Vibrational Approach to the Dynamics and Structure of Protein Amyloids

Residue-Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation

(2018) Haiyang Liu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Aggregation-induced conformation changes dictate islet amyloid polypeptide (IAPP) membrane affinity

(2018) Anoop Rawat et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils

(2018) Ileana M. Pazos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Site-specific detection of protein secondary structure using 2D IR dihedral indexing: a proposed assembly mechanism of oligomeric hIAPP

(2018) Michał Maj et al.   Chemical Science

Toxic Amyloid Tape: A Novel Mixed Antiparallel/Parallel β-Sheet Structure Formed by Amyloid β-Protein on GM1 Clusters

(2018) Yuki Okada et al.   ACS Chemical Neuroscience

Structural features of α-synuclein amyloid fibrils revealed by Raman spectroscopy

(2017) Jessica D. Flynn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Amyloid β-Sheet Secondary Structure Identified in UV-Induced Cataracts of Porcine Lenses using 2D IR Spectroscopy

(2017) Tianqi O. Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Spectroscopic Signature for Stable β-Amyloid Fibrils versus β-Sheet-Rich Oligomers

(2017) Justin P. Lomont et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy

(2017) Justin P. Lomont et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP

(2017) Arnaldo L. Serrano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simple method to introduce an ester infrared probe into proteins

(2017) Ismail A. Ahmed et al.   PROTEIN SCIENCE

FTIR studies of the similarities between pathology induced protein aggregation in vivo and chemically induced protein aggregation ex vivo

(2017) Rebecca J. Tidy et al.   VIBRATIONAL SPECTROSCOPY

Pre-plaque conformational changes in Alzheimer’s disease-linked Aβ and APP

(2017) O. Klementieva et al.   Nature Communications

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

(2017) Steven J. Roeters et al.   Scientific Reports

Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer’s Disease

(2016) Andreas Nabers et al.   ANALYTICAL CHEMISTRY

Alpha-Synuclein Oligomers Interact with Metal Ions to Induce Oxidative Stress and Neuronal Death in Parkinson's Disease

(2016) Emma Deas et al.   ANTIOXIDANTS & REDOX SIGNALING

Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril

(2016) Marielle Aulikki Wälti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics

(2016) Andisheh Abedini et al.   eLife

Site-Specific Infrared Probes of Proteins

(2015) Jianqiang Ma et al.   Annual Review of Physical Chemistry

Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ1–23 using an unnatural amino acid

(2015) Haiyang Liu et al.   CHEMICAL COMMUNICATIONS

Transition Dipoles from 1D and 2D Infrared Spectroscopy Help Reveal the Secondary Structures of Proteins: Application to Amyloids

(2015) Emily B. Dunkelberger et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modulation of human IAPP fibrillation: cosolutes, crowders and chaperones

(2015) Mimi Gao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field

(2014) Ileana M. Pazos et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Aggregation Gatekeeper and Controlled Assembly of Trpzip β-Hairpins

(2014) Beatrice N. Markiewicz et al.   BIOCHEMISTRY

In Search of Aggregation Pathways of IAPP and Other Amyloidogenic Proteins: Finding Answers through NMR Spectroscopy

(2014) Hiren R. Patel et al.   Journal of Physical Chemistry Letters

How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy

(2014) Sean D. Moran et al.   Journal of Physical Chemistry Letters

Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

(2014) Luuk J. G. W. van Wilderen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy

(2014) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An alternative structural isoform in amyloid-like aggregates formed from thermally denatured human γD-crystallin

(2014) Sean D. Moran et al.   PROTEIN SCIENCE

Intrinsic Structural Heterogeneity and Long-Term Maturation of Amyloid β Peptide Fibrils

(2013) Jianqiang Ma et al.   ACS Chemical Neuroscience

ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins

(2013) Rabia Sarroukh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Insight into the Packing Pattern of β2 Fibrils: A Model Study of Glutamic Acid Rich Oligomers with 13C Isotopic Edited Vibrational Spectroscopy

