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List of works by William DeGrado

<i>De Novo</i> Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species

scientific article published on 29 December 2020

A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells ⬇️

scientific article published on 3 April 2017

A Photon-Free Approach to Transmembrane Protein Structure Determination ⬇️

scientific article published on October 15, 2011

A de Novo Designed Protein Mimics the Native State of Natural Proteins

article

A defined structural unit enables de novo design of small-molecule-binding proteins

scientific article published on 01 September 2020

A hierarchic approach to the design of hexameric helical barrels

scientific article published in May 2002

A long-lived Aβ oligomer resistant to fibrillization

scientific article published on 10 January 2018

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides

scientific article published in April 2004

A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D.

scientific article published in February 2009

A real-time all-atom structural search engine for proteins

scientific article

Activation of individual alphaIIbbeta3 integrin molecules by disruption of transmembrane domain interactions in the absence of clustering

scientific article published in April 2006

Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations

scientific article published in May 2003

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals

scientific article

Alpha-alpha linking motifs and interhelical orientations.

scientific article

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins

scientific article published on 23 September 2012

Amino acid propensities are position-dependent throughout the length of alpha-helices

scientific article published in April 2004

Amphiphilic polymethacrylate derivatives as antimicrobial agents

scientific article published in March 2005

An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses

scientific article published on 10 January 2017

An artificial di-iron oxo-protein with phenol oxidase activity

scientific article

An assay suitable for high throughput screening of anti-influenza drugs

scientific article

Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops

scientific article published in August 2005

Arylamide derivatives as allosteric inhibitors of the integrin alpha2beta1/type I collagen interaction

scientific article published on 5 May 2006

Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus

scientific article published on 17 October 2013

Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations

scientific article

Assessment of local friction in protein folding dynamics using a helix cross-linker

scientific article

Automated use of mutagenesis data in structure prediction

scientific article

Aβ and tau prion-like activities decline with longevity in the Alzheimer's disease human brain

scientific article published on 01 May 2019

Blue fluorescent amino acid for biological spectroscopy and microscopy

scientific article published on 22 May 2017

C-terminal juxtamembrane region of full-length M2 protein forms a membrane surface associated amphipathic helix

scientific article published on 14 January 2015

Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5 ⬇️

scientific article published on December 16, 2011

Catalytic efficiency of designed catalytic proteins

scientific article

Catalytic molten globules

scientific article published in Nature

Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics.

scientific article published in February 2006

Characterization of the monomeric form of the transmembrane and cytoplasmic domains of the integrin beta 3 subunit by NMR spectroscopy

scientific article

Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16.

scientific article

Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J.Am. Chem. Soc.2005,127, 1346−1347]

article

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces ⬇️

scientific article published on May 27, 2011

Computational Design of a β-Peptide That Targets Transmembrane Helices ⬇️

scientific article published on July 22, 2011

Computational biology: Biosensor design

scientific article published in May 2003

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

scientific article

Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore

scientific article published on 05 September 2013

Computational design and characterization of a monomeric helical dinuclear metalloprotein

scientific article published on December 2003

Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore

scientific article

Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation

scientific article published on 28 January 2015

Computational design of a protein crystal ⬇️

scientific article published on April 25, 2012

Computational design of a water-soluble analog of phospholamban

scientific article published in February 2003

Computational design of heterochiral peptides against a helical target

scientific article

Computational design of peptides that target transmembrane helices

scientific article published in March 2007

Computational design of water-soluble analogues of the potassium channel KcsA

scholarly article

Consensus motif for integrin transmembrane helix association

scientific article

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

scientific article published in March 2006

Cooperativity and specificity of association of a designed transmembrane peptide

scientific article

Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron

scientific article

Crystal structure of the drug-resistant S31N influenza M2 proton channel

scientific article

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.

scientific article

De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities

scientific article published on 11 April 2019

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles

scientific article published on 18 December 2017

De Novo Design of a Molecular Switch: Phosphorylation-dependent Association of Designed Peptides ⬇️

scientific article published on November 14, 2003

De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers

scholarly article

De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1.

scientific article

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.

scientific article published on 21 August 2017

De novo design of a single-chain diphenylporphyrin metalloprotein

scientific article published on 10 August 2007

De novo design of biomimetic antimicrobial polymers

scientific article

De novo design of drug-binding proteins with predictable binding energy and specificity

scientific article published on 04 April 2024

De novo designed synthetic mimics of antimicrobial peptides

scientific article

De novo protein design: from molten globules to native-like states

article

De novo protein design: what are we learning?

article

Deep mutational scanning reveals the structural basis for α-synuclein activity

scientific article published on 09 March 2020

Design and synthesis of multi-haem proteins

scientific article published in Nature

Design of a short thermally stable α-helix embedded in a macrocycle.

scientific article published on 7 February 2018

Design of a switchable eliminase ⬇️

scientific article published on April 11, 2011

Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment

scientific article

Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport

scientific article published on August 2017

Designed metalloprotein stabilizes a semiquinone radical

scientific article (publication date: April 2016)

