Well, mine is a beta-barrel protein called Green Fluorescent Protein. In such a case the movement of ion is very important. As the ion in side the barrel can quench the fluorescence. That's what I want to track.. <br><br>
<div class="gmail_quote">On Mon, May 30, 2011 at 4:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me in determining the binding affinity. So, my first objective can be achieved with it.<br>
<br>
Then what about the movement of ions into the barrel. Will it be possible to track it with MD coz the movement of ion is very important in my case. I don't want them to enter the barrel rather I want them to be on the surface of the barrel??<br>
<br>
</blockquote>
<br></div>
You can implement such restraints, or guide the ion through the channel, whichever you prefer. The literature is rich with studies of the movement of ions and small molecules through transporters and channels.<div><div>
</div><div class="h5"><br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>