(2013) Heng Chi et al.   BIOMACROMOLECULES

Length-dependent conformational transitions of polyglutamine repeats as molecular origin of fibril initiation

(2013) Benjamin S. Heck et al.   BIOPHYSICAL CHEMISTRY

Infrared Probes for Studying the Structure and Dynamics of Biomolecules

(2013) Heejae Kim et al.   CHEMICAL REVIEWS

Capturing inhomogeneous broadening of the –CN stretch vibration in a Langmuir monolayer with high-resolution spectra and ultrafast vibrational dynamics in sum-frequency generation vibrational spectroscopy (SFG-VS)

(2013) Luis Velarde et al.   JOURNAL OF CHEMICAL PHYSICS

A New Raman Spectroscopic Probe of Both the Protonation State and Noncovalent Interactions of Histidine Residues

(2013) Kevin W. Hoffman et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Study of the γD-Crystallin Protein Using Two-Dimensional Infrared (2DIR) Spectroscopy: Experiment and Simulation

(2013) A. R. Lam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sensitive, Site-Specific, and Stable Vibrational Probe of Local Protein Environments: 4-Azidomethyl-l-Phenylalanine

(2013) Christopher G. Bazewicz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Raman spectroscopy of proteins: a review

(2013) A. Rygula et al.   JOURNAL OF RAMAN SPECTROSCOPY

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient  -sheet

(2013) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toxic prefibrillar α-synuclein amyloid oligomers adopt a distinctive antiparallel β-sheet structure

(2012) María Soledad Celej et al.   BIOCHEMICAL JOURNAL

GM1 Cluster Mediates Formation of Toxic Aβ Fibrils by Providing Hydrophobic Environments

(2012) Saori Fukunaga et al.   BIOCHEMISTRY

The Amyloid State of Proteins in Human Diseases

(2012) David Eisenberg et al.   CELL

Carbon–Deuterium Bonds as Probes of Protein Thermal Unfolding

(2012) Wayne Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations

(2012) Cyril Falvo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ligand Binding Studied by 2D IR Spectroscopy Using the Azidohomoalanine Label

(2012) Robbert Bloem et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cysteine-linked aromatic nitriles as UV resonance Raman probes of protein structure

(2012) Colin L. Weeks et al.   JOURNAL OF RAMAN SPECTROSCOPY

Structural and Sequence Analysis of the Human γD-Crystallin Amyloid Fibril Core Using 2D IR Spectroscopy, Segmental 13C Labeling, and Mass Spectrometry

(2012) Sean D. Moran et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational Dynamics and Stability of HP35 Studied with 2D IR Vibrational Echoes

(2012) Jean K. Chung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macrocycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra

(2012) Ann Marie Woys et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Deamidation Accelerates Amyloid Formation and Alters Amylin Fiber Structure

(2012) Emily B. Dunkelberger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

(2012) Chris T. Middleton et al.   Nature Chemistry

Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human  D-crystallin amyloid fibrils

(2012) S. D. Moran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cyano Groups as Probes of Protein Microenvironments and Dynamics

(2011) Jörg Zimmermann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Vibrational solvatochromism and electrochromism of infrared probe molecules containing C≡O, C≡N, C=O, or C−F vibrational chromophore

(2011) Jun-Ho Choi et al.   JOURNAL OF CHEMICAL PHYSICS

Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy

(2011) Ricardo H. Pires et al.   JOURNAL OF MOLECULAR RECOGNITION

New Insights into the Coordination of Cu(II) by the Amyloid-B 16 Peptide from Fourier Transform IR Spectroscopy and Isotopic Labeling

(2011) Youssef El Khoury et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two-Dimensional IR Spectroscopy of Protein Dynamics Using Two Vibrational Labels: A Site-Specific Genetically Encoded Unnatural Amino Acid and an Active Site Ligand

