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PDB ID Mentions in PubMed Central Article count: 98

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PDB ID Mentions in PubMed Central

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Connectivity independent protein-structure alignment: a hierarchical approach.

(2006) BMC Bioinformatics 7

PubMed: 17118190 | PubMedCentral: PMC1683948 | DOI: 10.1186/1471-2105-7-510

The PDB ids of the protein pairs are: 1bgeB/2gmfA, 1cewI/1molA, 1cid/2rhe, 1crl/1ede, 1fxiA/1ubq, 1ten/1hhrB, 1tie/4fgf, 2azaA/1paz, 2sim/1nsbA, 3hlaB/2rhe, 1g61/1jdw.

Publication Year: 2006


Rapid detection of similarity in protein structure and function through contact metric distances.

(2006) Nucleic Acids Res 34

PubMed: 17130161 | PubMedCentral: PMC1702494 | DOI: 10.1093/nar/gkl788

Figure 1A illustrates this representation in human ubiquitin (PDB 1ubq).

2001 276 10185 11290 11087754 Figures and Tables Figure 1 ( A ) Contact vector representation of human ubiquitin (PDB 1ubq).

Publication Year: 2006


Implications from a network-based topological analysis of ubiquitin unfolding simulations.

(2008) PLoS One 3

PubMed: 18478068 | PubMedCentral: PMC2364640 | DOI: 10.1371/journal.pone.0002149

g001 Figure 1 The native structure of ubiquitin (PDB ID: 1UBQ).

Materials and Methods Molecular Dynamics Unfolding Simulations The native structure of ubiquitin obtained from the protein data bank (PDB ID: 1UBQ) was used in the unfolding simulations carried out using NAMD [29] .

Publication Year: 2008


Prospects for de novo phasing with de novo protein models.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19171972 | PubMedCentral: PMC2631639 | DOI: 10.1107/S0907444908020039

of models, large-scale ¶ Low-resolution models, 100 CPU days †† All-atom models, 100 CPU days †† All-atom models, large-scale †† Models, native ... onstraints ‡‡ Overall §§ 1be7 1bq9 H 3 51 1 43 3.5 × 10 5 1.7 × 10 7 — — — 0.882 0.882 1bq9 1bq9 P 2 1 2 1 2 1 51 1 43 3.5 × 10 5 1.7 × 10 7 — — — 0.627 0.627 2igd 1pgx P 2 1 2 1 2 1 55 1 46 2.7 × 10 5 4.2 × 10 5 — — 0.745 0.891 0.709 5cro 5cro H 32 55 4 70 2.6 × 10 5 7.4 × 10 5 — — 0.927 0.982 0.709 1hz5 1hz6 P 3 2 21 61 2 72 2.3 × 10 5 7.3 × 10 5 — 0.541 0.656 0.787 0.541 1hz6 1hz6 P 2 1 2 1 2 1 61 3 59 2.3 × 10 5 7.3 × 10 5 — 0.672 0.689 0.836 0.639 1a32 1a32 P 2 1 2 1 2 1 65 1 41 2.8 × 10 5 2.8 × 10 5 — 0.754 0.708 0.800 0.677 1ctf 1ctf P 4 3 2 1 2 68 1 47 2.4 × 10 5 3.2 × 10 5 — — — 0.882 0.515 1aar 1ubi P 1 71 2 35 2.0 × 10 5 5.4 × 10 7 — — — — 1.000 1f9j 1ubi I 4 1 22 71 2 60 2.0 × 10 5 5.4 × 10 7 — — — — 0.901 1ubq 1ubi P 2 1 2 1 2 1 71 1 33 2.0 × 10 5 5.4 × 10 7 — — 0.690 0.662 0.549 2fcq 1ubi P 4 3 32 71 2 58 2.0 × 10 5 5.4 × 10 7 — — — — 0.915 2ojr 1ubi P 3 2 21 71 1 73 2.0 × 10 5 5.4 × 10 7 — — — 0.549 0.549 1dt4 1dtj P 4 2 2 1 2 74 1 54 2.8 × 10 5 4.9 × 10 5 0.649 0.622 0.500 0.635 0.419 1dtj 1dtj C 2 74 4 60 2.8 × 10 5 4.9 × 10 5 — 0.635 0.716 0.811 0.635 1ig5 1ig5 P 4 3 2 1 2 75 1 43 2.3 × 10 5 8.3 × 10 6 — — — 0.307 0.307 1cm3 1opd P 2 1 85 1 28 2.3 × 10 5 8.4 × 10 6 — — — 0.753 0.459 1opd 1opd P 1 85 1 33 2.3 × 10 5 8.4 × 10 6 — — — 0.800 0.800 1a19 1a19 I 4 1 89 2 49 1.7 × 10 5 7.0 × 10 6 — — — 0.494 0.494 2hxx 1a19 C 2 89 2 46 1.7 × 10 5 7.0 × 10 6 — — — 0.674 0.674 1mb1 1bm8 P 4 1 2 1 2 99 1 51 1.6 × 10 5 9.2 × 10 5 — — — — 0.747 2hsh 1aiu C 2 105 1 35 1.5 × 10 5 4.4 × 10 5 — — 0.400 0.600 0.400 1m6t 256b C 222 1 106 1 43 1.8 × 10 5 1.5 × 10 5 — 0.453 0.443 0.491 0.283 256b 256b P 1 106 2 45 1.8 × 10 5 1.5 × 10 5 — — 0.660 0.594 0.585 2bc5 256b P 2 1 2 1 2 1 106 4 42 1.8 × 10 5 1.5 × 10 5 — 0.538 — 0.689 0.538 1elw 1elw P 4 1 117 2 47 1.5 × 10 5 1.1 × 10 5 — 0.453 0.521 0.897 0.436 1ab6 2chf P 3 1 128 2 57 1.2 × 10 5 3.5 × 10 6 — — 0.508 0.398 0.398 2fka 2chf F 432 128 1 79 1.2 × 10 5 3.5 × 10 6 — 0.430 0.359 0.367 0.313 3chy 2chf P 2 1 2 1 2 1 128 1 41 1.2 × 10 5 3.5 × 10 6 — — — 0.492 0.320 6chy 2chf P 2 1 2 1 2 1 128 2 43 1.2 × 10 5 3.5 × 10 6 — — 0.398 0.422 0.398 † F 1 Å is a measure of model accuracy: the fraction of C α atoms within 1 Å of the crystal structure of the modeled sequence.

For example, the benchmark includes four diffraction data sets for ubiquitin, in which the same pool of Rosetta models was tested for phasing, and the data set with the lowest solvent content (PDB code 1ubq ) was the only one for which a de novo model gave a successful Phaser solution.

Publication Year: 2009


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

We ran a Backrub Monte Carlo simulation at kT = 0.1 from the starting PDB conformation (using 1UBQ, which has the highest resolution (1.8 Å) of the unbound ubiquitin st... uctures; similar results were obtained for maximum segment length of 3 with PDB entries 1UBI and 1CMX and worse Q factors were obtained for PDB entries 1FXT, 1AAR, 1F9J, and 1TBE) for 10,000 steps with a maximum segment length of 3 or 12, matching the segment length used later.

Strategy to test relation 1 To test relation 1, our approach first uses unrestrained conformational sampling with the Backrub motional model to generate a large set of initial conformations, starting from the ubiquitin crystal structure (Protein Data Bank (PDB) code 1UBQ).

Gaussian Network Model Theoretical B-factors were calculated by applying the online Gaussian Network Model (oGNM) tool at http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm [69] to PDB structure 1UBQ using 1 node per residue and a cutoff of 10 Å for amino acid pairs.

The resulting ensemble consisted of 20 structures: 1XD3 chain B, 1BT0 chain A, 1EUV chain B, 1IYF, 1J8C, 1LM8 chain B, 1M94, 1NDD chain A, 1OQY, 1P1A, 1TGZ chain B, 1V5O, 1V5T, 1V86, 1WE6, 1WE7, 1WGD, 1WGG, 1WH3, and 1WM3 chain A. To create the C-alpha distance difference matrix we used the 66 positions that aligned in all 20 structures, which were (using 1UBQ numbering): 1–7, 9–16, 18–34, 36–46, 48–55, 57–64, 66–72.

