Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol

[1]  A. Bondar,et al.  Motions of the SecA protein motor bound to signal peptide: Insights from molecular dynamics simulations. , 2018, Biochimica et biophysica acta. Biomembranes.

[2]  A. Bondar Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics. , 2016, Seminars in cell & developmental biology.

[3]  K. Murzyn,et al.  Computer modelling studies of the bilayer/water interface. , 2016, Biochimica et biophysica acta.

[4]  A. Bondar,et al.  Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions. , 2016, Biochimica et biophysica acta.

[5]  Ana-Nicoleta Bondar,et al.  Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. , 2015, The journal of physical chemistry. B.

[6]  Sunhwan Jo,et al.  CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations , 2014, J. Comput. Chem..

[7]  H. Grubmüller,et al.  Anomalous surface diffusion of protons on lipid membranes. , 2014, Biophysical journal.

[8]  Oleksandr Sushko,et al.  Terahertz spectral domain computational analysis of hydration shell of proteins with increasingly complex tertiary structure. , 2013, The journal of physical chemistry. B.

[9]  Jeffery B. Klauda,et al.  Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. , 2012, Biochimica et biophysica acta.

[10]  S. White,et al.  Hydrogen bond dynamics in membrane protein function. , 2012, Biochimica et biophysica acta.

[11]  N. Agmon,et al.  Bioenergetics: Proton fronts on membranes. , 2011, Nature chemistry.

[12]  M. Asslaber,et al.  In search of a novel target — Phosphatidylserine exposed by non-apoptotic tumor cells and metastases of malignancies with poor treatment efficacy , 2011, Biochimica et biophysica acta.

[13]  P. Pohl,et al.  Protons migrate along interfacial water without significant contributions from jumps between ionizable groups on the membrane surface , 2011, Proceedings of the National Academy of Sciences.

[14]  Alexander D. MacKerell,et al.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.

[15]  V. Bankaitis,et al.  The Sec14 superfamily and mechanisms for crosstalk between lipid metabolism and lipid signaling. , 2010, Trends in biochemical sciences.

[16]  F. Sterpone,et al.  Water hydrogen-bond dynamics around amino acids: the key role of hydrophilic hydrogen-bond acceptor groups. , 2010, The journal of physical chemistry. B.

[17]  D. Paparo,et al.  Dielectric relaxation dynamics of water in model membranes probed by terahertz spectroscopy. , 2009, Biophysical journal.

[18]  M. Karttunen,et al.  Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study. , 2009, The journal of physical chemistry. B.

[19]  D. Tobias,et al.  Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations. , 2008, Biophysical journal.

[20]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[21]  Tony Yeung,et al.  Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization , 2008, Science.

[22]  Martin Gruebele,et al.  An extended dynamical hydration shell around proteins , 2007, Proceedings of the National Academy of Sciences.

[23]  S. Sligar,et al.  Nanodiscs unravel the interaction between the SecYEG channel and its cytosolic partner SecA , 2007, The EMBO journal.

[24]  I. Vattulainen,et al.  Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions. , 2007, Biophysical journal.

[25]  R. Righini,et al.  Heterogeneity of water at the phospholipid membrane interface. , 2007, The journal of physical chemistry. B.

[26]  Sagar A. Pandit,et al.  Aqueous solutions next to phospholipid membrane surfaces: insights from simulations. , 2006, Chemical reviews.

[27]  M. Berkowitz,et al.  Structure and dynamics of water at the interface with phospholipid bilayers. , 2005, The Journal of chemical physics.

[28]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[29]  P. Comfurius,et al.  Surface exposure of phosphatidylserine in pathological cells , 2005, Cellular and Molecular Life Sciences CMLS.

[30]  M. Wolfe,et al.  Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[31]  T. Róg,et al.  Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. , 2005, Biophysical journal.

[32]  M. Klein,et al.  Hydrogen Bonding Structure and Dynamics of Water at the Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation , 2004 .

[33]  D. Tieleman,et al.  Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. , 2004, Biophysical journal.

[34]  D. Harries,et al.  Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt. , 2004, Biophysical journal.

[35]  Helmut Grubmüller,et al.  Multistep binding of divalent cations to phospholipid bilayers: a molecular dynamics study. , 2004, Angewandte Chemie.

[36]  Sagar A. Pandit,et al.  Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics. , 2003, Biophysical journal.

[37]  S. Ran,et al.  Phosphatidylserine is a marker of tumor vasculature and a potential target for cancer imaging and therapy. , 2002, International journal of radiation oncology, biology, physics.

[38]  M. Freeman,et al.  Drosophila Rhomboid-1 Defines a Family of Putative Intramembrane Serine Proteases , 2001, Cell.

[39]  J. Nagle,et al.  Structure of lipid bilayers. , 2000, Biochimica et biophysica acta.

[40]  Alexander D. MacKerell,et al.  An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids , 2000 .

[41]  G. Ford,et al.  Effect of age on plasma membrane asymmetry and membrane fluidity in human leukocytes and platelets. , 1999, The journals of gerontology. Series A, Biological sciences and medical sciences.

[42]  A. Smondyrev,et al.  Structure of dipalmitoylphosphatidylcholine/cholesterol bilayer at low and high cholesterol concentrations: molecular dynamics simulation. , 1999, Biophysical journal.

[43]  Laxmikant V. Kale,et al.  NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .

[44]  A. Blume,et al.  Interactions at the lipid–water interface , 1998 .

[45]  A. Dicko,et al.  Study by infrared spectroscopy of the conformation of dipalmitoylphosphatidylglycerol monolayers at the air–water interface and transferred on solid substrates , 1998 .

[46]  M Feig,et al.  Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. , 1998, Biophysical journal.

[47]  G von Heijne,et al.  Anionic phospholipids are determinants of membrane protein topology , 1997, The EMBO journal.

[48]  A. Kusumi,et al.  Hydrogen Bonding of Water to Phosphatidylcholine in the Membrane As Studied by a Molecular Dynamics Simulation: Location, Geometry, and Lipid-Lipid Bridging via Hydrogen-Bonded Water , 1997 .

[49]  A. Schroit,et al.  Pathophysiologic implications of membrane phospholipid asymmetry in blood cells. , 1997, Blood.

[50]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[51]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[52]  B. Brooks,et al.  Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .

[53]  I. Muegge,et al.  Residence Times and Lateral Diffusion of Water at Protein Surfaces: Application to BPTI , 1995 .

[54]  A. Schroit,et al.  Exposure of phosphatidylserine in the outer leaflet of human red blood cells. Relationship to cell density, cell age, and clearance by mononuclear cells. , 1994, The Journal of biological chemistry.

[55]  Herman J. C. Berendsen,et al.  Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force , 1993 .

[56]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[57]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[58]  S H White,et al.  Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. , 1992, Biophysical journal.

[59]  Ronald L. Rivest,et al.  Introduction to Algorithms , 1990 .

[60]  J. Teissié,et al.  Lateral proton conduction at a lipid/water interface. Effect of lipid nature and ionic content of the aqueous phase. , 1987, European journal of biochemistry.

[61]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[62]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[63]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[64]  M. Gutman,et al.  Proton fronts on membranes , 2022 .