A Simtk Project Wiki

Welcome to your blank Simtk project wiki. Feel free to replace this wiki page with an introduction to your project and links to future wiki pages. (HelpOnPageCreation lists all the ways you can create a new page.)

Members of your project have full permissions to read, write, revert and delete pages. If you visit any non-existing page URL, you'll be shown a variety of templates for pages. You can choose among the following, from most permissive to most restrictive:

PublicWriteTemplate -- Anyone can edit this page. Deletes and reverts are limited to project members.
PublicReadTemplate -- Anyone can read the wiki page. Only your project's members can edit the page.
SimtkReadTemplate -- Any Simtk.org registered user can read the wiki page. Only your project's members can edit the page.

The default is to create an empty page which is only accessible to project members funny quotes dental implants funny jokes hilarious quotes nursery rhymes funny facebook status. If you want to force all wiki pages to be public or have some special permissions, contact a Simtk.org webmaster( webmaster@simtk.org ).

In addition to quickly adding new pages using templates, you can manually modify permissions for a page by adding or editing an Access Control List (ACL) statement at the top of the wiki page. (The details are here)

Each Simtk.org registered member can have permissions set by using the camel case version of their Simtk full name. For example, "John Doe" can have permissions set as JohnDoe:

#acl +JohnDoe:read

The above will let John Doe read the wiki page.

Interesting starting points:

RecentChanges: see where people are currently working
WikiSandBox: feel free to change this page and experiment with editing
FindPage: search or browse the database in various ways
SyntaxReference: quick access to wiki syntax
SiteNavigation: get an overview over this site and what it contains

This wiki farm is part of Simtk.org

How to use this site

A Wiki is a collaborative site, anyone can contribute and share:

Edit any page by pressing Edit at the top or the bottom of the page
Create a link to another page with joined capitalized words (like WikiSandBox) or with ["quoted words in brackets"]
Search for page titles or text within pages using the search box at the top of any page
See HelpForBeginners to get you going, HelpContents for all help pages.

To learn more about what a WikiWikiWeb is, read about WhyWikiWorks and the WikiNature. Also, consult the HelpMiscellaneous/FrequentlyAskedQuestions page.

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Computer-aided engineering of chimeric myosin VI

Probing the reverse directionality of myosin VI

Myosin VI moves toward the (-) end of actin filaments, despite sharing extensive sequence and structural homology with (+) end directed myosins. A unique insert between the converter domain and the lever arm was proposed to provide the structural basis of directionality reversal (J. Menetrey, et al, Nature 2005). Single molecule analysis of truncated versions of myosin VI strongly supports this model (Z. Bryant, D. Altman, and J.A. Spudich, PNAS 2007). To further explore the structural determinants of directionality, we designed a series of myosin VI constructs with artificial lever arms fused at different locations beyond the converter domain. Computational modeling including molecular dynamics simulation was used to predict the behavior of chimeric designs and select optimal fusion locations. In vitro motility assays were used to characterize the directionality and velocity of the chimeras. Our results demonstrated that the calmodulin-bound distal portion of the unique insert is not an integral structural or mechanistic component of the reverse stroke. Furthermore, we showed that as few as 18 residues are required to change the directionality of myosin funny quotes dental implants funny jokes hilarious quotes nursery rhymes funny facebook status.

Model structures of chimeric constructs were first predicted computationally. We have examined constructs fused at 5 different locations, i.e. residue numbers 789, 790, 791, 792, and 793 of myosin VI. Model structures predicted 789 and 793 to have structural collisions. We then ran molecular dynamics simulation for constructs 790, 791, and 792. The construct 792 showed the artificial lever arm unwinds a key alpha-helix in the myosin converter domain, while 790 and 791 were structurally stable for at least 2 ns. Construct 790 appeared to have the least structure hindrance if myosin undergoes conformational changes. In vitro motility assay was used to test all these constructs. Basically, one observed the movement of actin filaments driven by myosin attached on the glass surface in this assay. Experiments showed indeed that constructs 789, 792, and 793 could not move the actin filaments, while 790 and 791 were active.

[Results of simulations] funny quotes dental implants funny jokes hilarious quotes nursery rhymes funny facebook status