This correspondence in pattern of flexibility holds despite the different motional amplitudes of these ensembles: 2.0 Å and 0.9 Å pair-wise RMSD to the 1UBQ X-ray structure, respectively, for the UBQ subfamily ensemble and the RDC-optimized Backrub ensemble.

(B) and (C): Low-scoring designed sequences on the fixed backbone of the X-ray structure 1UBQ (orange); on non-RDC-optimized Backrub ensembles with maximum segment length of 12 with kT = 0.3 (green), kT = 1.2 (blue), and kT = 4.8 (cyan); and (B) low-scoring designed sequences on the ubiquitin X-ray ensemble (red), or (C) sequences from the UBQ subfamily (brown).

Low-scoring designed sequences on the fixed backbone of the X-ray structure 1UBQ (orange); on non-RDC-optimized Backrub ensembles with maximum segment length of 12 with kT = 0.3 (green), kT = 1.2 (blue), and kT = 4.8 (cyan); and sequences from the UBQ family (brown) for (A) aligned and (B) only core residues; or low-scoring designed sequences on the 100 ns MD ensemble (red) for (C) aligned and (D) only core residues.

Publication Year: 2009


Deuterium isotope effects on 15N backbone chemical shifts in proteins.

(2009) J Biomol NMR 44

PubMed: 19455282 | PubMedCentral: PMC2697368 | DOI: 10.1007/s10858-009-9316-0

The residue labels are according to the 15 N chemical shifts Molecular geometry X-PLOR (Brünger 1987 ) calculations were performed on the X-ray crystal structure of ubiquitin [PDB ID: 1ubq] (V... jay-Kumar et al.

Publication Year: 2009


Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases.

(2009) PLoS Comput Biol 5

PubMed: 19696882 | PubMedCentral: PMC2719061 | DOI: 10.1371/journal.pcbi.1000476

E) Ribbon representation of human ubiquitin (PDB ID: 1UBQ).

Publication Year: 2009


Copper-triggered aggregation of ubiquitin.

(2009) PLoS One 4

PubMed: 19756145 | PubMedCentral: PMC2737635 | DOI: 10.1371/journal.pone.0007052

A) Mapping the effects of paramagnetic Cu II binding on the Ub NMR signals (PDB ID 1UBQ): Ub residues whose signals are broadened beyond detection are colored in blue for the primary site (Met1) and i... red for the secondary site (His68); Lys63 is also shown; B) Aggregation profile of Ub obtained with the program PASTA.

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 Figure 3 is illustrated the structure of the backbone turn segment between Phe 45 and Lys 48 from model 19 of the 2NR2 ensemble and the corresponding segment from the X-ray structure (PDB code 1UBQ... ( 56 )).

When residues 2−72 of these models are superimposed on the coordinates of the X-ray structure used to initiate the NMR relaxation-restrained molecular dynamics (PDB code 1UBQ ( 56 )), the backbone rmsd values were found to range from 0.57 to 0.87 Å.

Panel A is drawn from model 19 of the NMR relaxation-restrained 2NR2 ensemble ( 30 ), while panel B is from the X-ray structure 1UBQ ( 49 ).

Publication Year: 2009


A unifying probabilistic framework for analyzing residual dipolar couplings.

(2008) J Biomol NMR 40

PubMed: 18095170 | PubMedCentral: PMC2758374 | DOI: 10.1007/s10858-007-9215-1

1998 ) and to those of the crystal structure 1UBQ (Vijay-Kumar et al.

 2 Posterior histograms for the elements calculated from the X-ray structure 1UBQ (panel A) and from the NMR structure 1D3Z (panel B).

 3 Ensembles generated by applying the sampled rotations to the average structure of the full simulation (A), the crystal structure 1UBQ (B) and the NMR structure 1D3Z (C).

Also shown as big grey dots are the axial and rhombic component obtained by maximum likelihood for all couplings observed in the first phase (ML) and for the N–H couplings only (ML) and by fitting the couplings to the NMR (1D3Z) and to the crystal structure (1UBQ) Elimination of the alignment tensor It is possible to eliminate the alignment tensor in the restraint energy and refine protein structures directly against observed dipolar couplings without any preanalysis (Moltke and Grzesiek 1999 ; Sass et al.

Distributions obtained from the crystal structure 1UBQ and from the NMR structure 1D3Z are shown as dashed and solid lines, respectively Histogram method Maximization of the conditional posterior probability of the Saupe tensor requires approximate knowledge of the coordinates and is therefore not applicable to a de novo structure determination.

Publication Year: 2008


Mechanical strength of 17,134 model proteins and cysteine slipknots.

(2009) PLoS Comput Biol 5

PubMed: 19876372 | PubMedCentral: PMC2759523 | DOI: 10.1371/journal.pcbi.1000547

The 190 structures (or 1.1% of all structure considered) with the top values of in units of are shown in Table 1 (the first 81 entries for which ) and Table S1 of the SI (proteins ranked 82 th... ough 190), together with the values of titin (1tit) and ubiquitin (1ubq) to provide a scale.

Publication Year: 2009


Toward a unified representation of protein structural dynamics in solution.

(2009) J Am Chem Soc 131

PubMed: 19919148 | PubMedCentral: PMC2779067 | DOI: 10.1021/ja907476w

Similarly, the AMD approach provides a mean trajectory-averaged J-coupling R-factor (0.143) that reproduces the couplings better than 1UBQ (0.153), and identically to 1D3Z (0.143) despite the fact tha... these scalar J-couplings were used in the refinement of 1D3Z .

In all cases, the free energy weighted extended conformational space ensembles reproduce the experimental observables to a substantially greater degree of accuracy than a control set of 5 ns standard MD simulations and provide better reproduction compared to the static X-ray crystal structure ( 1UBQ ).

The average RDC R-factor for the optimal AMD ensemble is better than the X-ray crystal structure for ubiquitin ( 1UBQ )( 47 ) (0.116).

Publication Year: 2009


The ubiquitin landscape at DNA double-strand breaks.

(2009) J Cell Biol 187

PubMed: 19948475 | PubMedCentral: PMC2779242 | DOI: 10.1083/jcb.200908074

1UBQ ; Vijay-Kumar, et al., 1987 ).

Publication Year: 2009


Crystallographic structure of ubiquitin in complex with cadmium ions.

(2009) BMC Res Notes 2

PubMed: 20003470 | PubMedCentral: PMC2804574 | DOI: 10.1186/1756-0500-2-251

The structure was determined by molecular replacement with the program MOLREP [ 5 ] using the monomeric Ub structure (PDB ID code 1UBQ ) as a search probe.

Publication Year: 2009


SeqRate: sequence-based protein folding type classification and rates prediction.

(2010) BMC Bioinformatics 11 Suppl 3

PubMed: 20438647 | PubMedCentral: PMC2863059 | DOI: 10.1186/1471-2105-11-S3-S1

Chromosomal protein Ubiquitin (PDB ID: 1UBQ) has a sequence length of 76 amino acids and experimental folding rate of 7.3 (in natural-base logarithm scale) in the unit of sec-1.

Publication Year: 2010


RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

(2010) Nucleic Acids Res 38

PubMed: 20462859 | PubMedCentral: PMC2896185 | DOI: 10.1093/nar/gkq369

The output (bottom) features the backbone traces of 10 generated ensemble members in green and a representation of the dynamic regions of an Ubiquitin ensemble (from blue to white to red with increasi... g variability) mapped onto the ubiquitin starting structure (PDB ID code: 1UBQ).

Publication Year: 2010


A new crystal form of Lys48-linked diubiquitin.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66

PubMed: 20823512 | PubMedCentral: PMC2935213 | DOI: 10.1107/S1744309110027600

The crystal structure of monoubiquitin (PDB code 1ubq ; Vijay-Kumar et al. , 1987 ▶ ) was used as a search model, excluding the flexible residues 73–76.

Publication Year: 2010


Structural transformation of the tandem ubiquitin-interacting motifs in ataxin-3 and their cooperative interactions with ubiquitin chains.

(2010) PLoS One 5

PubMed: 20949063 | PubMedCentral: PMC2951365 | DOI: 10.1371/journal.pone.0013202

The Ub structure is referenced from the crystal structure (PDB code: 1UBQ).

