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List of works by John E Straub

"Strange kinetics" in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c.

scientific article

A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization

scientific article

Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model

scientific article published on 15 March 2021

Aerosol-OT Surfactant Forms Stable Reverse Micelles in Apolar Solvent in the Absence of Water

scientific article published on 06 March 2019

Aqueous urea solution destabilizes Abeta(16-22) oligomers

scholarly article

Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins

scientific article published on 23 June 2020

Cellular prion protein targets amyloid-β fibril ends via its C-terminal domain to prevent elongation

scientific article

Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles

article

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

scientific article published on 5 June 2017

Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant

scientific article published on July 2002

Coarse-Grained Model of Coil-to-Helix Kinetics Demonstrates the Importance of Multiple Nucleation Sites in Helix Folding

scientific article published on 01 May 2006

Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides

scientific article

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables ⬇️

scientific article published on August 14, 2011

Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures.

scientific article published in September 2017

Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides

scientific article published on 01 April 2019

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities

scientific article published on 30 July 2020

Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers

scientific article published on 25 February 2021

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model

scientific article published in January 2009

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

scientific article published in March 2009

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.

scientific article

Diversity of solvent dependent energy transfer pathways in heme proteins

scientific article

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires ⬇️

scientific article published on November 22, 2010

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers

article

Dynamics of Methionine Ligand Rebinding in Cytochrome c ⬇️

scientific article published on April 6, 2012

Dynamics of locking of peptides onto growing amyloid fibrils

scholarly article

Effects of Membrane Heterogeneity and Aggregation on the Lateral Migration and Colocalization of Proteins

scholarly article

Efficient calculation of the free energy for protein partitioning using restraining potentials

scientific article published in 2022

Efforts toward developing direct probes of protein dynamics

scientific article published in May 2006

Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations

scientific article

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems

scientific article published on 10 November 2018

Entropic stabilization of proteins by TMAO

scientific article (publication date: 17 November 2011)

Exploring the Solid–Liquid Phase Change of an Adapted Dzugutov Model Using Generalized Replica Exchange Method ⬇️

scientific article published on April 10, 2012

Exploring the Structure and Stability of Cholesterol Dimer Formation in Multicomponent Lipid Bilayers

scientific article published on 30 July 2019

Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture

scientific article published on 01 May 2019

Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles

scientific article

Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers

scientific article published on 20 October 2016

Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization.

scientific article

Freezing Transitions of Nanoconfined Coarse-Grained Water Show Subtle Dependence on Confining Environment

scientific article published on 24 February 2016

Generalized replica exchange method

scientific article

Generalized simulated tempering for exploring strong phase transitions ⬇️

scientific article published on October 21, 2010

Gravitational smoothing as a global optimization strategy

scientific article published on 01 August 2002

Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein

scientific article published on 02 November 2020

Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.

scientific article published on 24 August 2016

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide ⬇️

scientific article published on May 19, 2011

Influence of membrane lipid composition on the structure and activity of γ-secretase

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

scientific article

Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles

scientific article published on 17 August 2021

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

scientific article

JCP Emerging Investigator Special Collection 2019

scientific article published on 01 September 2020

Limit of metastability for liquid and vapor phases of water.

scientific article

Long time dynamic simulations: exploring the folding pathways of an Alzheimer's amyloid Abeta-peptide

scientific article

Mean First-Passage Time Calculations for the Coil-to-Helix Transition: The Active Helix Ising Model†

article

Membrane-Protein Interactions Are Key to Understanding Amyloid Formation

scientific article published on 01 February 2014

Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways

article published in the Proceedings of the National Academy of Sciences of the United States of America

Mode-specific vibrational energy relaxation of amide I' and II' modes in N-methylacetamide/water clusters: intra- and intermolecular energy transfer mechanisms

scientific article published in April 2009

Molecular Insights into Human Hereditary Apolipoprotein A-I Amyloidosis Caused by the Glu34Lys Mutation

scientific article published on 19 September 2018

Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin

scientific article published on 06 March 2007

Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

scholarly article

Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials

scientific article published on 01 January 2005

On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes

scientific article published on 17 May 2022

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

scientific article published on 24 June 2016

Optimal replica exchange method combined with Tsallis weight sampling

scientific article published on April 2009

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method

scientific article published in March 2013

Orientational potentials extracted from protein structures improve native fold recognition

scientific article published on April 2004

Principles governing oligomer formation in amyloidogenic peptides

scientific article

Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization

scientific article

Probing the structure and dynamics of confined water in AOT reverse micelles

scientific article published on 06 June 2013

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins ⬇️

scientific article published on 17 May 2014

Protein folding in a reverse micelle environment: The role of confinement and dehydration ⬇️

scientific article published on February 7, 2011

Publisher's Note: “Protein folding in a reverse micelle environment: The role of confinement and dehydration” [J. Chem. Phys. 134, 055107 (2011)]

scientific article

Publisher’s Note: “Generalized simulated tempering for exploring strong phase transitions” [J. Chem. Phys. 133, 154101 (2010)].

scientific article published on 25 October 2010

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

scientific article published on 19 October 2018

Relationship between protein folding thermodynamics and the energy landscape

scientific article published on 4 March 2009

Replica Exchange Statistical Temperature Molecular Dynamics Algorithm ⬇️

scientific article published on May 15, 2012

Replica exchange statistical temperature Monte Carlo

scientific article published on March 2009

Resilience of the iron environment in heme proteins.

scientific article

Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles

scientific article published on 6 November 2014

Role of water in protein aggregation and amyloid polymorphism

scientific article published on 15 July 2011

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

scientific article published on 15 April 2019

Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide

scientific article published on June 2009

Spatio-temporal hierarchy in the dynamics of a minimalist protein model

scientific article published on December 2013

Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein.

scientific article published on 15 August 2016

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models

scientific article

Statistical-temperature Monte Carlo and molecular dynamics algorithms

scientific article published in August 2006

Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A

scientific article published on 06 February 2020

Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide

scientific article published in January 2003

Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection

scientific article

Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization.

scientific article published on 24 April 2018

Structure of APP-C991-99and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing

scientific article published on 18 July 2007

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

scientific article published on 14 May 2008

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

scientific article published on December 2009

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

scientific article

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

scientific article published on 01 April 2006

Toward a Molecular Theory of Early and Late Events in Monomer to Amyloid Fibril Formation ⬇️

scientific article published on January 1, 2011

Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature.

scientific article published on 08 January 2014

Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations

scientific article published on March 2009

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

scientific article published on 29 June 2020

Vibrational energy relaxation in proteins

scientific article

Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways

scientific article published on 22 September 2007

Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C.

scientific article

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