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PDB ID Mentions in PubMed Central Article count: 7

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PDB ID Mentions in PubMed Central

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A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

(2009) PLoS Comput Biol 5

PubMed: 19478996 | PubMedCentral: PMC2682763 | DOI: 10.1371/journal.pcbi.1000393

The RDC-optimized Backrub ensemble, the MD-EAR ensembles (1XQQ, 2NR2 and EROS PDB code: 2K39) and, the ubiquitin X-ray ensemble and the ensemble of MD structures have improved Q-factors over the best ... ingle structure ( Figure 3C ).

RDC-optimized Backrub ensembles match RDC measurements comparably to or better than other methods We compared the Q-factor of the RDC-optimized Backrub ensemble to the Q-factors from various other ubiquitin ensembles ( Figure 3C ): the Self-Consistent RDC-based Model-free (SCRM) description (an analytical description of the RDCs with five parameters per residue that does not provide an explicit all atom structural representation of the motions) [35] , an ensemble of 46 X-ray structures of ubiquitin alone and in different complexes (henceforth called the ubiquitin X-ray ensemble) as used in reference [4] , three sets of NMR structures (1D3Z, 1UD7, and 1G6J), three molecular dynamics (MD) ensemble-average-restraint (EAR) ensembles (1XQQ, 2NR2, EROS PDB code 2K39) [4] , [57] , [58] , and snapshots from a 100-nanosecond MD simulation [63] .

Publication Year: 2009


Accessing ns-micros side chain dynamics in ubiquitin with methyl RDCs.

(2009) J Biomol NMR 45

PubMed: 19652920 | PubMedCentral: PMC2728246 | DOI: 10.1007/s10858-009-9354-7

The ensemble represents therefore an intermediate between 1d3z which has not been optimized to match conformational averaging seen by RDCs and 2k39 where backbone and side chain RDCs were utilized.

Table 3 Conformational heterogeneity for methyl groups from the average structure and dynamic ensembles of ubiquitin and correlation with RDC-derived average spherical harmonics PDB Number of conformers Positional rmsd of all methyl group carbons Av ± st dev order parameter Pearson correlation (< Y 2,M > ) rmsd (< Y 2,M > ) References 1d3z 10 0.54 ± 0.23 Å 0.87 ± 0.19 0.8379 0.0758 Cornilescu et al. ( 1998 ) 1xqq 128 1.76 ± 0.32 Å 0.59 ± 0.27 0.8497 0.0597 Lindorff-Larsen et al. ( 2005 ) 2nr2 144 1.43 ± 0.24 Å 0.66 ± 0.21 0.8748 0.0588 Richter et al. ( 2007 ) 2k39 116 2.28 ± 0.43 Å 0.45 ± 0.29 0.8568 0.0496 Lange et al. ( 2008 ) « brub » 50 1.77 ± 0.28 Å 0.59 ± 0.26 0.8092 0.0648 Friedland et al.

(2009) Figure  6 displays a per-residue comparison of the order parameters from the highly restrained lowest-energy average NMR structures ( pdb:1d3z ), from the three dynamically-refined ensembles ( pdb:1xqq, 2nr2 and 2k39 ) and from the “Backrub”-generated ensembles (“ brub ”) with those obtained from the MFA.

 7 Eight representative examples of methyl bearing ubiquitin side chain heterogeneity from average structure ( pdb:1d3z ), from backrub-ensemble ( brub ), from dynamic ensembles ( pdb:1xqq, 2nr2, 2k39 ) and from ensembles generated by rotamer model-fitting of the average spherical harmonics resulting from the Model-free Analysis (MFA).

The EROS ensemble ( pdb:2k39 ) is also a dynamically refined structure, with the important difference that the ensemble refinement is not performed against order parameters but rather against orientational restraints provided from RDCs (including backbone D NH and methyl group D CC ).

 6 Order parameters plotted against residue position as back-calculated from different structural ensembles ( blue: 1d3z , green : 2nr2 , yellow : 1xqq , red : 2k39 , cyan : “backrub”-ensemble ( brub ), black : MFA) In comparison, the dynamic ensembles pdb:1xqq and pdb:2nr2 show a much higher level of conformational heterogeneity, by virtue of their refinement against not only backbone but also side chain (methyl group) relaxation-based order parameters.

