1. PcrA Helicase, a Prototype ATP-Driven Molecular Motor
Markus Dittrich, Klaus Schulten 
Structure 
Volume 14, Issue 9, Pages (September 2006)
DOI: /j.str
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2. Figure 1 Structural Alignment of PcrA and F1-ATPase
(A) Depicted are the aligned X-ray structures of the 1A and 1B domains of PcrA and the βTP subunit of F1-ATPase colored by Q-Value (O'Donoghue and Luthey-Schulten, 2005). In (A), the color scheme from red to white to blue indicates a structural alignment quality ranging from good to weak.
(B) Shown is a close-up view of the aligned catalytic sites of PcrA (red) and F1-ATPase (blue) with bound ADP in van der Waals representation; conserved residues (Walker motifs A and B) are highlighted in licorice representation.
(C) Shown are the two parts of the sequence alignment that contain a stretch of two or more consecutive conserved residues; the upper panel corresponds to the Walker A or P loop motif, and the lower one corresponds to the Walker B motif.
Structure  , DOI: ( /j.str )
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3. Figure 2 Key States along the ATP Hydrolysis Pathway
Shown are the conformations of the quantum mechanically treated part of the QM/MM subsystem in the reactant (RS), transition (TS1/TS2), intermediate (IS1/IS2), and product (PS) states of ATP hydrolysis pathways 1 and 2.
Structure  , DOI: ( /j.str )
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4. Figure 3 ATP Hydrolysis Reaction Pathways in PcrA and F1-ATPase
Shown are schematic views of the catalytic core region of the reactant, transition, and product states for PcrA (top) and F1-ATPase (bottom). Depicted are important catalytic site residues; their nominal charge is indicated if applicable. Also shown is the location of binding pocket residues in their respective protein subunits, 1A/2A and α/β for PcrA and F1-ATPase, respectively. The arrows in the reactant and transition states for both PcrA and F1-ATPase outline the proton relay mechanism responsible for efficient ATP hydrolysis in each case.
Structure  , DOI: ( /j.str )
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5. Figure 4 Energetics of ATP Hydrolysis in PcrA
Shown are the energies of the states RS, TS1, TS2, IS1, IS2, B1, and PS during the ATP hydrolysis reaction in the catalytic site of PcrA along pathways 1 and 2 (the corresponding structures are shown in Figure 2). In addition to the product state energy of the wt, the energies of mutants Q254G and Q254N (with and without an additional water molecule; see Experimental Procedures) are also given.
Structure  , DOI: ( /j.str )
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6. Figure 5
Electrostatic Interaction between ATP and the Protein Environment in PcrA
(A and B) Shown are the (A) difference in the electrostatic interaction between RS and TS1 and the (B) difference between the two transition states, TS1 and TS2.
Structure  , DOI: ( /j.str )
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7. Figure 6 QM/MM Subsystem for PcrA
The simulation model includes the nucleotide located in the center that is shown in van der Waals representation. The protein surrounding the binding pocket is shown in cartoon representation, a single strand of DNA is shown in licorice representation, and the solvent water is depicted in line representation.
Structure  , DOI: ( /j.str )
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