Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics.

[1]  U. Morbiducci,et al.  Aminoacid substitutions in the glycine zipper affect the conformational stability of amyloid beta fibrils , 2020, Journal of biomolecular structure & dynamics.

[2]  Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level. , 2019, The Journal of chemical physics.

[3]  J. Tuszynski,et al.  The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils , 2019, Front. Bioeng. Biotechnol..

[4]  H. Nemade,et al.  Electric Field Disruption of Amyloid Aggregation: Potential Noninvasive Therapy for Alzheimer's Disease. , 2019, ACS chemical neuroscience.

[5]  J. Basurto,et al.  Recent Advances by In Silico and In Vitro Studies of Amyloid-β 1-42 Fibril Depicted a S-Shape Conformation , 2018 .

[6]  Gianvito Grasso,et al.  Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol , 2018, International journal of molecular sciences.

[7]  J. Götz,et al.  Amyloid-β and Tau in Alzheimer's Disease: Novel Pathomechanisms and Non-Pharmacological Treatment Strategies. , 2018, Journal of Alzheimer's disease : JAD.

[8]  U. Morbiducci,et al.  Cell penetrating peptide modulation of membrane biomechanics by Molecular dynamics. , 2018, Journal of biomechanics.

[9]  M. Guo,et al.  Ultrasound‐induced changes in structural and physicochemical properties of β‐lactoglobulin , 2018, Food science & nutrition.

[10]  P. Derreumaux,et al.  Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study , 2018 .

[11]  J. Tuszynski,et al.  Conformational Dynamics and Stability of U-Shaped and S-Shaped Amyloid β Assemblies , 2018, International journal of molecular sciences.

[12]  J. Tuszynski,et al.  Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. , 2018, Biophysical journal.

[13]  Feng Wu,et al.  High-intensity focused ultrasound in the treatment of breast tumours , 2018, Ecancermedicalscience.

[14]  Gianvito Grasso,et al.  Josephin Domain Dimerization on a Gold Surface: Evidences for a Double‐Step Binding Pathway , 2017 .

[15]  Christian A. Söldner,et al.  Role of the N-terminus for the stability of an amyloid-β fibril with three-fold symmetry , 2017, PloS one.

[16]  G. Schröder,et al.  Fibril structure of amyloid-β(1–42) by cryo–electron microscopy , 2017, Science.

[17]  J. Tuszynski,et al.  Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics , 2017, Biology Direct.

[18]  P. Derreumaux,et al.  Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils. , 2016, The Journal of chemical physics.

[19]  J. Tuszynski,et al.  Characterization of the AXH domain of Ataxin‐1 using enhanced sampling and functional mode analysis , 2016, Proteins.

[20]  Jürgen Götz,et al.  Ultrasound treatment of neurological diseases — current and emerging applications , 2016, Nature Reviews Neurology.

[21]  J. Tuszynski,et al.  Conformational fluctuations of the AXH monomer of Ataxin‐1 , 2016, Proteins.

[22]  Jack A. Tuszynski,et al.  Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates , 2016, PLoS Comput. Biol..

[23]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[24]  J. Tuszynski,et al.  Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations , 2015, Molecules.

[25]  Joo Ha Hwang,et al.  Emerging HIFU applications in cancer therapy , 2015, International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group.

[26]  Jürgen Götz,et al.  Scanning ultrasound removes amyloid-β and restores memory in an Alzheimer’s disease mouse model , 2015, Science Translational Medicine.

[27]  Ruth Nussinov,et al.  Aβ(1–42) Fibril Structure Illuminates Self-recognition and Replication of Amyloid in Alzheimer’s , 2015, Nature Structural &Molecular Biology.

[28]  R. Kamm,et al.  Multiscale impact of nucleotides and cations on the conformational equilibrium, elasticity and rheology of actin filaments and crosslinked networks , 2015, Biomechanics and Modeling in Mechanobiology.

[29]  Haohao Fu,et al.  Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes. , 2015, The journal of physical chemistry letters.

[30]  Jack A. Tuszynski,et al.  Investigation of the Josephin Domain Protein-Protein Interaction by Molecular Dynamics , 2014, PloS one.

[31]  Hisashi Okumura,et al.  Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations. , 2014, Journal of the American Chemical Society.

