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PDBsum entry 2k3b

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protein links
Structural protein PDB id
2k3b
Jmol
Contents
Protein chain
59 a.a. *
* Residue conservation analysis
PDB id:
2k3b
Name: Structural protein
Title: Seeing the invisible: structures of excited protein states by relaxation dispersion nmr
Structure: Actin-binding protein. Chain: a. Fragment: sh3 domain. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Gene: abp1. Expressed in: escherichia coli.
NMR struc: 10 models
Authors: P.Vallurupalli,F.D.Hansen,L.E.Kay
Key ref:
P.Vallurupalli et al. (2008). Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci U S A, 105, 11766-11771. PubMed id: 18701719 DOI: 10.1073/pnas.0804221105
Date:
30-Apr-08     Release date:   29-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15891  (ABP1_YEAST) -  Actin-binding protein
Seq:
Struc:
 
Seq:
Struc:
592 a.a.
59 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1073/pnas.0804221105 Proc Natl Acad Sci U S A 105:11766-11771 (2008)
PubMed id: 18701719  
 
 
Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy.
P.Vallurupalli, D.F.Hansen, L.E.Kay.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Probing chemical shifts and residual anisotropic interactions in the invisible, excited state. (A) Stick model of a polypeptide chain fragment highlighting the dipolar (^1HN-^15N, ^1H^α-^13C^α, ^1HN-^13CO) and chemical shift anisotropy (^13CO) interactions of the invisible, excited state that are probed (arrows), as well as the chemical shifts (^1HN, ^15N, ^13C^α and ^13CO) that are measured (balls) by the relaxation dispersion NMR experiments that were recorded for the present work. (B–F) Typical relaxation dispersion profiles recorded on samples of ^15N,^2H- (B, C, and F), ^13C^α- (D), or ^15N,^13CO,^2H- (E) labeled Abp1p SH3 domain and substoichiometric amounts of Ark1p peptide (≈5–10% by mole fraction, depending on the sample) at static magnetic field strengths of 500 and 800 MHz (red and blue points, respectively), 25°C, along with global fits of the data to a model of two-site chemical exchange (solid lines).
Figure 3.
Solution structure of the invisible, Ark1p-peptide bound conformation of the Abp1p SH3 domain. (A) Ensemble of 10 starting structures generated from high temperature molecular dynamics of the apo-Abp1p SH3 domain x-ray structure (22), as described in the text. Regions in gray are fixed to the x-ray structure, because Δϖ[RMS] ≈ 0. The pair-wise rmsd values of the backbone C^α, CO and N atoms of regions 1 (red), 2 (blue) and 3 (green) are 5.8 ± 1.6, 3.7 ± 1.0, 2.6 ± 0.7 Å, respectively (10.4 ± 1.6, 8.6 ± 1.2, 3.8 ± 0.6 Å with respect to the apo-Abp1p1 SH3 domain x-ray coordinates). (B) Ensemble of the 10 lowest energy structures generated using (φ, ψ) restraints exclusively, as described in the text. Pair-wise rmsd values of regions 1, 2 and 3 are 3.1 ± 1.4, 3.8 ± 2.4 and 1.2 ± 0.7 Å, respectively. (C) As in B, but including restraints from residual anisotropic interactions as measured using a single alignment media (Pf1). The rmsd values of 0.39 ± 0.12, 0.30 ± 0.11 and 0.20 ± 0.06 Å are calculated for regions 1–3 (0.47 ± 0.10, 0.76 ± 0.14 and 0.53 ± 0.07 Å to the reference structure of the bound form). Inset, ribbon diagram of the apo-Abp1p SH3 domain x-ray structure; all conformers in the figure are in the same orientation. All of the rmsd values reported are calculated by superimposing the “fixed” regions (gray in Fig. 2C); the fixed regions are not included in the computation.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21857680 G.Bouvignies, P.Vallurupalli, D.F.Hansen, B.E.Correia, O.Lange, A.Bah, R.M.Vernon, F.W.Dahlquist, D.Baker, and L.E.Kay (2011).
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.
  Nature, 477, 111-114.
PDB codes: 2lc9 2lcb