(2011) Megan C. Thielges et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Covalently Bound Azido Groups Are Very Specific Water Sensors, Even in Hydrogen-Bonding Environments

(2011) Marta P. Wolfshorndl et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules

(2011) Matthias M. Waegele et al.   Journal of Physical Chemistry Letters

Modulating Accidental Fermi Resonance: What a Difference a Neutron Makes

(2011) Jacob S. Lipkin et al.   Journal of Physical Chemistry Letters

Isotope-assisted vibrational circular dichroism investigations of amyloid β peptide fragment, Aβ(16–22)

(2011) Ganesh Shanmugam et al.   JOURNAL OF STRUCTURAL BIOLOGY

2DIR Spectroscopy of Human Amylin Fibrils Reflects Stable β-Sheet Structure

(2011) Lu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Islet Amyloid Polypeptide, Islet Amyloid, and Diabetes Mellitus

(2011) Per Westermark et al.   PHYSIOLOGICAL REVIEWS

Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy

(2011) A. Ghosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Residue-Specific Vibrational Echoes Yield 3D Structures of a Transmembrane Helix Dimer

(2011) A. Remorino et al.   SCIENCE

Structural Insights into the Oligomerization and Architecture of Eukaryotic Membrane Pore-Forming Toxins

(2011) Ariel E. Mechaly et al.   STRUCTURE

Modulation ofp-Cyanophenylalanine Fluorescence by Amino Acid Side Chains and Rational Design of Fluorescence Probes of α-Helix Formation

(2010) Humeyra Taskent-Sezgin et al.   BIOCHEMISTRY

Molecular mechanism of Thioflavin-T binding to amyloid fibrils

(2010) Matthew Biancalana et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Suppression of IAPP fibrillation at anionic lipid membranes via IAPP-derived amyloid inhibitors and insulin

(2010) Daniel Sellin et al.   BIOPHYSICAL CHEMISTRY

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

(2010) Rabia Sarroukh et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Residue-Specific, Real-Time Characterization of Lag-Phase Species and Fibril Growth During Amyloid Formation: A Combined Fluorescence and IR Study of p-Cyanophenylalanine Analogs of Islet Amyloid Polypeptide

(2010) Peter Marek et al.   JOURNAL OF MOLECULAR BIOLOGY

Nitrile Bonds as Infrared Probes of Electrostatics in Ribonuclease S

(2010) Aaron T. Fafarman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

2D-IR Study of a Photoswitchable Isotope-Labeled α-Helix

(2010) Ellen H. G. Backus et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Residue-specific structural kinetics of proteins through the union of isotope labeling, mid-IR pulse shaping, and coherent 2D IR spectroscopy

(2010) Chris T. Middleton et al.   METHODS

2D IRphoton echo of azido-probes for biomolecular dynamics

(2010) Matthew J. Tucker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Discriminating early stage A 42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study

(2010) W. Zhuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential effects of phe19 and phe20 on fibril formation by amyloidogenic peptide Aβ16-22 (Ac-KLVFFAE-NH2)

(2010) Hideyo Inouye et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Probing Protein Folding Using Site-Specifically Encoded Unnatural Amino Acids as FRET Donors with Tryptophan

(2009) Shigeki J. Miyake-Stoner et al.   BIOCHEMISTRY

Morphology and Secondary Structure of Stable β-Oligomers Formed by Amyloid Peptide PrP(106−126)

(2009) Patrick Walsh et al.   BIOCHEMISTRY

Interpretation ofp-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study

(2009) Humeyra Taskent-Sezgin et al.   BIOCHEMISTRY

The Ability of Rodent Islet Amyloid Polypeptide To Inhibit Amyloid Formation by Human Islet Amyloid Polypeptide Has Important Implications for the Mechanism of Amyloid Formation and the Design of Inhibitors