Of the five ensembles, the pdb:2k39 boasts together with pdb:1xqq the best correlation (Pearson correlation r  = 0.857) and by quite a big margin the best overall agreement (rmsd = 0.0496) with the MFA results.

Publication Year: 2009


Peptide conformer acidity analysis of protein flexibility monitored by hydrogen exchange.

(2009) Biochemistry 48

PubMed: 19722680 | PubMedCentral: PMC2754664 | DOI: 10.1021/bi901219x

In contrast, two of the three most acidic conformers for the Asp 52 amide in the 2K39 ensemble have trans χ 1 rotamers.

For seven of these eight residues, the NMR relaxation-restrained 2NR2 ensemble predicts no solvent accessibility, while the predicted acidity for the one conformer with a solvent-exposed Phe 4 amide is more than 4.5 pH units higher in the 2K39 ensemble than for the 2NR2 ensemble.

Although neither the amide of Ile 44 nor that of Phe 45 become solvent-exposed in any of the models in the 2NR2 ensemble, the predicted amide p K a values of Gly 47 and Lys 48 for that ensemble also overestimate the hydrogen exchange rates for these residues to a similar degree as predicted by the 2K39 ensemble.

Peptide conformer acidities were predicted for residues in which the amide hydrogen is exposed to solvent by more than 0.5 Å 2 in at least 50% of the models in the NMR relaxation-restrained 2NR2 ensemble (panel A) and the NMR residual dipolar coupling-restrained 2K39 ensemble (panel B).

In addition to the residues with a solvent-exposed amide in only a single 2K39 ensemble structure, overestimation of the hydrogen experimental amide exchange rates also occurs for a substantial fraction of the other amides which are exposed to solvent above 0.5 Å 2 in less than half of the 2K39 ensemble models.

Continuum Dielectric Calculations Static accessibility calculations for all backbone amides were carried out on the 144 ubiquitin conformations in the 2NR2 ensemble ( 40 ) and the 116 protein structures in the 2K39 ensemble ( 41 ).

The residues with backbone amides that are buried in the X-ray structures, yet have substantially overestimated hydrogen exchange rates predicted from the 2K39 ensemble, are spread throughout the ubiquitin sequence (Figure 8 ).

Continuum Dielectric Analysis of Highly Solvent-Exposed Amides in NMR-Restrained Ensembles Poisson−Boltzmann continuum dielectric calculations were performed on the 144 ubiquitin structures of the NMR relaxation-restrained ensemble (PDB code 2NR2 ( 40 )) and the 116 structures of the NMR residual dipolar coupling-restrained ensemble (PDB code 2K39 ( 41 )).

With the previously reported NMR-restrained molecular dynamics ensembles of ubiquitin (PDB codes 2NR2 and 2K39 ) used as representations of the Boltzmann-weighted conformational distribution, nearly all of the exchange rates for the highly exposed amides were more accurately predicted than by use of the high-resolution X-ray structure.

Publication Year: 2009


Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling.

(2010) J Am Chem Soc 132

PubMed: 20958032 | PubMedCentral: PMC2974370 | DOI: 10.1021/ja106173n

Even though the AXES fit to the static, lowest energy NMR structure (1D3Z;( 25 ) χ = 3.05) suggests that this model is a better representation of the average ubiquitin structure in solution, t... e fact that fits to the entire 1XQQ and 2K39 ensembles are better than those to their individual members indicates that these ensembles correctly capture dynamic processes in the protein.

Remarkably, fits to the previously extensively studied dynamic ensemble representations of ubiquitin 23 , 24 yield lower χ values when fitting these entire ensembles simultaneously, than when fitting each member of the ensemble separately, followed by averaging of these χ values (χ ensemble = 5.06 and 4.98 for PDB entries 1XQQ( 23 ) and 2K39,( 24 ) respectively, vs ⟨χ⟩ = 5.36 for 1XQQ and ⟨χ⟩ = 6.01 for 2K39; SI ), despite far fewer adjustable parameters in the fitting procedure (4 for the ensemble fit; N *4 for an N -member ensemble).