21424227 G.Bouvignies, P.Vallurupalli, M.H.Cordes, D.F.Hansen, and L.E.Kay (2011).
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
  J Biomol NMR, 50, 13-18.  
21280116 G.M.Clore (2011).
Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation.
  Protein Sci, 20, 229-246.  
21214861 M.Bieri, A.H.Kwan, M.Mobli, G.F.King, J.P.Mackay, and P.R.Gooley (2011).
Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.
  FEBS J, 278, 704-715.  
21144739 T.R.Sosnick, and D.Barrick (2011).
The folding of single domain proteins--have we reached a consensus?
  Curr Opin Struct Biol, 21, 12-24.  
21501688 Y.Kodama, M.L.Reese, N.Shimba, K.Ono, E.Kanamori, V.Dötsch, S.Noguchi, Y.Fukunishi, E.Suzuki, I.Shimada, and H.Takahashi (2011).
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
  J Struct Biol, 174, 434-442.  
20715194 C.Cogliati, L.Ragona, M.D'Onofrio, U.Günther, S.Whittaker, C.Ludwig, S.Tomaselli, M.Assfalg, and H.Molinari (2010).
Site-specific investigation of the steady-state kinetics and dynamics of the multistep binding of bile acid molecules to a lipid carrier protein.
  Chemistry, 16, 11300-11310.  
20829478 D.M.Korzhnev, T.L.Religa, W.Banachewicz, A.R.Fersht, and L.E.Kay (2010).
A transient and low-populated protein-folding intermediate at atomic resolution.
  Science, 329, 1312-1316.
PDB code: 2kzg
21152000 F.Morcos, S.Chatterjee, C.L.McClendon, P.R.Brenner, R.López-Rendón, J.Zintsmaster, M.Ercsey-Ravasz, C.R.Sweet, M.P.Jacobson, J.W.Peng, and J.A.Izaguirre (2010).
Modeling conformational ensembles of slow functional motions in Pin1-WW.
  PLoS Comput Biol, 6, e1001015.  
20696393 P.Robustelli, K.Kohlhoff, A.Cavalli, and M.Vendruscolo (2010).
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.
  Structure, 18, 923-933.  
20033258 R.Auer, D.F.Hansen, P.Neudecker, D.M.Korzhnev, D.R.Muhandiram, R.Konrat, and L.E.Kay (2010).
Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1rho methods.
  J Biomol NMR, 46, 205-216.  
20385578 Z.Ren, H.Wang, and R.Ghose (2010).
Dynamics on multiple timescales in the RNA-directed RNA polymerase from the cystovirus phi6.
  Nucleic Acids Res, 38, 5105-5118.  
19841630 A.J.Baldwin, and L.E.Kay (2009).
NMR spectroscopy brings invisible protein states into focus.
  Nat Chem Biol, 5, 808-814.  
19846313 A.K.Mittermaier, and L.E.Kay (2009).
Observing biological dynamics at atomic resolution using NMR.
  Trends Biochem Sci, 34, 601-611.  
19223165 D.Russel, K.Lasker, J.Phillips, D.Schneidman-Duhovny, J.A.Velázquez-Muriel, and A.Sali (2009).
The structural dynamics of macromolecular processes.
  Curr Opin Cell Biol, 21, 97.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
19522466 L.K.Picton, S.Casares, A.C.Monahan, A.Majumdar, and R.B.Hill (2009).
Evidence for conformational heterogeneity of fission protein Fis1 from Saccharomyces cerevisiae.
  Biochemistry, 48, 6598-6609.  
19448976 P.Lundström, H.Lin, and L.E.Kay (2009).
Measuring 13Cbeta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy.
  J Biomol NMR, 44, 139-155.  
19289032 P.Neudecker, P.Lundström, and L.E.Kay (2009).
Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding.
  Biophys J, 96, 2045-2054.  
19319480 P.Vallurupalli, D.F.Hansen, P.Lundström, and L.E.Kay (2009).
CPMG relaxation dispersion NMR experiments measuring glycine 1H alpha and 13C alpha chemical shifts in the 'invisible' excited states of proteins.
  J Biomol NMR, 45, 45-55.  
  20948662 S.R.Van Doren (2009).
Nuclear magnetic resonance captures the elusive.
  F1000 Biol Rep, 1, 0.  
20001053 S.Ulzega, M.Verde, F.Ferrage, and G.Bodenhausen (2009).
Heteronuclear double resonance in nuclear magnetic resonance spectroscopy: Relaxation of multiple-quantum coherences.
  J Chem Phys, 131, 224503.  
19629713 V.Chevelkov, U.Fink, and B.Reif (2009).
Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy.
  J Biomol NMR, 45, 197-206.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.