Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12

Abstract

Molecular dynamics simulations have been used to characterise the binding of the fatty acid ligand palmitate in the barley lipid transfer protein 1 (LTP) internal cavity. Two different palmitate binding modes (1 and 2), with similar protein-ligand interaction energies, have been identified using a variety of simulation strategies. These strategies include applying experimental protein-ligand atom-atom distance restraints during the simulation, or protonating the palmitate ligand, or using the vacuum GROMOS 54B7 force-field parameter set for the ligand during the initial stages of the simulations. In both the binding modes identified the palmitate carboxylate head group hydrogen bonds with main chain amide groups in helix A, residues 4 to 19, of the protein. In binding mode 1 the hydrogen bonds are to Lys 11, Cys 13, and Leu 14 and in binding mode 2 to Thr 15, Tyr 16, Val 17, Ser 24 and also to the OH of Thr 15. In both cases palmitate binding exploits irregularity of the intrahelical hydrogen-bonding pattern in helix A of barley LTP due to the presence of Pro 12. Simulations of two variants of barley LTP, namely the single mutant Pro12Val and the double mutant Pro12Val Pro70Val, show that Pro 12 is required for persistent palmitate binding in the LTP cavity. Overall, the work identifies key MD simulation approaches for characterizing the details of protein-ligand interactions in complexes where NMR data provide insufficient restraints. V C 2012 Wiley Periodicals, Inc.

Molecular Dynamics Simulations of Bromodomains Reveal Binding‐Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl‐Lysine

“…For example, the discovery of multiple metastable states of the ligand in silico has also shed light onto discrepancies in the experimentally determined binding modes, as reported for the Staphylococcus aureus Sortase A interaction with the LPATG sorting signal 68. Atomistic simulations can also provide information when the experimental data are missing, as shown by Smith and co‐workers: three MD‐based strategies were devised to identify the binding modes of palmitate to the barley lipid transfer protein where the NOE restraints were not sufficient to clearly define the details of the ligand binding site 69…”

Deriving Structural Information from Experimentally Measured Data on Biomolecules

“…[128].A lthough the proposed structure of the complex of the barley lipid transfer protein 1(LTP) in complex with the fatty acid ligand palmitate was based on the use of 25 protein-ligand NOE restraints, [128] these were not sufficient to identify the details of the ligand binding site using the calculation protocol applied. [129] Thet wo modes have similar protein-ligand interaction energies suggesting that both are significantly populated. [129] Using different sets of restraints (omitting hydrogen-bond restraints), different protonation states and force-field parameters two alternative palmitate binding modes characterized by different hydrogen-bonding patterns,w ere identified for palmitate.…”

“…[129] Using different sets of restraints (omitting hydrogen-bond restraints), different protonation states and force-field parameters two alternative palmitate binding modes characterized by different hydrogen-bonding patterns,w ere identified for palmitate. [129] Thet wo modes have similar protein-ligand interaction energies suggesting that both are significantly populated. In these binding modes the palmitate head group is not involved in as alt bridge or hydrogen bond to the side chain of Cys 9a sh ad been previously suggested.…”

Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle

“…Der Palmitinsäure-Ligand wanderte aus der inneren Kavität heraus, wodurch er für das Lçsungsmittel frei zugänglich wurde. [129] Durch Verwendung von unterschiedlichen Sätzen an Beschränkungen (ohne solche für Wasserstoffbrücken), verschiedenen Protonierungszuständen und Kraftfeldparametern, konnten zwei alternative Bindungsmoden für Palmitinsäure identifiziert werden. [129] Diese zeichnen sich durch unterschiedliche Muster von Wasserstoffbrücken aus.…”

“…[129] Durch Verwendung von unterschiedlichen Sätzen an Beschränkungen (ohne solche für Wasserstoffbrücken), verschiedenen Protonierungszuständen und Kraftfeldparametern, konnten zwei alternative Bindungsmoden für Palmitinsäure identifiziert werden. [129] Diese zeichnen sich durch unterschiedliche Muster von Wasserstoffbrücken aus. Beide Moden besitzen ähnliche Energien für die Protein-Ligand-Wechselwirkung, was darauf hindeutet, dass beide Zustände maßgeblich besetzt sind.…”