Publication Year: 2010


What lessons can be learned from studying the folding of homologous proteins?

(2010) Methods 52

PubMed: 20570731 | PubMedCentral: PMC2965948 | DOI: 10.1016/j.ymeth.2010.06.003

Class (fold) Superfamily Protein (species) Method of investigation PDB code Experimental references Comparative references a All-α (Acyl-CoA binding protein-like) Acyl-CoA binding protein ACBP... (Cow) Φ-Value analysis 2ABD [93,94] [94] ACBP (Rat) WT kinetics 2ABD b [93] ACBP (Yeast) Φ-Value analysis 2ABD b [94] 

 All-α (Acyl carrier protein-like) Colicin E immunity proteins Im7 ( E. coli ) Φ-Value analysis 1AYI [28] [29] Im9 ( E. coli ) Φ-Value analysis 1IMQ [29,30,95] 

 All-α (Cytochrome c ) Cytochrome c Cytochrome c (Horse) Hydrogen exchange 1HRC [96] [97] Cytochrome c 2 ( R. capsulatus ) WT kinetics 1C2R [98] Cytochrome c 551 ( P. aeruginosa ) Minimal Φ-value analysis 2PAC [99] Cytochrome c 552 ( H. thermophilus ) WT kinetics 1AYG [100] Cytochrome c 552 ( T. thermophilus ) WT kinetics 1C52 [101] Mitochondrial cytochrome c (Yeast) WT kinetics 1YCC [102] 

 All-α (Four-helical up-and-down bundle) Cytochromes Cytochrome b 562 ( E. coli ) Hydrogen exchange 1APC [103] FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) FRB (Human) WT kinetics 1AUE [104] 

 All-α (DNA/RNA-binding 3-helical bundle) Homeodomain-like DNA-binding domain of human telomeric protein hTRF1 (Human) WT kinetics 1BA5 [47] [47] En-Hd (Drosophila) Φ-Value analysis 1ENH [7,105] c-Myb DNA-binding domain (Mouse) Φ-Value analysis 1IDY [47] Rap1 (Human) WT kinetics 1FEX [47] 

 All-α (Globin-like) Globin-like Leghemoglobin (Soybean) Hydrogen exchange 1FSL [106] [106] Myoglobin (Sperm whale) Hydrogen exchange 1A6M [107] 

 All-α (peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex E3 binding domain of dihydrolipoamide acetyltransferase [E3BD] ( B. stearothermophilus ) Φ-Value analysis 1EBD [58] [59] E3-binding domain of dihydrolipoamide succinyltransferase [BBL] ( E. coli ) Φ-Value analysis 1BBL [59] POB ( P. aerophilium ) Φ-Value analysis 1BBL b [60] 

 All-α (ROP-like) ROP protein ROP ( E. agglomerans ) WT kinetics 1ROP b [4] [4] ROP ( E. coli ) WT kinetics 1ROP [4] ROP ( P. vulgaris ) WT kinetics 1ROP b [4] 

 All-α (spectrin repeat-like) Spectrin repeat Alpha chain R15 (Chicken) Φ-Value analysis 1U5P [46] [46] Alpha chain R16 (Chicken) Φ-Value analysis 1CUN [81] Alpha chain R17 (Chicken) Φ-Value analysis 1CUN [45] 

 α/β (α/β knot) α/β knot YbeA ( E. coli ) Φ-Value analysis 1NS5 [108] [108] YibK ( H. influenzae ) Φ-Value analysis 1J85 [109] 

 α/β (Dihydrofolate reductase-like) Dihydrofolate reductase-like Dihydrofolate reductase ( E. coli ) WT kinetics, Ligand binding 1RA9 [110] [110] Dihyrofolate reductase ( L. casei ) WT kinetics, Ligand binding 3DFR [110] Dihydrofolate reductase (Human) WT kinetics, Ligand binding 1KMV [110] 

 α/β (flavodoxin-like) CheY-like CheY ( E. coli ) Φ-Value analysis 1EAY [111] [112] Flavoproteins Apoflavodoxin ( A. vinelandii ) WT kinetics 1YOB [113] Flavodoxin ( Anabaena pcc 7119 ) Φ-Value analysis 1FTG [112] 

 α/β (Phosphoglycerate kinase) Phosphoglycerate kinase Phosphoglycerate kinase ( B. stearothermophilus ) Minimal Φ-value analysis 1PHP [114] Phosphoglycerate kinase (Yeast) WT kinetics 3PGK [115] 

 α/β (RNase-H-like Motif) RNase-H-like RNase-H ( E.coli ) Hydrogen exchange Limited mutagenesis 1F21 [168,169] RNase-H ( T. thermophilus ) Hydrogen exchange 1RIL [170] [170,171] RNase-H ( C. tepidum ) WT kinetics 3H08 [171] 

 α/β (TIM β/α-barrel) Ribulose-phosphate binding barrel Trptophan synthase α-subunit [αTS] ( E. coli ) WT kinetics 1V7Y [116] [117] Indole-3-glycerophosphate synthase [sIGPS] ( S. solfataricus ) WT kinetics, Hydrogen exchange 1IGS [118,119] 

 Xylose isomerase-like IOLI ( B. subtilis ) WT kinetics 1I60 [117] 

 α + β (Ferredoxin-like) Acyl-phosphatase-like AcP (Human) Φ-Value analysis 1APS b [26,120] [26,65,121] HypF ( E. coli ) WT kinetics 1GXU [121] Protease propeptides/inhibitors Procarboxy-peptidase A2 (Human) Φ-Value analysis 1O6X [27] Ribosomal protein S6 S6 ( A. aeolicus ) Φ-Value analysis 2J5A [65] S6 ( T. thermophilus ) Φ-Value analysis 1RIS [69] RNA binding domain (RBD) U1A (Human) Φ-Value analysis 1FHT [13] 

 α + β (β-hairpin-α-hairpin repeat) Ankyrin repeat AnkyrinR D34 (Human) Minimal Φ-value analysis 1N11 [122] [123] Ankyrin repeats in tumor suppressor p16 (Human) Φ-Value analysis 1BI7 [52] Cell-cycle inhibitor p19ink4D (Human) WT kinetics 1BD8 [124] Myotrophin (Rat) Φ-Value analysis 2MYO [51] Neurogenic locus notch receptor domain (Drosophila) Minimal Φ-value analysis, WT redesign 1OT8 [125,126] 

 α + β (Cell-cycle regulatory proteins) Cell-cycle regulatory proteins CksHs1 (Human) Φ-Value analysis 1BUH [70] [70] CksHs2 (Human) WT kinetics 1CKS [127] Suc1 ( S. pombe ) Φ-Value analysis 1PUC [128] 

 α + β (Lysozyme-like) Lysozyme-like Lysozyme (Hen Egg White) WT kinetics 1E8L [129] [130] α-Lactalbumin (Bovine) WT kinetics 1F6S [130] α-Lactalbumin (Goat) Minimal Φ-value analysis, Hydrogen exchange 1HFY [131,132] [131] Milk lysozyme (Dog) Hydrogen exchange 1EL1 [131,133] 

 α + β (β-grasp: ubiquitin-like) Immunoglobulin-binding domains Protein G ( Streptococcus ) Φ-Value analysis 2IGD [42] [42,134,135] Immunoglobulin light chain-binding domain of Protein L ( P. magnus ) Φ-Value analysis 2PTL [41] Ubiquitin-like c-Raf1 RBD (Human) Φ-Value analysis 1RFA [134,135] Ubiquitin (Human) Minimal Φ-value analysis 1UBQ [136] Ubiquitin (Yeast) Φ-Value analysis 1Q0W [137] 

 All-β (Ig-like β-sandwich) Fibronectin type III CAfn2 ( B. circulans ) Φ-Value analysis 1K85 [19] [15,19] FnIII-9 (Human) WT kinetics 1FNF [138] FnIII-10 (Human) Φ-Value analysis 1FNF [16] TNfn3 (Human) Φ-Value analysis 1TEN [18] Immunoglobulin TI I27 (Human) Φ-Value analysis 1TIT [17] CD2 (Rat) Minimal Φ-value analysis 1HNG [37] Various antibody domains (V L , C L , C H 2, C H 3) WT kinetics [139–142] [142] 