(2009) Ping Cao et al.   BIOCHEMISTRY

Inhibiting Islet Amyloid Polypeptide Fibril Formation by the Red Wine Compound Resveratrol

(2009) Rajesh Mishra et al.   CHEMBIOCHEM

2D IR photon echo study of the anharmonic coupling in the OCN region of phenyl cyanate

(2009) Matthew J. Tucker et al.   CHEMICAL PHYSICS LETTERS

5-Cyanotryptophan as an infrared probe of local hydration status of proteins

(2009) Matthias M. Waegele et al.   CHEMICAL PHYSICS LETTERS

Carbon-deuterium vibrational probes of peptide conformation: Alanine dipeptide and glycine dipeptide

(2009) C. S. Miller et al.   JOURNAL OF CHEMICAL PHYSICS

The Common Architecture of Cross-β Amyloid

(2009) Thomas R. Jahn et al.   JOURNAL OF MOLECULAR BIOLOGY

Strategies for Extracting Structural Information from 2D IR Spectroscopy of Amyloid: Application to Islet Amyloid Polypeptide

(2009) David B. Strasfeld et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamical Transition in a Small Helical Peptide and Its Implication for Vibrational Energy Transport

(2009) Ellen H. G. Backus et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Applications of 2D IR Spectroscopy to Peptides, Proteins, and Hydrogen-Bond Dynamics†

(2009) Yung Sam Kim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

K3 Fragment of Amyloidogenic β2-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis

(2009) Mirela Mustata et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Using Two Fluorescent Probes to Dissect the Binding, Insertion, and Dimerization Kinetics of a Model Membrane Peptide

(2009) Jia Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FTIR analysis of GPCR activation using azido probes

(2009) Shixin Ye et al.   Nature Chemical Biology

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

(2009) Beth A. Lindquist et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

2D IR provides evidence for mobile water molecules in  -amyloid fibrils

(2009) Y. S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution

(2009) S.-H. Shim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amide I Two-Dimensional Infrared Spectroscopy of Proteins

(2008) Ziad Ganim et al.   ACCOUNTS OF CHEMICAL RESEARCH

Small-Molecule Inhibitors of Islet Amyloid Polypeptide Fibril Formation

(2008) Rajesh Mishra et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dynamics of Liquids, Molecules, and Proteins Measured with Ultrafast 2D IR Vibrational Echo Chemical Exchange Spectroscopy

(2008) M.D. Fayer   Annual Review of Physical Chemistry

Using an Amino Acid Fluorescence Resonance Energy Transfer Pair To Probe Protein Unfolding: Application to the Villin Headpiece Subdomain and the LysM Domain†

(2008) Julie M. Glasscock et al.   BIOCHEMISTRY

β-Azidoalanine as an IR Probe: Application to Amyloid Aβ(16-22) Aggregation

(2008) Kwang-Im Oh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nitrile Groups as Vibrational Probes: Calculations of the CN Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran

(2008) Beth A. Lindquist et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Investigation of an unnatural amino acid for use as a resonance Raman probe: detection limits and solvent and temperature dependence of the νCN band of 4-cyanophenylalanine

(2008) Colin L. Weeks et al.   JOURNAL OF RAMAN SPECTROSCOPY

Tracking Fiber Formation in Human Islet Amyloid Polypeptide with Automated 2D-IR Spectroscopy

(2008) David B. Strasfeld et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Optical properties of amyloid stained by Congo red: History and mechanisms

(2008) Alexander J. Howie et al.   MICRON

Amyloid-β protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory

(2008) Ganesh M Shankar et al.   NATURE MEDICINE

Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from A 40

(2008) Y. S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of Protein Fibril Formation: Nucleated Polymerization with Competing Off-Pathway Aggregation

(2007) Evan T. Powers et al.   BIOPHYSICAL JOURNAL

FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils

(2004) Giorgia Zandomeneghi et al.   PROTEIN SCIENCE