Publication Year: 2010


Discovering conformational sub-states relevant to protein function.

(2011) PLoS One 6

PubMed: 21297978 | PubMedCentral: PMC3030567 | DOI: 10.1371/journal.pone.0015827

For comparison, we use to study the anharmonicity observed in ubiquitin motions from s long MD simulation [22] (see Materials and Methods section) and also from experimental ensembles ... 116 NMR structures revealing up to s dynamics [Protein Data Bank (PDB) code: 2K39] [11] , and 44 X-ray crystallographic structures).

Publication Year: 2011


Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition.

(2011) J Am Chem Soc 133

PubMed: 21634390 | PubMedCentral: PMC3686050 | DOI: 10.1021/ja200461n

Table 1 Level of Agreement with NMR Parameters and Structural Analysis of Previously Reported Static ( 1UBQ 18 and 1D3Z ( 11 )) and Dynamic ( 2K39 7 ) Representations of Ubiquitin, ERNST, a and an Ens... mble Obtained Using Unbiased MD b   1UBQ 1D3Z 2K39 MD ERNST NMR Parameter c Validation Q ( D HNC′ ) 0.29 0.21 d 0.23 0.27 0.23 Q ( D NC′ ) 0.22 0.18 d 0.18 0.19 0.18 rmsd( 3 J ϕ )/Hz e 0.42 0.38 0.45 0.46 0.36 rmsd( 3h J NC′ )/Hz f 0.15 0.23 0.13 0.10 0.09 rmsd( R NH,NH )/Hz f 1.05 0.57 0.50 0.83 0.46 rmsd( R NH,CαHα )/Hz f 2.10 1.76 1.66 1.87 1.61 Structural Parameter g Structural Analysis ⟨rmsd ij ⟩ (Å) n.a. n.a. 1.39 0.88 0.83 rmsd from 1UBQ (Å) 0 0.38 0.55 0.42 0.40 rmsd from 1D3Z (Å) 0.38 0 0.48 0.39 0.33 a Coordinates have been deposited in the PDB with code 2KOX .

22 The only structural models of ubiquitin that gave relatively accurate values of R NH,NH and R NH,CαHα are those that were restrained with NH RDCs ( 1D3Z , 2K39 , and ERNST).

The level of agreement is comparable to those for static structures (PDB code 1D3Z ) and dynamic ensembles (PDB code 2K39 ) that, unlike ERNST, were refined using some of these RDCs.

Publication Year: 2011


Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

(2013) PLoS One 8

PubMed: 24391900 | PubMedCentral: PMC3877219 | DOI: 10.1371/journal.pone.0084123

a (CamShift) (CamShift) (ProCS) (ProCS) PDB-ID 1 H RMSD 1 H RMSD RMSD Q-factor b 2KOX 0.29 0.84 0.68 0.86 0.12 0.04 c 2K39 0.34 0.82 0.98 0.77 0.13 0.07 d 2KN5 0.23 0.91 0.71 0.82 0.12 0.22 e 2NR2 0.4... 0.74 1.35 0.64 0.14 0.25 f 1XQQ 0.38 0.81 0.92 0.77 0.14 0.38 g 1D3Z 0.41 0.79 1.00 0.71 0.30 0.06 h 1UBQ 0.40 0.77 0.92 0.72 0.22 0.22 i 1UBI 0.40 0.77 0.97 0.73 0.33 0.25 j 1OGW 0.36 0.73 0.84 0.73 0.17 0.26 k OPLS + ProCS 0.32 0.79 0.17 0.98 0.14 0.27 k OPLS + CamShift 0.32 0.90 1.15 0.86 0.17 0.27 k OPLS 0.48 0.78 1.11 0.78 0.18 0.29 a Chemical shifts RMSD and values are calculated for the residues for which spin-spin coupling constants have been measured.

Publication Year: 2013