 All-β (Lipocalins) Lipocalins CRABP I (Mouse) WT kinetics 2CBR [143,144] [32,143] CRBP II (Rat) WT kinetics 1OPA [143] IFABP (Rat) Minimal Φ-value analysis 1IFC [31,32,143,145] ILBP (Rat) Minimal Φ-value analysis 1O1V b [31,32] 

 All-β (OB-fold) Nucleic acid-binding proteins Bc-Csp ( B. caldolyticus ) Φ-Value analysis 1C9O [146,147] [146,148] CspA ( E. coli ) Hydrogen exchange 1MJC [149] Bs-CspB ( B. subtilis ) Φ-Value analysis 1CSP [150] Tm-Csp ( T. maritima ) WT kinetics 1G6P [148] 

 All-β (PDZ domain-like) PDZ domain-like PDZ2 domain from PTP-BL (Mouse) Φ-Value analysis 1GM1 [57] [151] Third PDZ domain from synaptic protein PSD-95 (Rat) Hydrogen exchange Φ-value analysis 1BE9 [151,152] 

 All-β (SH3-like barrel) Chromo domain-like DNA-binding protein Sso7d ( S. solfataricus ) Φ-Value analysis 1SSO [153] [21,153] SH3-domain α-Spectrin SH3-domain (Chicken) Φ-Value analysis, WT redesign 1SHG [22,154] Fyn proto-oncogene tyrosine kinase SH3-domain (Chicken) Φ-Value analysis, NMR dispersion 1FYN b [23,24,155,156] Actin binding protein ABP1 (Yeast) NMR dispersion 1JO8 [21] Phosphatidylinositol 3-kinase SH3-domain (Cow) WT kinetics 2PNI [157] c-src protein tyrosine kinase (Chicken) Φ-Value analysis 1SRM [25] 

 All-β (WW domain-like) WW domain Formin Binding Protein 28 (Mouse) Φ-Value analysis 1E0L [8,158]   Mitotic rotamase PIN1 (Human) Φ-Value analysis 1PIN [48,159] Yap65 WW domain (Human) WT kinetics 1JMQ [160] 

 Coiled coil proteins (Parallel coiled-coil) Leucine zipper domain GCN4 (Yeast) WT kinetics, Minimal Φ-value analysis 2BNI [161,162] c-Jun (Human) Dimer thermodynamics 1JUN [163] c-Fos (Human) Dimer thermodynamics 1FOS [163] a Comparative references are those in which the folding mechanisms/pathways of homologous proteins are compared and discussed.

Publication Year: 2010


Improved side-chain torsion potentials for the Amber ff99SB protein force field.

(2010) Proteins 78

PubMed: 20408171 | PubMedCentral: PMC2970904 | DOI: 10.1002/prot.22711

Simulations of HEWL, BPTI, Ubq, and GB3 were initiated from PDB 22 entries 6LYT, 5PTI, 1UBQ, and 1P7E solvated in cubic water boxes containing 10,594, 4215, 6080, and 5156 water molecules, respectivel... .

Publication Year: 2010


Potentials of mean force for protein structure prediction vindicated, formalized and generalized.

(2010) PLoS One 5

PubMed: 21103041 | PubMedCentral: PMC2978081 | DOI: 10.1371/journal.pone.0013714

Sampling from TorusDBN was done conditional on the amino acid sequence of ubiquitin (76 residues, PDB code 1UBQ).

Publication Year: 2010


CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.

(2010) BMC Struct Biol 10

PubMed: 21034466 | PubMedCentral: PMC2987814 | DOI: 10.1186/1472-6807-10-39

For ubiquitin, the starting conformer was the X-ray structure (PDB ID 1UBQ [ 55 ]) available; for SGCI, we used the fifth (representative) conformer in its deposited NMR-derived structure (PDB ID 1KGM... [ 46 ]).

pdb) plus COCO-derived conformers 20 this study U_1XQQ DER ensemble 128 [ 14 ] U_2NR2 MUMO ensemble 144 [ 15 ] U_2K39 EROS ensemble 116 [ 10 ] U_ISD ISD ensemble (ensemble provided as an example with the ISD 1.1 package) 25 [ 26 ] U_NNR NOE(2)+S 2 (8)+RDC(8) restrained ensemble 32 this study U_CNS RECOORD ensemble calculated with CNS 25 [ 34 ] U_CNW RECOORD ensemble calculated with CNS in water 25 [ 34 ] U_CYA RECOORD ensemble calculated with CYANA 25 [ 34 ] U_CYW RECOORD ensemble calculated with CYANA in water 25 [ 34 ] U_1UBQMD 5ns MD simulation started from the X-ray structure 1UBQ 32 this study U_1G6J Ubiquitin in reverse micelles 32 [ 36 ] U_1V80 Ubiquitin at 30 bar 10 [ 37 ] U_1V81 Ubiquitin at 3000 bar 10 [ 37 ] U_2JZZ Solid-state NMR structure 20 [ 38 ] Figure 2 Ribbon representation of human ubiquitin ensembles generated for this study .

Publication Year: 2010


Residual dipolar couplings: are multiple independent alignments always possible?

(2011) J Biomol NMR 49

PubMed: 21184138 | PubMedCentral: PMC3020303 | DOI: 10.1007/s10858-010-9457-1

1996 )) and b ubiquitin (pdb code 1UBQ (Vijay-Kumar et al.

Publication Year: 2011


Discovering conformational sub-states relevant to protein function.

(2011) PLoS One 6

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

Starting with eight different crystal structures [PDB codes: 1UBQ; 1P3Q (chain U); 1S1Q (chain B); 1TBE (chain B); 1YIW (chain A); 2D3G (chain B); 2FCQ (chain B); and 2G45 (chain B)] t... at covered the structural diversity of ubiquitin's conformation, stable MD trajectories were generated.

Publication Year: 2011


Site-resolved measurement of water-protein interactions by solution NMR.

(2011) Nat Struct Mol Biol 18

PubMed: 21196937 | PubMedCentral: PMC3058360 | DOI: 10.1038/nsmb.1955

Two crystal structures for wild type human ubiquitin are available (PDB codes 1UBQ and 1UBI) 27 , 33 .

Two views of the backbone ribbon of a crystallographic structure of human ubiquitin (PDB code 1UBQ) are shown.

To illustrate the degree of correspondence between the long-lived hydration waters detected by NMR to the locations of the defined waters common to both crystal structures of ubiquitin, a color-coded ribbon diagram of 1UBQ is shown in Figure 4 .

Waters that are common between the two crystal structures (1UBQ and 1UBI) are shown as spheres.

Publication Year: 2011


Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction.

(2011) Nat Chem Biol 7

PubMed: 21196936 | PubMedCentral: PMC3078768 | DOI: 10.1038/nchembio.501

Figure 5 Fiber decompaction is a specific property of the ubiquitin protein a , Surface rendering of the X-ray structure of ubiquitin (1UBQ, left) 49 and the NMR structure of Hub1 (1M94, right, includ... ng the C-terminal RGG residues) 50 .

Publication Year: 2011


In silico elucidation of the recognition dynamics of ubiquitin.

(2011) PLoS Comput Biol 7

PubMed: 21533067 | PubMedCentral: PMC3080845 | DOI: 10.1371/journal.pcbi.1002035

The crystal structure of ubiquitin (PDB code 1UBQ) [45] was employed as the initial conformation.

Since residues 73–76 of ubiquitin in 2D3G are missing, the ubiquitin conformation of 1UBQ was used for this simulation by superimposing the backbone of residues 2–71 to chain A of the structure 2D3G.

Publication Year: 2011


The energy computation paradox and ab initio protein folding.

(2011) PLoS One 6

PubMed: 21541343 | PubMedCentral: PMC3081830 | DOI: 10.1371/journal.pone.0018868

Methods Interacting Fragment Database Generation In order to generate a reference database of fragment-based interacting systems involved in protein folds, we examined a native fold of ubiquitin (PDBI... : 1UBQ) [31] in detail.

Publication Year: 2011


SHIFTX2: significantly improved protein chemical shift prediction.

(2011) J Biomol NMR 50

PubMed: 21448735 | PubMedCentral: PMC3085061 | DOI: 10.1007/s10858-011-9478-4

To evaluate SHIFTX2 in the context of protein structure refinement, we simulated the structure refinement process by generating 15 randomly perturbed structures for ubiquitin (PDB entry 1UBQ) by progr... ssively altering the backbone ϕ/ψ angles of the native protein.

This graph illustrates the correlation coefficients calculated via SHIFTX + , SHIFTY+ and SHIFTX2 using 16 different 1UBQ structures (15 randomized and 1 native structure).

Publication Year: 2011


Implementation of force distribution analysis for molecular dynamics simulations.

(2011) BMC Bioinformatics 12

PubMed: 21501475 | PubMedCentral: PMC3094238 | DOI: 10.1186/1471-2105-12-101

(A) A fit of ubiquitin (PDB code 1UBQ ) with and without applied external strain.

Publication Year: 2011


Rational design of protein stability: effect of (2S,4R)-4-fluoroproline on the stability and folding pathway of ubiquitin.

(2011) PLoS One 6

PubMed: 21625626 | PubMedCentral: PMC3095602 | DOI: 10.1371/journal.pone.0019425

Replacement of Pro with (4R)-FPro has been simulated using the crystal structure coordinates of wt ubiquitin (PDB: 1UBQ).

g001 Figure 1 Tertiary structure of human ubiquitin according to the 1.8 Å crystal structure (1UBQ.

Publication Year: 2011


The essential functions of NEDD8 are mediated via distinct surface regions, and not by polyneddylation in Schizosaccharomyces pombe.

(2011) PLoS One 6

PubMed: 21655279 | PubMedCentral: PMC3105002 | DOI: 10.1371/journal.pone.0020089

Figures were made using MacPyMOL on NEDD8 (PDB 1NDD) and ubiquitin (PDB 1UBQ).

Publication Year: 2011


A new view of the bacterial cytosol environment.

(2011) PLoS Comput Biol 7

PubMed: 21695225 | PubMedCentral: PMC3111478 | DOI: 10.1371/journal.pcbi.1002066

Although ubiquitin (PDB code 1UBQ) is a eukaryotic protein, it was chosen owing to its small size and large amount of literature dedicated to its study [25] – [27] .

Ubiquitin (PDB code 1UBQ) is a eukaryotic protein, it was chosen owing to its small size and large amount of literature dedicated to its study [25] – [27] .

Publication Year: 2011


QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin.

(2011) Bioinformatics 27

PubMed: 21685101 | PubMedCentral: PMC3117343 | DOI: 10.1093/bioinformatics/btr248

Briefly, eight crystal structures of ubiquitin (PDB codes: 1UBQ, 1P3Q, 1S1Q, 1TBE, 1YIW, 2D3G, 2G45 and 2FCQ) were used for our simulation.

Publication Year: 2011


Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures.

(2011) J Mol Biol 411

PubMed: 21645520 | PubMedCentral: PMC3171141 | DOI: 10.1016/j.jmb.2011.05.033

The following labels apply: start—molecular replacement solution; unrestr—structure refined without external restraints; restr—structure refined using corrections calculated ac... ording to Busing–Levy equations as restraints (the restraints were calculated for PDB ID 1H8K from the 1SHG model and for PDB ID 3EFU from the 1UBQ model); restr or —structure refined from unrestr 0 using distances without any corrections as restraints.

Publication Year: 2011


Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.

(2011) Eur Biophys J 40

PubMed: 22089251 | PubMedCentral: PMC3222826 | DOI: 10.1007/s00249-011-0754-8

1UBQ and 1D3Z are the X-ray crystallography structure and the NMR average solution structure ( purple and red ), respectively.

Publication Year: 2011


Structural analysis of the UBA domain of X-linked inhibitor of apoptosis protein reveals different surfaces for ubiquitin-binding and self-association.

(2011) PLoS One 6

PubMed: 22194841 | PubMedCentral: PMC3240630 | DOI: 10.1371/journal.pone.0028511

The HADDOCK calculations of XIAP-UBA/Ub complex were started with the coordinates of human ubiquitin (PDB code: 1UBQ) and the averaged structure of the XIAP UBA domain (residues 365–423, PDB c... de: 2KNA).

The mono-ubiquitin structure was retrieved from Protein Data Bank (PDB code: 1UBQ).

Publication Year: 2011


Deciphering the preference and predicting the viability of circular permutations in proteins.

(2012) PLoS One 7

PubMed: 22359629 | PubMedCentral: PMC3281007 | DOI: 10.1371/journal.pone.0031791

Well-defined protein splitting sites for PCA (see [77] for a summary), protein trans-splicing [75] , [76] and domain insertion [28] include residue 35 of ubiquitin (PDB entry: 1UBQ), 197 and 198 of &#... 003b2;-lactamase (PDB entry: 1TEM), 106 of DHFR, 102 and 123 and 131 of intein (PDB entry: 2KEQ), 438 of firefly luciferase (PDB entry: 1BA3), 158 of green fluorescent protein (GFP; PDB entry: 1GFL), and 145 of enhanced yellow fluorescent protein (PDB entry: 1YFP).

Publication Year: 2012


SProt: sphere-based protein structure similarity algorithm.

(2011) Proteome Sci 9 Suppl 1

PubMed: 22166105 | PubMedCentral: PMC3289081 | DOI: 10.1186/1477-5956-9-S1-S20

Figure 1 An example of an aa-sphere This example demonstrates an aa-sphere for the 26-th amino acid of Ubiquitin [PDB:1UBQ].

Publication Year: 2011


OneG: a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions.

(2012) PLoS One 7

PubMed: 22412877 | PubMedCentral: PMC3296725 | DOI: 10.1371/journal.pone.0032465

The k rc values of NHs in ubiquitin (PDB ID: 1UBQ) and cardiotoxin III have been calculated using the OneG and the data have been compared with the k rc values of NHs in the proteins as determined by ... anual calculation ( Figure 2 ).

Publication Year: 2012


Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

(2012) J Chem Theory Comput 8

PubMed: 22582031 | PubMedCentral: PMC3348677 | DOI: 10.1021/ct200909j

The systems used consisted of partially folded TRPCage 52 (304 atoms), ubiquitin 53 , 54 (1231 atoms, PDB code 1UBQ ), apo-myoglobin (2492 atoms), and nucleosome (25 095 atoms, PDB code 1KX5 )...

We focus on root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the C α backbone carbon atoms with respect to the crystal structure (PDB code 1UBQ ( 53 , 54 )).

Publication Year: 2012


PubMed ID is not available.

Published in 2012

PubMedCentral: PMC3378902

The FANCI and monoubiquitylated FANCD2 complex were depicted based on the crystal structures of mouse ID complex (PDB ID: 3S4W) and human ubiquitin (PDB ID: 1UBQ).

Publication Year: 2012


Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.

(2012) Nature 489

PubMed: 22842904 | PubMedCentral: PMC3442243 | DOI: 10.1038/nature11376

A lower resolution (3 Å) data set for the heterotrimer was solved by finding a single RNF4 RING domain (PDB 2XEU) 3 , followed by E2 UbcH5a (2YHO) 14 and ubiquitin (1UBQ, truncated at residue ... 72) 32 .

Publication Year: 2012


Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection.

(2012) PLoS Comput Biol 8

PubMed: 23055911 | PubMedCentral: PMC3464204 | DOI: 10.1371/journal.pcbi.1002704

Additional simulations starting from two x-ray structures without binding partner (1UBI [25] and 1UBQ [26] ) were conducted for comparison.

PDB code binding partner reference 1NBF Ubiquitin carboxyl-terminal hydrolase 7 (HAUSP) [12] 1P3Q CUE domain of Vacuolar protein sorting associated protein (Vps9p) [13] 1S1Q Tumor susceptibility gene 101 protein (TSG101) [14] 1UBI none (unbound reference) [25] 1UBQ none (unbound reference) [26] 1UZX UEV domain of Vps23 [15] 1XD3 Ubiquitin Carboxyl-terminal esterase L3 (UCH-L3) [16] 2D3G UIM from hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs-UIM) [17] 2FIF Rab5 GDP/GTP exchange factor [18] 2G45 Ubiquitin carboxyl-terminal hydrolase 5 [19] 2HTH Vacuolar protein sorting protein 36 [20] 2IBI Ubiquitin carboxyl-terminal hydrolase 2 [21] 2OOB E3 ubiquitin-protein ligase CBL-B [22] Structures used for simulation setup.

An unbound reference ensemble was created from simulation trajectories based on the unbound x-ray structures 1UBI and 1UBQ and these unbound control trajectories.

Publication Year: 2012


The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method.

(2012) J Biomol NMR 54

PubMed: 23001323 | PubMedCentral: PMC3483107 | DOI: 10.1007/s10858-012-9662-1

2000 ) (human ubiquitin, PDB identifier 1ubq (Vijay-Kumar et al.

Publication Year: 2012


Similarities between protein folding and granular jamming.

(2012) Nat Commun 3

PubMed: 23093180 | PubMedCentral: PMC3493650 | DOI: 10.1038/ncomms2177

Methods Computational details The initial co-ordinates for the simulations were crystal structures of ubiquitin (PDB id 1UBQ 55 ), titin (1TIT 56 ) and calmodulin (1LJK 57 ) obtained from the Protein ... ata Bank.

Publication Year: 2012


Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.

(2012) J Chem Theory Comput 8

PubMed: 23180979 | PubMedCentral: PMC3503459 | DOI: 10.1021/ct200390j

o 115.04 63.77 51.27 1.91 0.38 0.12 a The test proteins (PDB code) are trp ( 1l2y ), drk ( 2a36 ), ubq ( 1ubq ), if3c ( 1tig ), lys ( 1aki ), and talin ( 2jsw ).

Publication Year: 2012


Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

(2012) EURASIP J Bioinform Syst Biol 2012

PubMed: 22793672 | PubMedCentral: PMC3524763 | DOI: 10.1186/1687-4153-2012-8

2008 2008 Institute of Electrical and Electronics Engineers, Hangzhou, China pp. 74 79 Vijay Kumar S Bugg CE Cook WJ Structure of ubiquitin refined at 1.8 A resolution J Mol Biol 1987 194 531 544 10.1... 16/0022-2836(87)90679-6 3041007 Vijay Kumar S Bugg CE Cook WJ 1UBQ Structure of ubiquitin refined at 1.8 angstroms resolution http://www.rcsb.org/pdb/explore/explore.do?structureId=1ubq Hicke L Schubert HL Hill CP Ubiquitin-binding domains Nat Rev Mol Cell Biol 2005 6 610 621 10.1038/nrm1701 16064137 Varadan R Assfalg M Haririnia A Raasi S Pickart C Fushman D Solution conformation of Lys63-linked di-ubiquitin chain provides clues to functional diversity of polyubiquitin signaling J Biol Chem 2004 279 7055 7063 14645257 Varadan R Walker O Pickart C Fushman D Structural properties of polyubiquitin chains in solution J Mol Biol 2002 324 637 647 10.1016/S0022-2836(02)01198-1 12460567 Cook WJ Jeffrey LC Carson M Chen Z Pickart CM Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2) J Biol Chem 1992 267 16467 16471 1322903 Branden C Tooze J Introduction to Protein Structure 1999 Garland Publishing Inc., New York, NY pp. 9 10 McClendon CL Friedland G Mobley DL Amirkhani H Jacobson MP Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles J Chem.

Using the secondary structure revealed in the X-ray diffraction 1.8 angstrom solved structure 1UBQ [ 37 , 38 ] available from the Protein Data Bank, of the representative attribute clusters in each branch, we observe that (a) 11 out of 14 clusters included loops or turns; (b) 9 out of 14 included beta strands; and (c) 5 out of 14 included helices.

The 3D structure of ubiquitin is shown in Figure 3A , using the solved structure 1UBQ.

(A) The 3D structure of ubiquitin, using the 1UBQ solved structure.

For better visualization of the module locations and the major branch node-forming clusters on the sequence, Figure 4 shows the modules as boxes superimposed over the sequence with its color-coded secondary structure (taken from the 1UBQ model).

The location of the major clusters associated with the four major modules is shown, for clarity, on two identical secondary structure ribbons, taken from model 1UBQ.

Publication Year: 2012


BetaSearch: a new method for querying ?-residue motifs.

(2012) BMC Res Notes 5

PubMed: 22839199 | PubMedCentral: PMC3532365 | DOI: 10.1186/1756-0500-5-391

For example, the sheet ID of the first β -matrix in chain A of ubiquitin [PDB:1UBQ] is “1UBQA_SHEET_000”.

Publication Year: 2012


Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function.

(2013) Nat Struct Mol Biol 20

PubMed: 23178454 | PubMedCentral: PMC3537887 | DOI: 10.1038/nsmb.2430

Ubiquitin (1UBQ) conformers shown in colors.

Publication Year: 2013


Enzyme-catalyzed protein crosslinking.

(2013) Appl Microbiol Biotechnol 97

PubMed: 23179622 | PubMedCentral: PMC3546294 | DOI: 10.1007/s00253-012-4569-z

The cartoon depicted in the center was created with the program PyMOL and shows the structure of ubiquitin (PDB ID: 1ubq) (Schrodinger 2010 ) One of the most extensively studied cellular protein cross... inking events is the enzyme-catalyzed covalent tethering of ubiquitin to target proteins.

Publication Year: 2013


MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry.

(2012) BMC Struct Biol 12

PubMed: 23153250 | PubMedCentral: PMC3557227 | DOI: 10.1186/1472-6807-12-29

pdb [ 25 ] and 1UBQ.

Publication Year: 2012


On the binding affinity of macromolecular interactions: daring to ask why proteins interact.

(2013) J R Soc Interface 10

PubMed: 23235262 | PubMedCentral: PMC3565702 | DOI: 10.1098/rsif.2012.0835

( a , b ) Crystallographically determined structures of ubiquitin (PDB entries 1UBQ and 1UBI), along with their corresponding crystallographic water molecules.

Publication Year: 2013


ISG15: leading a double life as a secreted molecule.

(2013) Exp Mol Med 45

PubMed: 23579383 | PubMedCentral: PMC3641400 | DOI: 10.1038/emm.2013.36

The structural information was obtained from the protein data bank (PDB): ubiquitin (PDB code: 1UBQ) and ISG15 (PDB code: 1Z2M).

Publication Year: 2013


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 .

The ensemble refinement protocol was started from the X-ray structure of ubiquitin (PDB code 1UBQ ( 18 )) and consisted of simulated annealing (SA) cycles [for details, see the Supporting Information (SI)].

8 For this purpose, we carried out ensemble simulations starting from the X-ray structure of ubiquitin ( 1UBQ ) using the SA protocol described in the SI and ensemble sizes ranging from 1 to 128.

Publication Year: 2011


Protein analysis by time-resolved measurements with an electro-switchable DNA chip.

(2013) Nat Commun 4

PubMed: 23839273 | PubMedCentral: PMC3719012 | DOI: 10.1038/ncomms3099

Protein dimensions (x, y, z) were measured from pdb entries with Pymol (The PyMOL Molecular Graphics system, Version, 1.5.0.4 Schrödinger LLC; (CA: 3LXE, Ub: 1UBQ, INFα: 1ITF, DHFR: 2W... M, chloramphenicol acetyl transferase: 1PD5, ERK2: 4GT3).

Publication Year: 2013


Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning.

(2013) J Chem Theory Comput 9

PubMed: 23894231 | PubMedCentral: PMC3719162 | DOI: 10.1021/ct400279d

We now put this into practice by performing molecular dynamics (MD) simulations of the three proteins described previously (PDB: 1UBQ, 1MHN, 6LYT) using force fields based on our calculated DDEC charg... s.

We have utilized the linear-scaling nature of our DDEC implementation to calculate DDEC charges of three proteins: ubiquitin, the SMN Tudor Domain, and hen egg lysozyme (PDB: 1UBQ, 1MHN, 6LYT).

Figure 10 Backbone C α root-mean-square deviation (RMSd) with respect to the initial experimental PDB structure for 1UBQ, 1MHN, and 6LYT, with running averages taken over 50 ps windows.

Publication Year: 2013


Interactions between HIV-1 Vif and human ElonginB-ElonginC are important for CBF-? binding to Vif.

(2013) Retrovirology 10

PubMed: 23988114 | PubMedCentral: PMC3765967 | DOI: 10.1186/1742-4690-10-94

The conserved EloB N-terminal was named the UbL domain because it bears marked sequence similarity to ubiquitin [ 48 ], and its tertiary structure (shown in red, PDB code: 3DCG) is strikingly similar ... o that of ubiquitin (shown in green, PDB code: 1UBQ) when aligned using software PyMol ( http://pymol.org/ , Figure  5 B) [ 28 , 72 ].

Publication Year: 2013


Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10.

(2013) PLoS Pathog 9

PubMed: 24086134 | PubMedCentral: PMC3784475 | DOI: 10.1371/journal.ppat.1003639

( A ) A ribbon representation of Ubq (1UBQ.

Publication Year: 2013


The architecture of Trypanosoma brucei tubulin-binding cofactor B and implications for function.

(2013) FEBS J 280

PubMed: 23627368 | PubMedCentral: PMC3806363 | DOI: 10.1111/febs.12308

Fig 4 Structural overlay of Tb TBC-B Ubl (blue) and ubiquitin (PDB code 1UBQ; pink).

Although remarkably similar in structure to ubiquitin (rmsd of 0.83 Å over 41 Cα atoms with PDB code 1UBQ), the Tb TBC-B Ubl domain shares only 10% sequence identity.

Publication Year: 2013


Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP.

(2013) Nature 503

PubMed: 24141947 | PubMedCentral: PMC3838313 | DOI: 10.1038/nature12638

Data were reduced using Xia2 from the CCP4 suite and the structure of the complex was determined by molecular replacement in Phaser 31 using the apo structure and ubiquitin (1UBQ.

Publication Year: 2013


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

Structural refinement using OPLS and ProCS for ubiquitin results in ensembles with average H O distances that have an RMSD within 0.02 Å of those found in the X-ray structures 1UBQ and 1UBI (b... th 1.80 Å X-ray resolution) and 0.04 Å from the ubiquitin structure 1OGW (1.30 Å X-ray resolution) in which the leucine residues 50 and 67 have been replaced by fluoro leucine.

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 0.44 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.

The following crystal structures obtained from the PDB were used as starting structures in the simulations: 1PGB (Protein G), 1UBQ (Ubiquitin) and 1MHN (SMN Tudor Domain).

ProCS CamShift Bond length Structures a 1 H RMSD 1 H RMSD deviation b RMSD Ubiquitin Ensembles: CamShift + OPLS 0.79 ppm - 0.03 Å 0.17 Hz Ubiquitin Ensembles: CamShift + OPLS - 0.50 ppm 0.37 Å 0.17 Hz Ubiquitin Ensembles: OPLS (no chemical shifts) 1.56 ppm 0.60 ppm 0.41 Å 0.18 Hz 1UBQ X-ray starting structure 1.22 ppm 0.51 ppm - 0.22 Hz SMN Tudor Domain Ensembles: ProCS + OPLS 0.93 ppm - 0.09 Å 0.24 Hz SMN Tudor Domain Ensembles: CamShift + OPLS - 0.46 ppm 0.17 Å 0.23 Hz SMN Tudor Domain Ensembles: OPLS (no chemical shifts) 1.47 ppm 0.61 ppm 0.22 Å 0.23 Hz 1MHN X-ray starting structure 1.09 ppm 0.65 ppm - 0.24 Hz Protein G Ensembles: ProCS + OPLS 0.69 ppm - 0.06 Å 0.14 Hz Protein G Ensembles: CamShift + OPLS - 0.52 ppm 0.38 Å 0.18 Hz Protein G Ensembles: OPLS (no chemical shifts) 1.54 ppm 0.68 ppm 0.37 Å 0.20 Hz 1PGB X-ray starting structure 1.21 ppm 0.55 ppm - 0.17 Hz a The ensembles are obtained from MCMC simulations using either OPLS-AA/L with the GB/SA solvent model (OPLS) force field energy or OPLS energy plus a chemical shift energy term from from either ProCS or CamShift.

Publication Year: 2013


Ranking and compacting binding segments of protein families using aligned pattern clusters.

(2013) Proteome Sci 11

PubMed: 24564874 | PubMedCentral: PMC3907781 | DOI: 10.1186/1477-5956-11-S1-S8

Our resulting APCs Figure 7 The three-dimensional structure of the ubiquitin protein, with PDB ID 1UBQ from the protein data bank, has seven binding residues: Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, ... nd Lys63 .

Figure 7 : The three-dimensional structure of the ubiquitin protein, with PDB ID 1UBQ from the protein data bank, has seven binding residues: Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, and Lys63.

Publication Year: 2013


E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.

(2013) Nat Struct Mol Biol 20

PubMed: 23955022 | PubMedCentral: PMC3941643 | DOI: 10.1038/nsmb.2655

The h/ceOTUB1-Ubal complex (PDB ID: 4DHZ), UBCH5B (PDB ID: 2ESK), and ubiquitin (PDB ID: 1UBQ) were used as search models.

Publication Year: 2013


Specific non-local interactions are not necessary for recovering native protein dynamics.

(2014) PLoS One 9

PubMed: 24625758 | PubMedCentral: PMC3953337 | DOI: 10.1371/journal.pone.0091347

To compare surface fluctuations in CND and ENM we have used all the above 26 structures and additionally Ubiquitin structure (1UBQ [53] , chain A, residues 1 to 72).

Publication Year: 2014


Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.

(2014) J Am Chem Soc 136

PubMed: 24568736 | PubMedCentral: PMC3954408 | DOI: 10.1021/ja4132642

Table 1 Experimental Validation Statistics for Different Structural Representations of Ubiquitin a structure current (2MJB) 1D3Z 20 2KOX 18 2NR2 26 1UBQ 27 , d ⟨X-ray⟩ d , e RC... A b  (ppb) 6.5/15.7/8.9 b 7.2/14.9/9.4 b 9.2/17.5/11.1 b 10.6/17.4/12.1 b 11.6/24.7/14.3 b 6.2/13.9/8.1 b Q NH c  (%) 5.9/8.3/6.6 8.9/15.3/10.5 6.5/7.7/6.8 18.1/35.9/22.8 14.7/28.3/17.6 11.6/14.6/12.2 Q CαCβ (%) 9.3/22.2/11.7 10.8/29.4/14.6 10.5/21.1/12.4 12.5/16.9/13.2 17.3/37.8/21.3 9.9/14.3/10.4 3 J HNHα f  (Hz) 0.43/0.77/0.50 0.49/0.56/0.50 0.58/0.89/0.65 0.84/1.43/0.97 0.66/1.17/0.77 0.50/0.83/0.57 a For Q2-V70.

Publication Year: 2014


Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.

(2014) Biochemistry 53

PubMed: 24724799 | PubMedCentral: PMC4020902 | DOI: 10.1021/bi500116x

38 Despite poor sequence conservation, 15.8% and 11.8% sequence identity with the human and rat USP11 UBL domain respectively, the domains align to ubiquitin (PDB code 1UBQ( 39 )) with an RMSD of 1.6 ... #x000c5; over 70 Cα positions.

Publication Year: 2014


Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.

(2014) PLoS Pathog 10

PubMed: 24854014 | PubMedCentral: PMC4031219 | DOI: 10.1371/journal.ppat.1004113

The structure elements were generated using the X-ray crystal structure of ubiquitin (pdb: 1UBQ).

Phases for the complex were obtained from a molecular replacement solution using a monomer of the unbound PLpro structure (PDB entry: 2FE8) and free ubiquitin (PDB entry: 1UBQ) as search models using Phaser [64] , which identified one unique molecular replacement solution of the complex.

Publication Year: 2014


Extensive conformational heterogeneity within protein cores.

(2014) J Phys Chem B 118

PubMed: 24564338 | PubMedCentral: PMC4065209 | DOI: 10.1021/jp4105823

Ubiquitin A total of 1000 simulations were started from PDB 1UBQ, 33 for an aggregate of 2.3 ms of dynamics.

Publication Year: 2014


Bayesian weighting of statistical potentials in NMR structure calculation.

(2014) PLoS One 9

PubMed: 24956116 | PubMedCentral: PMC4067304 | DOI: 10.1371/journal.pone.0100197

The dotted black line indicates the average Q-factor of the crystal structure (PDB code: 1ubq).

The dotted black line indicates the average Q-factor of the crystal structure (PDB code: 1ubq).

Publication Year: 2014


The role of the selective adaptor p62 and ubiquitin-like proteins in autophagy.

(2014) Biomed Res Int 2014

PubMed: 25013806 | PubMedCentral: PMC4075091 | DOI: 10.1155/2014/832704

Other helical structures are blue (Protein Data Bank (PDB) accession codes: 1UBQ [ 105 ], 4GDK [ 106 ], and 1UGM [ 107 ], resp.)

Publication Year: 2014


PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

(2014) PLoS Comput Biol 10

PubMed: 24992446 | PubMedCentral: PMC4081019 | DOI: 10.1371/journal.pcbi.1003691

We used the structure of Ub monomer (PDB: 1UBQ) resolved by X-ray crystallography [54] as the reference conformation for structure-based model (SBM).

Publication Year: 2014


Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

(2014) J Phys Chem B 118

PubMed: 24479585 | PubMedCentral: PMC4103960 | DOI: 10.1021/jp409805p

Table 1 Protein Molecular Weight, Secondary Structure in Terms of Helical and β-Sheet Composition, Surface Composition in Terms of the Total Time-Averaged OH-Bond Population of the Hydrophobe,... H-Bond Donor or H-Bond Acceptor Sites, and Total Charge     secondary structure relative OH-bond population     molecular weight (kDa) helical β-sheet hydrophobe donor acceptor total charge ubiquitin 9 23% 34% 68% 15% 17% 0 lysozyme 14 40% 10% 72% 15% 13% +8 subtilisin Carlsberg 27 28% 19% 71% 13% 16% –1 acetylcholinesterase 59 36% 17% 74% 14% 12% –9 The initial protein configurations were obtained from the crystallographic structures with PDB codes 4ARA (acetylcholinesterase), 1SCN (subtilisin Carlsberg), 2LYM (lysozyme), and 1UBQ (ubiquitin).

Publication Year: 2014


Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

(2014) PLoS Comput Biol 10

PubMed: 25057988 | PubMedCentral: PMC4109840 | DOI: 10.1371/journal.pcbi.1003719

(A) Ubiquitin (PDB code 1UBQ [57] ) displayed as ribbons with crystal waters.

Publication Year: 2014


A new statistical framework to assess structural alignment quality using information compression.

(2014) Bioinformatics 30

PubMed: 25161241 | PubMedCentral: PMC4147913 | DOI: 10.1093/bioinformatics/btu460

Comparison between DALI score, TM-Score and I -value on ambiguous alignments reported by Zu-Kang and Sippl (1996) Structures Residues Alignment A 1 Alignment A 2 S v. T | S | | T | DALI Score TM-Score... I ( A 1 , S , T ) Dali Score TM-Score I ( A 2 , S , T ) 2TMVP v. 256BA 154 106 262.8 0.4871 9611.2 bits 242.6 0.4744 9614.0 bits 1TNFA v. 1BMV1 152 185 265.1 0.3815 12577.1 bits 307.3 0.3947 12463.7 bits 1UBQ v. 1FRD 76 98 161.9 0.4790 6384.8 bits 146.1 0.4518 6409.8 bits 2RSLC v. 3CHY 119 128 182.6 0.3773 9159.8 bits 206.1 0.3768 9143.5 bits 3CHY v. 1RCF 128 169 377.5 0.4960 10983.0 bits 336.4 0.4855 10961.8 bits Note : For DALI and TM-score, the higher the score the better the alignment.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4165463

Inset in (a) shows the structures of cross-links P3 to P6, and inset in (b) shows the X-ray 3D structure of ubiquitin (PDB: 1UBQ).

Publication Year: 2014


Assembly, analysis and architecture of atypical ubiquitin chains.

(2013) Nat Struct Mol Biol 20

PubMed: 23563141 | PubMedCentral: PMC4176834 | DOI: 10.1038/nsmb.2547

Right , monoUb (pdb-id 1ubq 58 ).

Publication Year: 2013


Design and characterization of structured protein linkers with differing flexibilities.

(2014) Protein Eng Des Sel 27

PubMed: 25301959 | PubMedCentral: PMC4191447 | DOI: 10.1093/protein/gzu043

(B) Ribbon diagrams for domains used in structured linkers shown to scale (pdb codes: ZAG (1ZAG), β2m (1LDS), cTPR (2FO7), ubiquitin (1UBQ)).

, 1999 ), and β2-microgloblin (β2m; PDB code: 1LDS) and ubiquitin (Ub; PDB code: 1UBQ) as examples of small globular proteins (Fig.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4201340

The X-ray crystal structure of Ub (PDB: 1UBQ) shows glutamine 40 (Q40) oriented toward the C-terminus, and studies in yeast demonstrated that this residue can be substituted without deleterious effect... on Ub function.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4270946

(b) Consistent with the { 1 H – 15 N} hetNOE data, the crystal structure of Ub (PDB: 1UBQ ) is ordered at its αN-terminus and immediately forms a β -strand with residue Met1.

Publication Year: 2014


Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

(2014) Proteins 82

PubMed: 23818175 | PubMedCentral: PMC4282583 | DOI: 10.1002/prot.24350

For further optimization and validation of newly derived force field parameters, 800 ns MD simulations of GPGG, VAPG, Gly-Pro-Phe (GPF), 1.5 μs MD simulations of angiotensin II, 1 μs M... simulations of human ubiquitin (PDB entry 1UBQ), 48 600 ns and 1.5 μs MD simulations of AHM and 1.5 μs MD simulations of AHG were carried out.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4339119

This and the fact that there are no significant conformational differences between the phosphoUb structures in the crystal and a Ub reference structure [pdb-id 1ubq, RMSDs 0.45–0.69&#x... 00a0;Å (Vijay-Kumar et al , 1987 )] indicated that the major phosphoUb NMR species had crystallized.

E Comparison of Ub secondary structure [derived from pdb-id 1ubq (Vijay-Kumar et al , 1987 )] with the secondary structure predictions of major and minor phosphoUb forms as calculated from backbone chemical shifts using TALOS+ (Supplementary Fig S5).

Publication Year: 2014


The role of binding site on the mechanical unfolding mechanism of ubiquitin.

(2015) Sci Rep 5

PubMed: 25736913 | PubMedCentral: PMC4348633 | DOI: 10.1038/srep08757

We employed the AMBER99sb potential field 51 which utilizes an implicit solvent model for water in conjunction with the Protein Data Bank (PDB) ID 1UBQ for the native configuration of ubiquitin.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4353193

Ub (PDB: 1UBQ, yellow) [ 46 ] and Ube2W (PDB: 2A7L, gold) [ 48 ].

Structural representation of each Ub-SUMO2 substrate was created by using the Ub structure (PDB: 1UBQ, yellow) [ 46 ] and the SUMO2 structure (PDB: 1WM2, blue) [ 47 ] (the flexible N-terminus of SUMO2 is represented by a blue ribbon).

DUB assays were carried out for 1 h at 37°C. Figure 2 The UCH DUBs can cleave Ub from the N-terminus of polySUMO2 ( A ) Structural representation of the Ub-SUMO2x4ΔN11 substrate was created by using the Ub structure (PDB: 1UBQ, yellow) [ 46 ] and the SUMO2 structure (PDB: 1WM2, blue) [ 47 ] (the flexible N-terminus of SUMO2 is represented by a blue ribbon).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4367433

PDB IDs for ubiquitin and UFM1 are 1UBQ and 1WXS, respectively.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4370504

The crystal structure of Ub (PDB code: 1ubq) was used as the search model.

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4372068

(B) Structure of Ub (PDB entry 1ubq) showing the seven lysines (K6, K11, K27, K29, K33, K48, and K63) and the types of polymeric Ub (polyUb) chains that form due to the presence of these residues.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4372856

Structure modified from PDB ID: 1UBQ.

Structures modified from PDB ID: ; 1UBQ and ; 2B3P.

Publication Year: 2015


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