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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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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

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

Figure 1 shows the projection of the 1AP4 cMD and aMD trajectories into PC space as well as an overlay of the two.

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.

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

(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.

(C) Frame 9840 corresponds to the most open conformation sampled during the 1AP4 aMD simulation.

Principal Component Analysis The principal component analysis (PCA) was performed using the bio3D package in R. 33 A blast profile of the 1AP4 sequence revealed 1056 hits.

Simulation of NMR Observables On the basis of the MD trajectory of the Ca 2+ -bound system ( 1AP4 ), chemical shifts for the amide 1 H and the amide 15 N were calculated using the SHIFTX software.

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 ).

The Ca 2+ -bound system was modeled based on model 14 from pdb entry 1AP4 (89 residues, Ca 2+ -ion 4 ).

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

(B) Projection of the 1AP4 cMD trajectory (full blue circles) into the PC space is shown in density coloring where darker shades of blue indicate the more heavily sampled parts of the trajectory.

(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 ).

(C) Projection of the 1AP4 aMD trajectory (full blue circles) into the PC space is shown in density coloring.

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

(D) Projections of the 1AP4 cMD trajectory (full red circles) and the 1AP4 aMD trajectory (full blue circles) into the PC space are shown in density coloring, where darker shades of red and blue indicate the more heavily sampled parts of the trajectories.

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.

A principal component analysis of the conventional MD trajectory of the calcium bound TnC regulatory domain ( 1AP4 ) was performed.

(A) NMR structure of Ca 2+ -bound TnC ( 1AP4 ), (B) NMR structure of Ca 2+ -TnI-bound TnC ( 1MXL ), and (C) structure of frame 9840 of the 1AP4 aMD simulation are shown.

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