Abstracts of Articles in 2013


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  1. Molecular Recognition and Ligand Association.

  2. Molecular Basis of Calcium-sensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A multi-scale simulation study.

  3. Accelerated Molecular Dynamics: An efficient enhanced sampling method for biomolecular simulations.
  4. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations.
  5. Structural insight into the separate roles of IP4 and DAD in activation of histone deacetylase 3.
  6. Allosteric Networks in Thrombin Distinguish Procoagulant vs. Anticoagulant Activities.
  7. Antibacterial drug leads targeting isoprenoid biosynthesis.
  8. w-REXAMD: A Hamiltonian replica exchange approach to improve free energy calculations for systems with kinetically-trapped conformations

  9. Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

  10. Fluoroketone Inhibition of Ca++-Independent Phospholipase A2 through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics.

 

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Molecular Recognition and Ligand Association

Baron, R., J.A. McCammon

Ann. Revs. Phys. Chem. in press (2013)


Molecular Basis of Calcium-sensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A multi-scale simulation study

Kekenes-Huskey, P.M., S. Lindert, J.A. McCammon

PLoS Comp. Biol. in press (2013)


Accelerated Molecular Dynamics: An efficient enhanced sampling method for biomolecular simulations

Pierce, L.C.T., W. Sinko, J.A. McCammon

Ramachandran Symposium Book in press (2013)


On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations

Rogers, K., J.M. Ortiz-Sanchez, R. Baron, M. Fajer, C.A.F. de Oliveira, J.A. McCammon

J. Chem. Theory Comput. in press (2013)


Structural insight into the separate roles of IP4 and DAD in activation of histone deacetylase 3

Arrar, M., R. Turnham, L. Pierce, C.A.F. de Oliveira, J.A. McCammon

Protein Sci. in press (2013)


Allosteric Networks in Thrombin Distinguish Procoagulant vs. Anticoagulant Activities

Gasper,P., B. Fuglestad, E. Komives, P. Markwick, J.A. McCammon

Proc. Natl. Acad. Sci. USA in press (2013)


Antibacterial drug leads targeting isoprenoid biosynthesis

Zhu, W., Y. Zhang, W. Sinko, M. Hensler, J. Olson, K.J. Molohon, S. Lindert, R. Cao, K. Li, K. Wang, Y. Wang, Y.L. Liu, A. Sankovsky, C.A.F. de Oliveira, D.A. Mitchell, V. Nizet, J.A. McCammon, E. Oldfield

Proc. Natl. Acad. Sci. USA in press (2013)


w-REXAMD: A Hamiltonian replica exchange approach to improve free energy calculations for systems with kinetically-trapped conformations

Arrar, M., M. Fajer, W. Sinko, C. de Oliveira, J.A. McCammon

J. Chem. Theory Comput. in press (2013)

 


Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

Setny, P., R. Baron, P. Kekenes-Huskey, J.A. McCammon, J. Dzubiella

Proc. Natl. Acad. Sci. USA in press (2013)

 


Fluoroketone Inhibition of Ca++-Independent Phospholipase A2 through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics.

Hsu, Y.H., D. Bucher, J. Cao, S. Li, S.W. Yang, G. Kokotos, V. Woods, J. McCammon, E. Dennis

J. Amer. Chem. Soc. in press (2013)

The mechanism of inhibition of Group VIA Ca2+-independent phospholipase A2 (iPLA2) by fluoroketone (FK) ligands is examined using a combination of deuterium exchange mass spectrometry (DXMS) and molecular dynamics (MD). Models for iPLA2 were built by homology with the known structure of patatin and equilibrated by extensive MD simulations. Empty pockets were identified during the simulations and studied for their ability to accommodate FK inhibitors. Ligand docking techniques showed that the potent inhibitor 1,1,1,3-tetrafluoro-7-phenylheptan-2-one (PHFK) forms favorable interactions inside an active site pocket where it blocks the entrance of phospholipid substrates. The polar fluoroketone head group is stabilized by hydrogen bonds with residues Gly486, Gly487, and Ser519. The nonpolar aliphatic chain and aromatic group are stabilized by hydrophobic contacts with Met544, Val548, Phe549, Leu560, and Ala640. The binding mode is supported by DXMS experiments showing an important decrease of deuteration in the contact regions in the presence of the inhibitor. The discovery of the precise binding mode of FK ligands to the iPLA2sub> should greatly improve our ability to design new inhibitors with higher potency and selectivity.

 

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