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PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Structure of the inhibitor W7 bound to the regulatory domain of cardiac troponin C.

(2009) Biochemistry 48

PubMed: 19419198 | PubMedCentral: PMC2697600 | DOI: 10.1021/bi9001826

We know that W7 binding stabilizes the open conformation of cNTnC·Ca 2+ 9 , 10 so the most inappropriate intraprotein NOEs for the docked complex would reflect the closed conformation of PDB e... try 1SPY ( 2 ).

Control calculations were also performed using the coordinates from PDB entries 1MXL and 1SPY (cNTnC·Ca 2+ , reflecting the closed conformation).

The choice of the initial coordinates and intraprotein NOEs of 1SPY gives an intraprotein NOE residual of 3.25 ± 0.65 kcal/mol (mean ± standard deviation over all 50 conformers) but does not minimize the docking residual (314 ± 38 kcal/mol).

For the choice of an inappropriate combination of initial coordinates and intraprotein NOEs (the initial coordinates from 1SPY with the intraprotein NOEs of 1MXL ), the intraprotein NOE residual is 58 ± 12 kcal/mol and the docking residual is 369 ± 76 kcal/mol.

Publication Year: 2009


Solution structure of the Apo C-terminal domain of the Lethocerus F1 troponin C isoform.

(2010) Biochemistry 49

PubMed: 20104876 | PubMedCentral: PMC3388720 | DOI: 10.1021/bi902094w

We show from left to right and from top to bottom the following: apo F1 CTnC (PDB entry 2k2a , blue), holo CTnC (PDB entry 2jnf , red), apo skCtnC in a complex with TnI and TnT (PDB entry 1yv0 , light... green), holo skCtnC in a complex with TnI and TnT (PDB entry 1ytz , brown), apo cNTnC (PDB entry 1spy , cyan), holo cNTnC (PDB entry 1apo , magenta), apo skNTnC (PDB entry 1tnp , gold), and holo skNTnC (PDB entry 1tnq , dark green).

Table 2 Interhelical Angles in Representative EF-Hands a protein PDB entry method I−II II−III III−IV I−IV apo NCaM 1dmo NMR 128 ± 3 130 ± 4 130 ± 4 121 ± 2 apo CCaM 1dmo NMR 137 ± 3 144 ± 3 132 ± 5 144 ± 3 apo skNTnC 1tnp NMR 130 ± 3 126 ± 5 125 ± 4 111 ± 2 apo cNTnC 1spy NMR 139 ± 3 115 ± 4 125 ± 5 117 ± 3 apo cNTnC 1a2x X-ray 138 119 136 121 holo cNTnC b 1ap4 NMR 136 ± 4 97 ± 4 119 ± 4 115 ± 2 apo F1 NTnC 2jnf NMR 133 ± 3 118 ± 2 124 ± 2 126 ± 3 apo F1 CTnC 2k2a NMR 135 ± 5 134 ± 4 132 ± 12 129 ± 7 holo F1 CTnC 2jnf NMR 103 ± 3 119 ± 2 127 ± 4 97 ± 2 holo NCaM 4cln X-ray 94 110 96 107 holo NCaM 1cll X-ray 87 112 96 99 holo NCaM 1g4y X-ray 96 111 90 115 holo NCaM 1cdl X-ray 88 112 91 104 holo CCaM 4cln X-ray 98 114 94 115 holo CCaM 1cll X-ray 97 112 95 109 apo CCaM c 1g4y X-ray 95 137 93 140 holo CCaM 1cdl X-ray 101 112 96 112 holo cCTnC 1a2x X-ray 99 120 109 112 holo cCTnC 1j1d X-ray 100 125 118 109 holo skNTnC 1tnq NMR 90 ± 3 100 ± 6 69 ± 5 109 ± 3 holo skNTnC 1ytz X-ray 105 101 94 116 apo skCTnC d 1yv0 X-ray 101 121 112 106 holo skCTnC 1ytz X-ray 106 123 111 114 apo CRLC e 1wdcB X-ray 103 146 104 144 apo CELC e 1wdcC X-ray 115 130 94 143 holo CAct e 1h8b NMR 96 ± 3 150 ± 4 93 ± 4 147 ± 3 a The values were calculated using the interhlx program freely available online ( http://nmr.uhnres.utoronto.ca/ikura/resources/data+sw/interhlx/ ).

Publication Year: 2010


Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study.

(2012) J Phys Chem B 116

PubMed: 22329450 | PubMedCentral: PMC3405770 | DOI: 10.1021/jp212173f

All systems were neutralized adding Na + counterions ( 1AP4 : 13 Na + , 1SPY : 15 Na + , 1MXL : 11 Na + ) and solvated using a TIP3P water box.

