Published in J Am Chem Soc on January 08, 2014
Impact of bilayer lipid composition on the structure and topology of the transmembrane amyloid precursor C99 protein. J Am Chem Soc (2014) 0.85
Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. J Am Chem Soc (2014) 0.84
Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the mechanism of receptor activation. Biochemistry (2014) 0.83
Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations. J Am Chem Soc (2016) 0.79
Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein. Proc Natl Acad Sci U S A (2016) 0.78
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochim Biophys Acta (2016) 0.77
Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins (2015) 0.75
Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein. J Phys Chem Lett (2016) 0.75
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Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta (2008) 1.76
Modeling the lipid component of membranes. Curr Opin Struct Biol (2002) 1.71
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Structural studies of the transmembrane C-terminal domain of the amyloid precursor protein (APP): does APP function as a cholesterol sensor? Biochemistry (2008) 1.54
Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem (2011) 1.43
Designed helical peptides inhibit an intramembrane protease. J Am Chem Soc (2003) 1.33
Independent generation of Abeta42 and Abeta38 peptide species by gamma-secretase. J Biol Chem (2008) 1.13
Systematic multiscale simulation of membrane protein systems. Curr Opin Struct Biol (2009) 1.12
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Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc (2009) 1.04
Molecular interactions of Alzheimer's Aβ protofilaments with lipid membranes. J Mol Biol (2012) 1.04
Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc (2009) 0.98
The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc (2013) 0.93
Resolving individual steps in the operation of ATP-dependent proteolytic molecular machines: from conformational changes to substrate translocation and processivity. Biochemistry (2008) 0.93
How the amyloid-β peptide and membranes affect each other: an extensive simulation study. Biochim Biophys Acta (2012) 0.88
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Abeta40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry (2005) 1.78
Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63
Flanking polyproline sequences inhibit beta-sheet structure in polyglutamine segments by inducing PPII-like helix structure. J Mol Biol (2007) 1.59
A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization. J Am Chem Soc (2003) 1.55
Evidence for novel beta-sheet structures in Iowa mutant beta-amyloid fibrils. Biochemistry (2009) 1.45
Peptide-based inhibitors of amyloid assembly. Methods Enzymol (2006) 1.44
A mutant chaperone converts a wild-type protein into a tumor-specific antigen. Science (2006) 1.44
Increasing the amphiphilicity of an amyloidogenic peptide changes the beta-sheet structure in the fibrils from antiparallel to parallel. Biophys J (2004) 1.41
Structure of substrate-free human insulin-degrading enzyme (IDE) and biophysical analysis of ATP-induced conformational switch of IDE. J Biol Chem (2007) 1.41
Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci (2004) 1.40
Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proc Natl Acad Sci U S A (2004) 1.34
Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci (2002) 1.19
Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A (2009) 1.15
Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. J Mol Biol (2004) 1.12
Entropic stabilization of proteins by TMAO. J Phys Chem B (2011) 1.09
Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. J Phys Chem B (2009) 1.08
Role of water in protein aggregation and amyloid polymorphism. Acc Chem Res (2011) 1.06
Glyoxalase 1 increases anxiety by reducing GABAA receptor agonist methylglyoxal. J Clin Invest (2012) 1.06
The Japanese mutant Aβ (ΔE22-Aβ(1-39)) forms fibrils instantaneously, with low-thioflavin T fluorescence: seeding of wild-type Aβ(1-40) into atypical fibrils by ΔE22-Aβ(1-39). Biochemistry (2011) 1.05
Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc (2009) 1.04
Statistical-temperature Monte Carlo and molecular dynamics algorithms. Phys Rev Lett (2006) 1.03
Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol (2008) 1.01
Probing the role of backbone hydrogen bonding in beta-amyloid fibrils with inhibitor peptides containing ester bonds at alternate positions. Biochemistry (2003) 1.00
Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.99
Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc (2009) 0.98
Mechanism of cis-inhibition of polyQ fibrillation by polyP: PPII oligomers and the hydrophobic effect. Biophys J (2009) 0.95
Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. J Phys Chem B (2009) 0.95
Vibrational energy relaxation in proteins. Proc Natl Acad Sci U S A (2005) 0.94
