Structure of ubiquitin refined at 1.8 Å resolution

Vijay‐Kumar, Senadhi; Bugg, Charles E.; Cook, William J.

doi:10.1016/0022-2836(87)90679-6

Cited by 1,661 publications

(1,735 citation statements)

References 38 publications

Supporting

Mentioning

1,641

Contrasting

Unclassified

Order By: Relevance

“…Hen egg white lysozyme (PDB code 6LYT 36 ) and ubiquitin (PDB code 1UBQ 37,38 ) simulations were run under the same conditions as the short peptides described above, but with truncated octahedral periodic boundary conditions including 4350 and 3300 water molecules respectively. Equilibration was done in multiple steps, with positional restraints on all heavy atoms in the crystal structure gradually released from 2 to 0 kcal/mol-Å 2 .…”

Section: Calculation Of Nmr Order Parametersmentioning

confidence: 99%

See 1 more Smart Citation

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

View full text Add to dashboard Cite

The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "AMBER" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems.

show abstract

Section: Calculation Of Nmr Order Parametersmentioning

confidence: 99%

“…This is another small and well characterized protein of 76 residues with a known crystal structure 37,38 , for which NMR relaxation parameters were also determined experimentally 65 . Based on the crystal structure, the C-terminal region extends away from and makes few contacts with the remainder.…”

Section: Force Field Validationmentioning

confidence: 99%

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

View full text Add to dashboard Cite

show abstract

“…The tether (387–405) that partly occludes the RING1 binding site in the starting coordinates was allowed to move. Coordinates for ubiquitin (PDB code 1UBQ; Vijay‐Kumar et al , 1987) and UbcH7 (PDB code 4Q5E; Grishin et al , 2014) were used to sequentially dock the UbcH7 and Ub moieties untethered according to restraints and using a single unambiguous restraint between the C‐terminal G76 of ubiquitin and the catalytic C86K of UbcH7 to create the UbcH7‐Ub conjugate in the complex. Upper distance limits of 4.0 Å were set for ambiguous distance restraints, while the unambiguous distance restraint was set to 6.8 Å.…”

Section: Methodsmentioning

confidence: 99%

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

et al. 2018

View full text Add to dashboard Cite

The E3 ligase parkin ubiquitinates outer mitochondrial membrane proteins during oxidative stress and is linked to early‐onset Parkinson's disease. Parkin is autoinhibited but is activated by the kinase PINK1 that phosphorylates ubiquitin leading to parkin recruitment, and stimulates phosphorylation of parkin's N‐terminal ubiquitin‐like (pUbl) domain. How these events alter the structure of parkin to allow recruitment of an E2~Ub conjugate and enhanced ubiquitination is an unresolved question. We present a model of an E2~Ub conjugate bound to the phospho‐ubiquitin‐loaded C‐terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re‐modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a weak interaction of the pUbl domain with the RING0 domain and rearrange the location of the RING2(Rcat) domain to drive parkin activity.

show abstract

“…Moreover, high-resolution crystal structures or NMR structural data are available, making them ideal candidates for such an investigation. [36][37][38][39][40] Albumin, known to transport numerous important biomolecules and drugs in the cytoplasm, 41 and transferrin, which controls the level of free iron in biological fluids, may react immediately with the metallaprisms, if they are administrated intravenously. Cytosolic proteins also possess important functions: cytochrome c is involved in apoptotic pathways, 42 while ubiquitin is relevant in posttranslational modifications together with the proteasome system, 43 and myoglobin is the primary oxygen-carrying pigment of muscle tissues.…”

Section: Introductionmentioning

confidence: 99%

Interactions of arene ruthenium metallaprisms with human proteins

2015

View full text Add to dashboard Cite

Interactions between three hexacationic arene ruthenium metallaprisms, [( p-cymene) 6+ , and a series of human proteins including human serum albumin, transferrin, cytochrome c, myoglobin and ubiquitin have been studied using NMR spectroscopy, mass spectrometry and circular dichroism spectroscopy. All data suggest that no covalent adducts are formed between the proteins and the metallaprisms. Indeed, in most cases electrostatic interactions, leading to precipitation of protein-metallaprism aggregates, have been observed. In addition, with the smallest proteins, ubiquitin, myoglobin and cytochrome c, the presence of the hexacationic arene ruthenium metallaprisms induces structural changes of the proteins, as emphasized by circular dichroism. The results suggest that proteins are certainly a biological target for these metalla-assemblies.

show abstract

Structure of ubiquitin refined at 1.8 Å resolution

Cited by 1,661 publications

References 38 publications

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

Interactions of arene ruthenium metallaprisms with human proteins

Contact Info

Product

Resources

About