Rg cutoffs that were decided as a class to represent:
- a folded polymer:
- an unfolded or extended polymer:
How well does Rg work to keep track of how folded the polymers are?
5.) Describe in complete, descriptive sentences what you did to solve your challenge. Did it work? How do you know?
Alright, so to start off we changed from our molecule from 0.01eV to 0.2eV. I also changed my temperature to the maxium T available, 340K. Looking at differences between 0 and 1, it's clear that polymer 1 can fold without any additional help from the program. By simply letting it run about at 340K, I was able to get a radius of 3.98. After letting polymer 1 run for about two minutes, the graph for radius was horizontal, without any significant changes. For polymer 0, I went ahead and added solvent molecules (+1 selection). These were able to force the polymer to a folded state. However, even though my radius values hovered between 3.9 and 4.1 the entire time, I was unable to get a linear/horizontal progression like for polymer 1. In order to get a more linear progression, I had to change the charges on the polymer particle. For the first six, I made the charges postive, and for the next six I made them negative, then repeat for the next 12 particles in the polymer chain. Then, I added solvent molecules (+2), which crushed the polymer into a folded state. If I changed the mass of the solvent molecules (i.e. MW of 10,000), I really sandwiched them together. However, the radius is still not linear, but on a small scale it looks like a sine curve.
6.) If your solution could have worked better, what else would you try?
I'm pretty sure if I made the solvent molecules heavier, and heavier, and heavier, then eventually I would smother them to death. This would really crush the molecules together, probably giving me an even smaller radius, though I doubt by much. However, another thing I would like to try is making the polymer a small molecular weight (1 g/mol) and all positive. Then, make huge solvent molecules with a molecular weight of 1,000,000 g/mol that are negatively charged. This sounds like a lot of work, so I'll just leave it to speculation. Without actually changing the charges, I could try varying solvent combinations like somebody else suggested to try and smother them regardless. Maybe use a smaller, more realistic molecular weight while I'm at it.
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