NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.
A Model of Interdomain Mobility in a Multidomain Protein
Structural Properties of Polyubiquitin Chains in Solution
THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS. FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 10%. CHAIN A CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C- TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER, BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION AND TRANSLATION AND NO CONSTRAINTS REPRESENTING THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR DATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE.
UBIQUITIN, LYS48-LINKED POLYUBIQUITIN, POLYUBIQUITIN, SIGNALING PROTEIN