The NMR structures of 1AP4 , 1SPY , and 1MXL are shown as filled green, red, and blue circles, respectively.

These cutoffs resulted in 7 ( 1AP4 ), 9 ( 1SPY ), and 8 ( 1MXL ) clusters that represented at least 90% of the respective trajectories.

This minimum coincides with projection of the 1AP4 and 1SPY crystal structures, suggesting a significant energetic barrier to sampling the TnI-bound state.

The apo system was modeled based on model 13 from pdb entry 1SPY (89 residues 4 ).

The fully solvated systems contained 24 316 ( 1AP4 ), 26 756 ( 1SPY ), and 25 994 ( 1MXL ) atoms, respectively.

The NMR structures of 1AP4 , 1SPY , and 1MXL are shown as filled green, red, and blue circles, respectively.

(B) Projections of the Ca 2+ -bound TnC for the 1AP4 cMD trajectory (full blue circles), the 1SPY cMD trajectory (full red circles), and the 1MXL cMD trajectory (full green circles) into the PC space are shown in density coloring, where darker shades of blue, red, and green indicate the more heavily sampled parts of the trajectories.

Backbone N–H order parameters were calculated from the 100 ns molecular dynamics simulation of the apo system ( 1SPY ) using the isotropic reorientational eigenmode dynamics (iRED) approach.

In the cMD simulations, the structures and dynamics of the apo ( 1SPY ) and Ca 2+ -bound ( 1AP4 ) systems are very similar, as seen by their virtually overlapping projections into PC space (Figure 3 ).

32 An rmsd cutoff of 1.6 Å ( 1AP4 ), 1.7 Å ( 1SPY ) and 1.8 Å ( 1MXL ) was chosen, respectively.

(C) Projections of the Ca 2+ -bound TnC for the 1AP4 aMD trajectory (full blue circles), the 1SPY aMD trajectory (full red circles), and the 1MXL aMD trajectory (full green circles) into the PC space are shown in density coloring, where darker shades of blue, red, and green indicate the more heavily sampled parts of the trajectories.

The quadrants along PC1 and PC2 describe apo and Ca 2+ -bound TnC structures (lower right, e.g., 1SPY , 1AP4 ) and Ca 2+ -TnI-bound TnC structures (left side, e.g., 1MXL , 2L1R ).

Publication Year: 2012


Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study.

(2012) PLoS Comput Biol 8

PubMed: 23209387 | PubMedCentral: PMC3510055 | DOI: 10.1371/journal.pcbi.1002777

This transition is observed in the and TnI -bound states of skeletal TnC [22] , but only in the TnI -bound form for cardiac TnC ; it is accompanied by a decrease in the / angle from 140 and 132 degree... (where the helices are nearly parallel) for the apo and -bound structures (PDB codes 1SPY/1AP4) to 102 to 121 degrees (where the helices approach perpendicularity) for various TnI -bound states (PDB codes 1MXL, 1J1E, 1LXF).

Materials and Methods Structure preparation and simulation -bound (1AP4) and -free (1SPY) NMR structures resolved by [14] were obtained from the Protein Data bank [31] .

Results Mutations slightly disrupt wild-type TnC structure Overall TnC structure To understand the impact of GOF- and LOF- associated mutations on the structure of the N-terminal regulatory domain of TnC and subsequent impact on affinity, we performed in silico mutations of the -bound (holo) and - free (apo) wild-type NMR structures (1AP4 and 1SPY).

Publication Year: 2012


Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints.

(2014) PLoS One 9

PubMed: 24558365 | PubMedCentral: PMC3928104 | DOI: 10.1371/journal.pone.0087135

The Ca 2+ based folding and unfolding of helix D is observed in the crystal structures of the cTnC N-domain in the Ca 2+ -free (1SPY.

In the Ca 2+ free crystal structure of cardiac troponin C, 1SPY.

Publication Year: 2014


Regulatory domain of troponin moves dynamically during activation of cardiac muscle.

(2014) J Mol Cell Cardiol 75

PubMed: 25101951 | PubMedCentral: PMC4169182 | DOI: 10.1016/j.yjmcc.2014.07.015

For the IT arm, the crystal structure of 1J1D [8] was used for models in both relaxation and active contraction; for the regulatory head, the NMR solution structures of 1SPY [16] and 1MXL [17] were us... d in the absence and presence of Ca 2+ , respectively.

Publication Year: 2014