2K3B

Seeing the Invisible: Structures of Excited Protein States by Relaxation Dispersion NMR

Summary for 2K3B

• Entry DOI: 10.2210/pdb2k3b/pdb
• NMR Information: BMRB: 16843
• Descriptor: Actin-binding protein (1 entity in total)
• Functional Keywords: cpmg, abp1p, ark1p, invisible state, acetylation, actin-binding, cytoplasm, cytoskeleton, phosphoprotein, sh3 domain, structural protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Cytoplasm, cytoskeleton, actin patch: P15891
• Total number of polymer chains: 1
• Total formula weight: 6993.48

Authors

Vallurupalli, P.,Hansen, F.D.,Kay, L.E. (deposition date: 2008-04-30, release date: 2008-07-29, Last modification date: 2024-05-29)

Primary citation

Vallurupalli, P.,Hansen, D.F.,Kay, L.E.
Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy
Proc.Natl.Acad.Sci.Usa, 105:11766-11771, 2008

PubMed Abstract: Molecular function is often predicated on excursions between ground states and higher energy conformers that can play important roles in ligand binding, molecular recognition, enzyme catalysis, and protein folding. The tools of structural biology enable a detailed characterization of ground state structure and dynamics; however, studies of excited state conformations are more difficult because they are of low population and may exist only transiently. Here we describe an approach based on relaxation dispersion NMR spectroscopy in which structures of invisible, excited states are obtained from chemical shifts and residual anisotropic magnetic interactions. To establish the utility of the approach, we studied an exchanging protein (Abp1p SH3 domain)-ligand (Ark1p peptide) system, in which the peptide is added in only small amounts so that the ligand-bound form is invisible. From a collection of (15)N, (1)HN, (13)C(alpha), and (13)CO chemical shifts, along with (1)HN-(15)N, (1)H(alpha)-(13)C(alpha), and (1)HN-(13)CO residual dipolar couplings and (13)CO residual chemical shift anisotropies, all pertaining to the invisible, bound conformer, the structure of the bound state is determined. The structure so obtained is cross-validated by comparison with (1)HN-(15)N residual dipolar couplings recorded in a second alignment medium. The methodology described opens up the possibility for detailed structural studies of invisible protein conformers at a level of detail that has heretofore been restricted to applications involving visible ground states of proteins.

PubMed: 18701719
DOI: 10.1073/pnas.0804221105

Experimental method

SOLUTION NMR