Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings

Simon, Katya; Xu, Jun; Kim, Chinpal; Skrynnikov, Nikolai R.

doi:10.1007/s10858-005-2601-7

Cited by 16 publications

(16 citation statements)

References 64 publications

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“…However, if those ensembles with RMSD larger than 2.5 Å are excluded (blue fit lines) then the gradient becomes almost zero, suggesting that for better structures, ensemble RMSD is a poor guide to accuracy. Similar comments have been made previously [14][15][16][17]40 .…”

Section: Comparison Between Ansurr and Conventional Nmr-based Predictsupporting

confidence: 84%

A method for validating the accuracy of NMR protein structures

Fowler

Sljoka

Williamson

2020

Preprint

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We present a method, Accuracy of NMR Structures using Random Coil Index and Rigidity (ANSURR), that measures the accuracy of NMR protein structures. It provides a residue-by-residue comparison of two measures of local rigidity: the Random Coil Index [RCI] (a measure of the extent to which backbone chemical shifts adopt random coil values); and local rigidity predicted by mathematical rigidity theory using the computational method Floppy Inclusion and Rigid Substructure Topology [FIRST], calculated from an NMR structural model. We compare RCI and FIRST using a correlation score (which assesses the location of secondary structure), and an RMSD score (which measures overall rigidity, and mainly assesses hydrogen bond correctness). We test the performance of ANSURR using: (a) structures refined in explicit solvent, which have much better RMSD score than unrefined structures, though similar correlation; (b) decoy structures generated for 89 NMR structures. The experimental NMR structures are usually better, though helical and sheet structures behave differently; (c) conventional predictors of structural accuracy such as number of restraints per residue, restraint violations, energy of structure, RMSD of the ensemble (precision of the calculation), Ramachandran distribution, and clashscore. Comparisons of NMR to crystal structures show that secondary structure is equally accurate in both, but crystal structures tend to be too rigid in loops, whereas NMR structures tend to be too floppy overall.

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Section: Comparison Between Ansurr and Conventional Nmr-based Predictsupporting

confidence: 84%

A method for validating the accuracy of NMR protein structures

Fowler

Sljoka

Williamson

2020

Preprint

View full text Add to dashboard Cite

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“…The level of agreement is expected for a crystal structure at this resolution (1.94 Å). 46,47 In particular, the RDC values for the residues 12−14 agree well between observed and calculated values ( Figure S8, Supporting Information).…”

Section: ■ Resultssupporting

confidence: 77%

Subtle Dynamics of holo Glutamine Binding Protein Revealed with a Rigid Paramagnetic Probe

et al. 2014

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Bacterial periplasmic binding proteins (PBPs) are involved in the translocation of small molecules in the periplasm. To unload, the two domains of a PBP open up, allowing the ligand to exit. However, it is not clear whether there are dynamics near the binding site which can facilitate the rapid dissociation of a ligand. To visualize such dynamics, we utilized paramagnetic relaxation enhancement (PRE) NMR and introduced a rigid paramagnetic probe to a PBP, glutamine-binding protein (QBP) with its cognate ligand bound. A paramagnetic Cu(II) ion is sandwiched between an engineered di-histidine motif at a helix and an NTA capping molecule. The afforded paramagnetic probe is so rigid that PRE values calculated from a single structure of holo QBP largely agree with the observed values. The remaining PRE discrepancies, however, manifest dynamics of a loop in the opposite domain from the paramagnetic probe. This loop packs against the glutamine ligand in the holo QBP and undergoes fluctuations upon ligand dissociation, as assessed by steered molecular dynamics simulations. As such, the loop dynamics, occurring for a small population in nanosecond to microsecond time scale, may be related to the ligand dissociation process. The rigid paramagnetic probe described herein can be grafted to other protein systems for structure and dynamics studies.

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“…76 It is worth mentioning that bicelle calculations in PALES have been programmed for DMPC/DHPC, so that the code implicitly accounts for the presence of 5 mM free DHPC in the solvent. 77, 78 To correct for this small contribution and, in addition, account for 0.3 wt% of free hexanol in solution 76 one should use a slightly altered value of the liquid crystal concentration. For instance, in the PALES calculations aimed at 5% PEG, r = 0.85 media the effective liquid crystal concentration should be set to 65 mg/ml.…”

Section: Methodsmentioning

confidence: 99%

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

2011

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Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domain-domain mobility. Due to its elongated shape, tandem SH3 efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. To test the accuracy of theoretical predictions, we prepared a number of tandem-SH3 samples in PEG/hexanol alignment media. These samples were used to measure backbone 1HN-15N residual dipolar couplings associated with the two globular domains within the tandem. The experimental alignment tensors determined in this fashion were compared with the results of the PALES-based simulations, broadly confirming the anticipated trends. The results of the comparison, however, fall short of quantitative agreement. In particular, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as a measure of domain-domain cooperativity, thus identifying the situations where two domains transiently interact with each other or become coupled through a partially structured linker.

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Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings

Cited by 16 publications

References 64 publications

A method for validating the accuracy of NMR protein structures

A method for validating the accuracy of NMR protein structures

Subtle Dynamics of holo Glutamine Binding Protein Revealed with a Rigid Paramagnetic Probe

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

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