Designed peptides that assemble into cross-α amyloid-like structures

scientific article published on 30 July 2018

Detection of drug-induced conformational change of a transmembrane protein in lipid bilayers using site-directed spin labeling

scientific article published on 19 November 2012

Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange

scientific article published on August 2003

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle

scientific article published on 7 April 2007

Development of a rotamer library for use in beta-peptide foldamer computational design

scientific article published on June 2010

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction ⬇️

scientific article published on October 11, 2012

Diiron-containing metalloproteins: Developing functional models

article

Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes

scientific article

Directly Activating the Integrin αIIbβ3 Initiates Outside-In Signaling by Causing αIIbβ3 Clustering

scientific article published on 07 April 2016

Discovery of Highly Potent Inhibitors Targeting the Predominant Drug-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel

scientific article published on 15 January 2016

Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus

scientific article

Discovery of potent small-molecule inhibitors of multidrug-resistant Plasmodium falciparum using a novel miniaturized high-throughput luciferase-based assay

scientific article

Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus

scientific article

Distinct synthetic Aβ prion strains producing different amyloid deposits in bigenic mice

scientific article

Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR.

scientific article

Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion

scientific article

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins

scientific article published in May 2005

Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores

scientific article

Engineered single- and multi-cell chemotaxis pathways in E. coli

scientific article

Engineering and design: editorial overview

scientific article published on 13 August 2009

Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy

scientific article published on 2 October 2007

Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule

scientific article published on 27 August 2018

Environment- and Sequence-Dependence of Helical Type in Membrane-Spanning Peptides Composed of β3-Amino Acids ⬇️

scientific article published on June 9, 2011

Erratum: Structural basis for the function and inhibition of an influenza virus proton channel

scientific article published in Nature

Exploring N-Arylsulfonyl-l-proline Scaffold as a Platform for Potent and Selective αvβ1 Integrin Inhibitors

scientific article published on 30 August 2016

Exploring Organosilane Amines as Potent Inhibitors and Structural Probes of Influenza A Virus M2 Proton Channel ⬇️

scientific article published on August 12, 2011

Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus

scientific article published on 05 April 2011

Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study

scientific article published on 14 February 2019

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

article

Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel.

scientific article

Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability This work was supported by a grant from the U.S. Army Research Office. Y. Tang is supported by a Whitaker Graduate Research Fellowship. We thank Dr. Ga

scientific article

Foldamers as versatile frameworks for the design and evolution of function

scientific article

Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs

scientific article published in August 2004

Functional Analysis of the Transmembrane Domain in Paramyxovirus F Protein-Mediated Membrane Fusion

scientific article (publication date: 13 February 2009)

Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly

scientific article published on 24 April 2019

Graphene Symmetry Amplified by Designed Peptide Self-Assembly

scientific article published on June 2016

Helix formation via conformation diffusion search

scientific article

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

scientific article

How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles

scientific article

Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors

scientific article

Identification of Interacting Hot Spots in the β3 Integrin Stalk Using Comprehensive Interface Design ⬇️

scientific article published on October 7, 2010

Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel

scientific article published on 09 July 2009

Infrared signature and folding dynamics of a helical beta-peptide

scientific article

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters

scientific article published on 12 September 2018

Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay

scientific article

Interactions of ADP-stimulated human platelets with PEGylated polystyrene substrates prepared by surface amidation.

scientific article

Lipid membranes supported on optically transparent nanosilicas: Synthesis and application in characterization of protein-membrane interactions ⬇️

scientific article published on December 3, 2010

Long-range interactions stabilize the fold of a non-natural oligomer

scientific article published in October 2002

Mechanistic insights from functional characterization of an unnatural His37 mutant of the influenza A/M2 protein

scientific article published on 22 November 2013

Molecular basis of ChvE function in sugar binding, sugar utilization, and virulence in Agrobacterium tumefaciens

scientific article published on 24 July 2009

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus

scholarly article

Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2.

scientific article published on 21 July 2011

Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins

scientific article published on 15 July 2015

Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer

scientific article published on 13 June 2009

Mutagenesis data in the automated prediction of transmembrane helix dimers

scientific article

NMR analysis of the αIIbβ3 cytoplasmic interaction suggests a mechanism for integrin regulation ⬇️

scientific article published on December 14, 2010

New design of helix bundle peptide-polymer conjugates

scientific article

Noncovalent self-assembly of a heterotetrameric diiron protein

scientific article

Nontoxic membrane-active antimicrobial arylamide oligomers.

scientific article

Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization

scientific article

Orientation, dynamics, and lipid interaction of an antimicrobial arylamide investigated by 19F and 31P solid-state NMR spectroscopy

scientific article

Oxygen reactivity of the biferrous site in the de novo designed four helix bundle peptide DFsc: nature of the "intermediate" and reaction mechanism

scientific article published on 24 June 2008

Packing of apolar side chains enables accurate design of highly stable membrane proteins

scientific article published on 01 March 2019

Peptide-Programmable Nanoparticle Superstructures with Tailored Electrocatalytic Activity.