[32]  J. Cummings,et al.  Alzheimer’s disease drug-development pipeline: few candidates, frequent failures , 2014, Alzheimer's Research & Therapy.

[33]  G. Bloom.  Amyloid-β and tau: the trigger and bullet in Alzheimer disease pathogenesis. , 2014, JAMA neurology.

[34]  Nick C Fox,et al.  Two phase 3 trials of bapineuzumab in mild-to-moderate Alzheimer's disease. , 2014, The New England journal of medicine.

[35]  E. Siemers,et al.  Phase 3 trials of solanezumab for mild-to-moderate Alzheimer's disease. , 2014, The New England journal of medicine.

[36]  D. Galimberti,et al.  Disease-modifying drugs in Alzheimer’s disease , 2013, Drug design, development and therapy.

[37]  Y. Goto,et al.  Acceleration of the depolymerization of amyloid β fibrils by ultrasonication. , 2013, Biochimica et biophysica acta.

[38]  P. Scheltens,et al.  Treating Alzheimer’s disease with monoclonal antibodies: current status and outlook for the future , 2013, Alzheimer's Research & Therapy.

[39]  Kullervo Hynynen,et al.  Amyloid-β plaque reduction, endogenous antibody delivery and glial activation by brain-targeted, transcranial focused ultrasound , 2013, Experimental Neurology.

[40]  Marco Agostino Deriu,et al.  A Hydrophobic Gold Surface Triggers Misfolding and Aggregation of the Amyloidogenic Josephin Domain in Monomeric Form, While Leaving the Oligomers Unaffected , 2013, PloS one.

[41]  Intravenous immunoglobulin and Alzheimer’s disease: what now? , 2013, Journal of Neuroinflammation.

[42]  B. Strooper,et al.  The amyloid cascade hypothesis for Alzheimer's disease: an appraisal for the development of therapeutics , 2011, Nature Reviews Drug Discovery.

[43]  F. Biscarini,et al.  Electric Field Effects on Short Fibrils of Aβ Amyloid Peptides. , 2010, Journal of chemical theory and computation.

[44]  B. Liu,et al.  [Study on the effect of ultrasound on the secondary structure of BSA by FTIR]. , 2010, Guang pu xue yu guang pu fen xi = Guang pu.

[45]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[46]  Yao-Sheng Tung,et al.  Microbubble-Size Dependence of Focused Ultrasound-Induced Blood–Brain Barrier Opening in Mice In Vivo , 2010, IEEE Transactions on Biomedical Engineering.

[47]  K. Koshiyama,et al.  Molecular dynamics simulation of structural changes of lipid bilayers induced by shock waves: Effects of incident angles. , 2008, Biochimica et biophysica acta.

[48]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[49]  Alberto Redaelli,et al.  Mechanical response and conformational changes of alpha-actinin domains during unfolding: a molecular dynamics study , 2007, Biomechanics and modeling in mechanobiology.

[50]  Martin Fechner,et al.  Speeding up parallel GROMACS on high‐latency networks , 2007, J. Comput. Chem..

[51]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[52]  R. Tycko,et al.  Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. , 2006, Biochemistry.

[53]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[54]  R. Riek,et al.  3D structure of Alzheimer's amyloid-β(1–42) fibrils , 2005 .

[55]  C. Ross,et al.  Protein aggregation and neurodegenerative disease , 2004, Nature Medicine.

[56]  Hyoung-Gon Lee,et al.  Lessons from the AN 1792 Alzheimer vaccine: lest we forget , 2004, Neurobiology of Aging.

[57]  P. Lansbury,et al.  Dissociation of amyloid fibrils of α-synuclein and transthyretin by pressure reveals their reversible nature and the formation of water-excluded cavities , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[58]  R. Leapman,et al.  A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. G. Powles,et al.  The collapsing bubble in a liquid by molecular dynamics simulations , 2002 .

[60]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[61]  T. Darden,et al.  Molecular dynamics simulations of biomolecules: long-range electrostatic effects. , 1999, Annual review of biophysics and biomolecular structure.

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

[63]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[64]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

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

[66]  J. Hardy,et al.  Alzheimer's disease: the amyloid cascade hypothesis. , 1992, Science.

[67]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

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

[69]  L. Rayleigh.  VIII. On the pressure developed in a liquid during the collapse of a spherical cavity , 1917 .