Generalized replica exchange method. J Chem Phys (2010) 0.93
Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin. J Phys Chem B (2007) 0.93
Helix-turn-helix peptides that form alpha-helical fibrils: turn sequences drive fibril structure. Biochemistry (2005) 0.93
Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models. J Chem Phys (2007) 0.93
Relationship between protein folding thermodynamics and the energy landscape. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.91
Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires. Proc Natl Acad Sci U S A (2010) 0.91
Strong synergy between mutant ras and HPV16 E6/E7 in the development of primary tumors. Oncogene (2004) 0.89
Site-specific effects of peptide lipidation on beta-amyloid aggregation and cytotoxicity. J Biol Chem (2007) 0.89
Efforts toward developing direct probes of protein dynamics. J Am Chem Soc (2006) 0.88
The specific amino acid sequence between helices 7 and 8 influences the binding specificity of human apolipoprotein A-I for high density lipoprotein (HDL) subclasses: a potential for HDL preferential generation. J Biol Chem (2008) 0.88
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide. J Comput Chem (2003) 0.88
Replica exchange statistical temperature Monte Carlo. J Chem Phys (2009) 0.86
Protein folding: sticky N17 speeds huntingtin pile-up. Nat Chem Biol (2010) 0.86
Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials. J Chem Phys (2005) 0.85
Generalized simulated tempering for exploring strong phase transitions. J Chem Phys (2010) 0.85
Spatial separation of beta-sheet domains of beta-amyloid: disruption of each beta-sheet by N-methyl amino acids. Biochemistry (2006) 0.84
Apolipoprotein A-I alpha -helices 7 and 8 modulate high density lipoprotein subclass distribution. J Biol Chem (2001) 0.84
Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. J Am Chem Soc (2014) 0.84
Replica exchange statistical temperature molecular dynamics algorithm. J Phys Chem B (2012) 0.83
Protein folding in a reverse micelle environment: the role of confinement and dehydration. J Chem Phys (2011) 0.82
Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables. J Chem Phys (2011) 0.82
Chaperone-like N-methyl peptide inhibitors of polyglutamine aggregation. Biochemistry (2010) 0.82
γδ T cell receptors recognize the non-classical major histocompatibility complex (MHC) molecule T22 via conserved anchor residues in a MHC peptide-like fashion. J Biol Chem (2012) 0.82
Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins. J Chem Phys (2006) 0.82
Resilience of the iron environment in heme proteins. Biophys J (2008) 0.81
High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold. J Mol Biol (2008) 0.81
Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C. Biophys J (2003) 0.81
Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide. J Phys Chem Lett (2011) 0.80
Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations. J Phys Chem B (2014) 0.80
Probing the structure and dynamics of confined water in AOT reverse micelles. J Phys Chem B (2013) 0.79
Optimal replica exchange method combined with Tsallis weight sampling. J Chem Phys (2009) 0.79
Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways. J Phys Chem B (2007) 0.78
Diversity of solvent dependent energy transfer pathways in heme proteins. J Phys Chem B (2009) 0.78
Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model. J Chem Phys (2009) 0.77
Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The nu(4) and nu(7) modes of iron-protoporphyrin IX and iron porphine. J Chem Phys (2009) 0.77
Novel semisynthetic method for generating full length beta-amyloid peptides. Biopolymers (2010) 0.77
Gravitational smoothing as a global optimization strategy. J Comput Chem (2002) 0.77
Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method. J Phys Chem B (2012) 0.76
Elucidation of the Aggregation Pathways of Helix-Turn-Helix Peptides: Stabilization at the Turn Region Is Critical for Fibril Formation. Biochemistry (2015) 0.76
Versatile cyclic templates for assembly of axially oriented ligands. Bioconjug Chem (2009) 0.75
Encapsulation and NMR on an aggregating peptide before fibrillogenesis. J Am Chem Soc (2006) 0.75
Exploring the Structure and Stability of Cholesterol Dimer Formation in Multicomponent Lipid Bilayers. J Comput Chem (2019) 0.75
Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models. J Chem Phys (2009) 0.75
Dynamics of methionine ligand rebinding in cytochrome c. J Phys Chem B (2012) 0.75
Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method. J Chem Phys (2013) 0.75
Mode-specific vibrational energy relaxation of amide I' and II' modes in N-methylacetamide/water clusters: intra- and intermolecular energy transfer mechanisms. J Phys Chem A (2009) 0.75
Spatio-temporal hierarchy in the dynamics of a minimalist protein model. J Chem Phys (2013) 0.75
"Strange kinetics" in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c. J Phys Chem B (2013) 0.75