scientific article published on 4 June 2018

Photoactivatable protein labeling by singlet oxygen mediated reactions

scientific article published on 12 May 2016

Photoinduced Electron Transfer and Fluorophore Motion as a Probe of the Conformational Dynamics of Membrane Proteins: Application to the Influenza A M2 Proton Channel ⬇️

scientific article published on March 14, 2011

Platelet factor 4 activity against P. falciparum and its translation to nonpeptidic mimics as antimalarials

scientific article

Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates

scientific article published on 10 December 2020

Polar Networks Control Oligomeric Assembly in Membranes

article

Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles

scientific article published in June 2003

Preorganization of molecular binding sites in designed diiron proteins

scientific article (publication date: April 2003)

Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor

scientific article

Protein-directed self-assembly of a fullerene crystal

scientific article published on 26 April 2016

Protein-protein interactions in the membrane: sequence, structural, and biological motifs

scientific article published on July 2008

Proton and cation transport activity of the M2 proton channel from influenza A virus

scientific article

Proton release from the histidine-tetrad in the M2 channel of the influenza A virus

scientific article published on 27 October 2014

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel

scientific article published on 12 July 2019

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

scientific article published on June 3, 2011

Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography

scientific article published in December 2005

Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers

scientific article published on 10 November 2007

SNAC-tag for sequence-specific chemical protein cleavage

scientific article published on 25 March 2019

Salt bridges: Geometrically specific, designable interactions ⬇️

scientific article published on January 5, 2011

Self-assembling dipeptide antibacterial nanostructures with membrane disrupting activity.

scientific article published on 8 November 2017

Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function

scientific article published on 21 January 2005

Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein.

scientific article

Short peptides self-assemble to produce catalytic amyloids

scientific article published on 16 March 2014

Signal transduction in histidine kinases: insights from new structures

scientific article published on 14 May 2015

Simulated Evolution of Emergent Chiral Structures in Polyalanine

article

Site-specific hydration status of an amphipathic peptide in AOT reverse micelles

scientific article published on 2 October 2007

Sliding helix and change of coordination geometry in a model di-MnII protein

scientific article (publication date: 27 January 2003)

Slow folding-unfolding kinetics of an octameric β-peptide bundle

scientific article published on 20 November 2013

Small molecule inhibitors of integrin alpha2beta1.

scientific article published on 04 October 2007

Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism

scholarly article

Solid-supported membrane technology for the investigation of the influenza A virus M2 channel activity

scientific article

Solution NMR Structure of a Designed Metalloprotein and Complementary Molecular Dynamics Refinement

scientific article

Specific aromatic foldamers potently inhibit spontaneous and seeded Aβ42 and Aβ43 fibril assembly

scientific article

Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy

scientific article published on 7 March 2011

Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity

scientific article published in November 2005

Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster

scientific article published on 01 August 2018

Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions.

scientific article published on 21 December 2017

Stimulated Photon Echoes from Amide I Vibrations

Structural basis for proton conduction and inhibition by the influenza M2 protein ⬇️

scientific article published on October 9, 2012

Structural basis for the function and inhibition of an influenza virus proton channel

scientific article

Structural biology. The flu's proton escort

scientific article

Structural heterogeneity and intersubject variability of Aβ in familial and sporadic Alzheimer's disease

scientific article published on 8 January 2018

Structural organization and interactions of transmembrane domains in tetraspanin proteins

scientific article

Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus.

scientific article

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus

scientific article

Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability

article

Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins

scientific article published on 24 July 2015

T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1.

scientific article published on 8 September 2005

Targeting integrin α5β1 ameliorates severe airway hyperresponsiveness in experimental asthma

scientific article published on 05 December 2016

Template-constrained cyclic sulfopeptide HIV-1 entry inhibitors

scientific article

The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases

scientific article

The design and evaluation of heparin-binding foldamers

scientific article

The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

scientific article

The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the M2 proton channel from the influenza A virus

scientific article published on July 2008

The leech product saratin is a potent inhibitor of platelet integrin alpha2beta1 and von Willebrand factor binding to collagen

scientific article published in March 2007

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

scientific article

The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives

scientific article published on January 2009

The αvβ1 integrin plays a critical in vivo role in tissue fibrosis

scientific article published on May 2015

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

scientific article

Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors

scientific article published on January 2011

Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion

scientific article

Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ

scientific article

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

scientific article

Use of phage display to probe the evolution of binding specificity and affinity in integrins

scientific article

Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers

scientific article

Using Thioamides To Site-Specifically Interrogate the Dynamics of Hydrogen Bond Formation in β-Sheet Folding ⬇️

scientific article published on May 2, 2012

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays

scientific article published on 19 August 2008

Using nitrile-derivatized amino acids as infrared probes of local environment

scientific article

Using two fluorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide

scientific article published on March 2009

X-ray Crystal Structure of the Influenza A M2 Proton Channel S31N Mutant in Two Conformational States: An Open and Shut Case

scientific article published on 11 July 2019

pH-induced conformational change of the influenza M2 protein C-terminal domain

scientific article published on 29 August 2008

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