Primary Citation PubMed: 19035630
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Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs.
(2013) PLoS Comput Biol 9
PubMed: 24367248 | PubMedCentral: PMC3868525 | DOI: 10.1371/journal.pcbi.1003395
While other local minima are present, the [Fe 4 S 4 ] 2+ (open,substrate-free) simulations sample energy wells near both the open (PDB ID: 3DNF) and closed (PDB ID: 3KE8) crystal structures along PC1 ... ut do not overlap with the latter, HMBPP-bound crystal structure.
Alignment procedures implemented in the RMSD and tRMSF calculations are performed with respect to the [Fe 3 S 4 ] + (open, substrate-free) IspH crystal structure (PDB ID: 3DNF  ), aligning to the backbone atoms of D1, as this domain is the most rigid in all simulations.
Crystal structures corresponding to [Fe 3 S 4 ] + (open, substrate-free) (white square, PDB ID: 3DNF) and [Fe 4 S 4 ] 2+ (closed, HMBPP-bound) IspH (white diamond, PDB ID: 3KE8) are also projected onto PC space  ,  .
Since we want our PCA to assess how well the different simulations sample conformational space with respect to the [Fe 3 S 4 ] + (open, substrate-free) and [Fe 4 S 4 ] 2+ (closed, HMBPP-bound) IspH crystal structures (PDB ID: 3DNF and 3KE8, respectively), we first align the two crystal structures using the STructural Alignment of Multiple Proteins (STAMP) procedure  , as implemented in the VMD MultiSeq plugin  ,  .
Methods Ligand parameterization for molecular dynamics simulation Since the questions under consideration in this study begin with open, substrate-free IspH protein, we use the [Fe 3 S 4 ] + (open, substrate-free) IspH crystal structure from Rekittke, et al (PDB ID: 3DNF) as a starting point  .
The A. aeolicus [Fe 3 S 4 ] + IspH structure (PDB ID: 3DNF; henceforth referred to as [Fe 3 S 4 ] + (open, substrate-free) IspH) assumes an open conformation, with a 10×20 Å cavity where the HMBPP molecule is expected to bind at the cluster  .
Publication Year: 2013
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