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PDB ID Mentions in PubMed Central Article count: 1

Citations in PubMed

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PDB ID Mentions in PubMed Central

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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 [23] ), 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 [23] , [28] .

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 [88] , as implemented in the VMD MultiSeq plugin [89] , [90] .

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 [23] .

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 [23] .

Publication Year: 2013