Search Results to John Straub, PhD

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One or more keywords matched the following properties of Straub, John

Research Expertise & Professional Interests John Straub explores protein dynamics and thermodynamics using theoretical and computational methods, with a particular focus on elucidating pathways for conformational change associated with protein energy transfer, signaling, folding, and aggregation. The Straub Group investigates fundamental aspects of protein dynamics and thermodynamics underlying the formation of protein structure, through folding and aggregation, and enabling protein function, through pathways of energy flow and signaling. Student and postdoctoral research scientists in the Straub Group work to develop and employ state-of-the-art computational methods while working in collaboration with leading experimental research groups. Kinetic and thermodynamic properties defining protein aggregation are elucidated through pioneering computational studies of the earliest stages of amyloid protein aggregation, including the formation of small oligomers (dimers through hexamers) from monomeric protein, and the production of monomeric protein from amyloid precursor proteins. Novel computational algorithms for enhanced sampling of conformational ensembles in complex biomolecular systems include effective approaches for global optimization and enhanced conformational sampling, in complex molecular systems, and novel coarse-grained models of proteins, for use in protein structure prediction. Novel computational approaches for the exploration of reaction dynamics allow for direct simulation of both ultrafast (quantum) and long-time (classical) dynamical events that translate how protein structure supports dynamical energy flow associated with protein function. Pathways and mechanism for energy and signal flow in proteins are explored using classical and quantum dynamical simulations. This includes fundamental aspects of energy transfer associated with ligand binding and redox events in a variety of heme protein systems, with the ultimate goal of relating protein dynamics to function. Professor Straub’s book, “Proteins: Energy, Heat and Signal Flow,” co-edited with David Leitner, captures the state-of-the-art in theoretical studies of protein dynamics and signaling.

One or more keywords matched the following items that are connected to Straub, John

Item TypeName
Concept Serum Amyloid A Protein
Concept Fungal Proteins
Concept Lipid Bilayers
Concept Lipids
Concept Membrane Lipids
Concept Protein Binding
Concept Protein Conformation
Concept Protein Denaturation
Concept Proteins
Concept Recombinant Proteins
Concept Protein Engineering
Concept Amyloid beta-Protein Precursor
Concept Protein Structure, Secondary
Concept Protein Structure, Tertiary
Concept Protein Folding
Concept PrPC Proteins
Concept Protein Structure, Quaternary
Concept Saccharomyces cerevisiae Proteins
Concept Amyloid Precursor Protein Secretases
Concept Protein Multimerization
Concept Protein Stability
Concept Hydrophobic and Hydrophilic Interactions
Concept Amyloidogenic Proteins
Concept Protein Unfolding
Concept Intrinsically Disordered Proteins
Concept Protein Aggregation, Pathological
Concept Protein Aggregates
Academic Article The interpretation of site-directed mutagenesis experiments by linear free energy relations.
Academic Article Molecular dynamics simulation of NO recombination to myoglobin mutants.
Academic Article Direct computation of long time processes in peptides and proteins: reaction path study of the coil-to-helix transition in polyalanine.
Academic Article Exploring the energy landscape in proteins.
Academic Article Theoretical probes of conformational fluctuations in S-peptide and RNase A/3''-UMP enzyme product complex.
Academic Article Long time dynamic simulations: exploring the folding pathways of an Alzheimer''s amyloid Abeta-peptide.
Academic Article Structural and dynamical analysis of the hydration of the Alzheimer''s beta-amyloid peptide.
Academic Article Development of novel statistical potentials for protein fold recognition.
Academic Article Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis.
Academic Article Energy landscape theory for Alzheimer''s amyloid beta-peptide fibril elongation.
Academic Article Simulation study of the structure and dynamics of the Alzheimer''s amyloid peptide congener in solution.
Academic Article A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization.
Academic Article Probing the origins of increased activity of the E22Q "Dutch" mutant Alzheimer''s beta-amyloid peptide.
Academic Article Orientational potentials extracted from protein structures improve native fold recognition.
Academic Article Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization.
Academic Article Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer''s beta-amyloid peptide compared to E22Q Dutch mutant.
Academic Article Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C.
Academic Article Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers.
Academic Article Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.
Academic Article Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways.
Academic Article Aqueous urea solution destabilizes Abeta(16-22) oligomers.
Academic Article Vibrational energy relaxation in proteins.
Academic Article Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin.
Academic Article Dissecting contact potentials for proteins: relative contributions of individual amino acids.
Academic Article Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.
Academic Article Efforts toward developing direct probes of protein dynamics.
Academic Article Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins.
Academic Article Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.
Academic Article Probing the mechanisms of fibril formation using lattice models.
Academic Article 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.
Academic Article 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.
Academic Article Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations.
Academic Article Dynamics of locking of peptides onto growing amyloid fibrils.
Academic Article Resilience of the iron environment in heme proteins.
Academic Article Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide.
Academic Article Principles governing oligomer formation in amyloidogenic peptides.
Academic Article Diversity of solvent dependent energy transfer pathways in heme proteins.
Academic Article 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.
Academic Article Relationship between protein folding thermodynamics and the energy landscape.
Academic Article Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires.
Academic Article Entropic stabilization of proteins by TMAO.
Academic Article Replica exchange statistical temperature molecular dynamics algorithm.
Academic Article Protein folding in a reverse micelle environment: the role of confinement and dehydration.
Academic Article Toward a molecular theory of early and late events in monomer to amyloid fibril formation.
Academic Article Factors governing fibrillogenesis of polypeptide chains revealed by lattice models.
Academic Article Role of water in protein aggregation and amyloid polymorphism.
Academic Article Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.
Academic Article Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles.
Academic Article Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection.
Academic Article Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.
Academic Article All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Academic Article Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aß(16-22) and Sup35(7-13) in AOT reverse micelles.
Academic Article Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature.
Academic Article Spatio-temporal hierarchy in the dynamics of a minimalist protein model.
Academic Article Membrane-Protein Interactions Are Key to Understanding Amyloid Formation.
Academic Article Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers.
Academic Article Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization.
Academic Article Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein.
Academic Article Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.
Academic Article Cellular prion protein targets amyloid-ß fibril ends via its C-terminal domain to prevent elongation.
Academic Article Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures.
Academic Article Molecular Insights into Human Hereditary Apolipoprotein A-I Amyloidosis Caused by the Glu34Lys Mutation.
Academic Article Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways.
Academic Article Influence of membrane lipid composition on the structure and activity of ?-secretase.
Academic Article Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation.
Academic Article Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.
Academic Article Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.
Academic Article Exploring the Structure and Stability of Cholesterol Dimer Formation in Multicomponent Lipid Bilayers.
Academic Article Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A.
Academic Article Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins.
Academic Article Differences in the free energies between the excited states of Aß40 and Aß42 monomers encode their aggregation propensities.
Grant Complex Role of Solvationin Protein Structure and Dynamics in Micelles and Membranes
Grant Probing the role of membrane domains and interfaces in protein assembly and function
Grant Probing the roles of membrane and cholesterol on Aß biogenesis and prion protein interactions

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