Primary Citation PubMed: 1512262
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Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation.
(2010) PLoS Comput Biol 6
PubMed: 20463873 | PubMedCentral: PMC2865513 | DOI: 10.1371/journal.pcbi.1000774
Materials and Methods Simulation setup The initial structures for the simulations starting from the R , R2 , and T state were taken from the protein data bank (PDB codes 1IRD  , 1B... B  and 2HHB  , respectively) and protonated using the pdb2gmx software.
Publication Year: 2010
Structure of the altitude adapted hemoglobin of guinea pig in the R2-state.
(2010) PLoS One 5
PubMed: 20811494 | PubMedCentral: PMC2927554 | DOI: 10.1371/journal.pone.0012389
Guinea pig hemoglobin (β1 = red, β2 = light red) and human hemoglobin (β1 = blue, β2 ... 003d; light blue) in the R2-state (PDB-code: 1BBB) were superimposed according to their C α -atoms.
The α1- and β2-subunit of guinea pig hemoglobin (α1 = light red) and human hemoglobin (α1 = light blue) in the R2-state (PDB-code: 1BBB,  ) were superimposed according to their C α -atoms.
Furthermore the position of His97 in human hemoglobin is shown in the T-state (grey, PDB-code: 1A3N,  ), R-state (orange, PDB-code: 1HHO,  ) and R2-state (light blue, PDB-code: 1BBB,  ).
The guinea pig hemoglobin structure is shown in cartoon representation, which is colored according to the distance between corresponding C α -atoms in guinea pig hemoglobin and the respective conformational state of human hemoglobin in (A) T-state (PDB-code: 1A3N,  ), (B) R-state (PDB-code: 1HHO,  ) and (C) R2-state (PDB-code: 1BBB,  ).
MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins.
(2014) J Appl Crystallogr 47
PubMed: 25242909 | PubMedCentral: PMC4119947 | DOI: 10.1107/S1600576714009959
Figure 4 Calculated solution difference scattering between human deoxy and carbonmonoxy hemoglobin crystal models ( 2hhb – 1bbb ), compared with experimental solution data from Cammarata et al... (2008 ▶ ).
The following structures were used (PDB codes in brackets): sperm whale deoxy myoglobin ( 2g0v , second state; Aranda et al. , 2006 ▶ ), sperm whale carbonmonoxy myoglobin ( 2g0r ; Aranda et al. , 2006 ▶ ), human deoxy hemoglobin ( 2hhb ) and human carbonmonoxy hemoglobin ( 1bbb ); these structures were used without cofactors.
In order to estimate the accuracy of difference scattering calculations from coarse-grained structures, the predicted difference scattering between the crystal structures of human deoxy hemoglobin (PDB code 2hhb ; Fermi et al. , 1984 ▶ ) compared with human carbonmonoxy hemoglobin (PDB code 1bbb ; Silva et al. , 1992 ▶ ), as calculated with all-atom and coarse-grained methods, are shown in Fig. 4 ▶ .
Publication Year: 2014
PubMed ID is not available.
Published in 2015
The B l ( q ) coefficients were evaluated to a maximum momentum transfer, q max , of 0.3 Å −1 (∼20 Å) for STMV (PDB code 1a34 ) and 0.6 Å... −1 (∼10 Å) for haemoglobin (PDB codes 1bbb and 2hbb ).
Figure 6 ( a ) FXS data calculated from the two haemoglobin crystal intermediates 1bbb (CO-haemoglobin; green and red cartoon and dotted lines) and 2hbb (deoxy-haemoglobin; blue cartoon and solid lines) in the Protein Data Bank.
Publication Year: 2015
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