User:Luis E Ramirez-Tapia/Sandbox 3

From Proteopedia

Revision as of 02:30, 26 April 2011

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground

Conformational Changes on T7 RNA polymerase

starting at the N-terminus, begins with a DNA-binding "headpiece", followed by a hinge region, then an N-terminal ligand-binding subdomain and a C-terminal ligand binding subdomain

....Transcription is a fundamental part of genetic regulation, the correct transcription of DNA to RNA depends of several factors like...., making the study of the transcriptional process more complicated, specially in higher organisms. The RNA polymerase of the bactereophage T7, overcomes the difficulty of studying the transcription process, mainly because it is a single unit enzyme that processes RNA with the affectivity as the polymerase from higher organisms. Still much of the mechanism is unknown, for example, during the Initial steps of transcription GREEN LINK an event called abortive cycling occurs (Figure X), where the small RNA transcripts (less than 12 bases) fall from the complex. This event will continue until the enzyme/DNA/RNA complex reach the elongation GREEN LINK phase, where a more stable enzyme/DNA/RNA complex is form. A mayor contributor of the stability of the complex is the formation of the RNA exit tunnel GREEN LINK.

One of the most striking characteristics of this enzyme is the HUGE conformational change of the N-terminus part GREEN LINK of the enzyme. There has been good advances in solving how the Subdomain H (alfa-helices in green) and the helices C1-C2 (yellow) refolds, specially thanks to a new intermediate state structure (PDB ID:3e2e) between the conformation and the complex, still there are some imporant details that are missing.

Using a energy minimization morphing software (Yale Morph), a morph between the INITIATION and the INTERMIDATE STATE structures was created. Press the BUTTON

If we try to use the three structures of the conformation change, an interesting event happen, Could you see what is the problem?. Hopefully someday we will be able to have a intermediate state between the enzyme/DNA/RNA complex with a 7 mer transcript and the elongation complex.

See Also

• Molecular Playground/T7 RNA Polymerase (7 mer int)