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.

2mor

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 17:02, 15 August 2018

A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings

Structural highlights

2mor is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1d3z
Gene:	UBC (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[UBC_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.^[1] ^[2]

Publication Abstract from PubMed

Residual dipolar couplings (RDCs) are parameters measured in nuclear magnetic resonance spectroscopy that can provide exquisitely detailed information about the structure and dynamics of biological macromolecules. We describe here a method of using RDCs for the structural and dynamical refinement of proteins that is based on the observation that the RDC between two atomic nuclei depends directly on the angle vartheta between the internuclear vector and the external magnetic field. For every pair of nuclei for which an RDC is available experimentally, we introduce a structural restraint to minimize the deviation from the value of the angle vartheta derived from the measured RDC and that calculated in the refinement protocol. As each restraint involves only the calculation of the angle vartheta of the corresponding internuclear vector, the method does not require the definition of an overall alignment tensor to describe the preferred orientation of the protein with respect to the alignment medium. Application to the case of ubiquitin demonstrates that this method enables an accurate refinement of the structure and dynamics of this protein to be obtained.

A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings.,Camilloni C, Vendruscolo M J Phys Chem B. 2014 Jun 4. PMID:24824082^[3]

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

References

↑ Huang F, Kirkpatrick D, Jiang X, Gygi S, Sorkin A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Mol Cell. 2006 Mar 17;21(6):737-48. PMID:16543144 doi:S1097-2765(06)00120-1
↑ Komander D. The emerging complexity of protein ubiquitination. Biochem Soc Trans. 2009 Oct;37(Pt 5):937-53. doi: 10.1042/BST0370937. PMID:19754430 doi:10.1042/BST0370937
↑ Camilloni C, Vendruscolo M. A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings. J Phys Chem B. 2014 Jun 4. PMID:24824082 doi:http://dx.doi.org/10.1021/jp5021824

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/2mor"

Categories: Human | Camilloni, C | Vendruscolo, M | Signaling protein | Ubiquitin

@@ Line 1: / Line 1: @@
 ==A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings==
 <StructureSection load='2mor' size='340' side='right' caption='[[2mor]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2mor]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MOR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2mor]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MOR FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d3z|1d3z]]</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=2mor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mor OCA], [http://pdbe.org/2mor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mor RCSB], [http://www.ebi.ac.uk/pdbsum/2mor PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2mor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mor OCA], [http://pdbe.org/2mor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mor RCSB], [http://www.ebi.ac.uk/pdbsum/2mor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2mor ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Camilloni, C]]
 [[Category: Vendruscolo, M]]
 [[Category: Signaling protein]]
 [[Category: Ubiquitin]]

2mor

From Proteopedia

Revision as of 17:02, 15 August 2018

A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox