This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2mwb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:35, 10 September 2015

FBP28 WW2 mutant W457F

Structural highlights

2mwb is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2mw9, 2mwa
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[TCRG1_HUMAN] Transcription factor that binds RNA polymerase II and inhibits the elongation of transcripts from target promoters. Regulates transcription elongation in a TATA box-dependent manner. Necessary for TAT-dependent activation of the human immunodeficiency virus type 1 (HIV-1) promoter.^[1] ^[2]

Publication Abstract from PubMed

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple beta-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.,Zhou R, Maisuradze GG, Sunol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18243-8. doi:, 10.1073/pnas.1420914111. Epub 2014 Dec 8. PMID:25489078^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sune C, Hayashi T, Liu Y, Lane WS, Young RA, Garcia-Blanco MA. CA150, a nuclear protein associated with the RNA polymerase II holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol Cell Biol. 1997 Oct;17(10):6029-39. PMID:9315662
↑ Goldstrohm AC, Albrecht TR, Sune C, Bedford MT, Garcia-Blanco MA. The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Mol Cell Biol. 2001 Nov;21(22):7617-28. PMID:11604498 doi:10.1128/MCB.21.22.7617-7628.2001
↑ Zhou R, Maisuradze GG, Sunol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18243-8. doi:, 10.1073/pnas.1420914111. Epub 2014 Dec 8. PMID:25489078 doi:http://dx.doi.org/10.1073/pnas.1420914111

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2mwb"

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[2mwb]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MWB FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2mw9|2mw9]], [[2mwa|2mwa]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mwb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mwb RCSB], [http://www.ebi.ac.uk/pdbsum/2mwb PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mwb OCA], [http://pdbe.org/2mwb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mwb RCSB], [http://www.ebi.ac.uk/pdbsum/2mwb PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2mwb" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

2mwb

From Proteopedia

Revision as of 18:35, 10 September 2015

FBP28 WW2 mutant W457F

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox