Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry.

(2012) PLoS Pathog 8

PubMed: 23144613 | PubMedCentral: PMC3493474 | DOI: 10.1371/journal.ppat.1002993

In the influenza A virus HA, T358 is indicated in the N terminus of HA2 and, after conformational rearrangement, in the fusion peptide (inset; PDB 2KXA [76] ); the corresponding residue E377 is indica... ed in influenza B virus HA2.

Publication Year: 2012


Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models.

(2013) PLoS Comput Biol 9

PubMed: 23505359 | PubMedCentral: PMC3591293 | DOI: 10.1371/journal.pcbi.1002950

The following conformational models were used as targets for the restrained simulations: the X-31 NMR structure in micelles by Han and co-workers [45] (PDB code 1IBN) for the kinked helix, the A/swine... Scotland/410440/94 NMR structure in micelles by Lorieau and co-workers [17] (PDB code 2KXA) for the helical hairpin, and the G1V X-31 NMR structure in micelles (PDB code 1XOP) by Li and co-workers [24] as an idealized straight helix.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4010296

Methods Starting Structures Starting coordinates for the HAFP hairpin were taken from the NMR structure 31 (PDB code 2KXA).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4384350

Superimposition of 2KXA and 2KSL conformations extracted from the SOM, as the ones displaying the minimum coordinates RMSD with respect to the first conformer of the corresponding PDB structures.

The introduction of this noise into the α helical and long-range constraints makes the i BP solution moving apart from the PDB structure, as the minimum RMSD to PDB structure changes from 1.1 to 2 Å for 2KXA, and from 3.0 to 4.3 Å for 2KSL.

In 2KSL and 2KXA SOMs, the protein conformations corresponding to the region displaying the smallest coordinate RMSD values with respect to the PDB structure, were extracted (Figure 7 ).

Table 2 Analysis of conformations obtained by the branch-and-pruning algorithm on the three proteins targets: 2JMY, 2KXA and 2KSL Proteins 2JMY 2JMY_1 2JMY_2 2KXA 2KSL Number of residues 15 15 15 24 51 Number of vertices 107 107 107 170 359 Definition of α helices 1-15 3-13 5-11 1-11, 13-23 4-11, 13-27, 29-36, 41-50 Position tolerance (Å) 0.2 0.2 0.2 0.2 0.2 Angle tolerance (°) 2 2 2 4 4 b value 4 4 4 8 4 Number of long-range constraints 0 0 0 1 3 Number of saved conformations 1 10000 10000 10000 10000 Number of generated conformations 1 633,937 928,399 3,380,964 491,498 CPU time - 1 min 1 min 25 min 31 min Number of violated constraints (> 1Å) 0 4.0 ± 2.1 11.6 ± 3.6 9.6 ± 2.9 12.8 ± 1.1 Maximum violation (Å) 0 3.3 ± 1.4 4.8 ± 0.7 3.7 ± 1.0 8.1 ± 0.6 Mininum RMSD from PDB structure (Å) 1.4 1.3 2.1 1.1 3.0 RMSD from PDB structure for minimum violated conformations (Å) 1.4 2.9 2.8 1.3 3.5 PROCHECK core residues (%) 100 65.7 ± 25.9 49.2 ± 7.6 60.4 ± 8.1 76.9 ± 2.4 allowed residues (%) 0 17.9 ± 9.7 40.9 ± 8.3 39.6 ± 8.0 21.3 ± 2.8 gen.allow.

The three examples we chose to illustrate the algorithm display an increasing structural complexity: (i) a single α helix, corresponding to the structure of peptide CM15 determined in micelles (PDB id: 2JMY [ 58 ]), (ii) an α helical hairpin (PDB id: 2KXA [ 59 ]), (iii) the insecticidial toxin TAITX-1a, formed as a bundle of four α helices, restrained by three disulphide bridges (PDB id: 2KSL).

Publication Year: 2015