faculty

Valerie Daggett

daggett@uw.edu

University of Washington,

Biophysical and Structural Biology

Computational Biology

Faculty Contact Information

Building: Foege Room: N310B Box: 355013 Phone: 206-685-7420

Lab Information

Location: University of Washington Building: Foege Room: N351A Box: 355013 Phone: 206-543-9305 http://depts.washington.edu/daglab

Accepting Students For:

Rotation, Autumn

Rotation, Spring

Rotation, Summer

Rotation, Winter

Permanent

Publications

The following publications were retrieved from PubMed:

Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin.

Powers JD, Yuan CC, McCabe KJ, Murray JD, Childers MC, Flint GV, Moussavi-Harami F, Mohran S, Castillo R, Zuzek C, Ma W, Daggett V, McCulloch AD, Irving TC, Regnier M.

Proc Natl Acad Sci U S A. 2019 May 20;

α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer's disease.

Shea D, Hsu CC, Bi TM, Paranjapye N, Childers MC, Cochran J, Tomberlin CP, Wang L, Paris D, Zonderman J, Varani G, Link CD, Mullan M, Daggett V.

Proc Natl Acad Sci U S A. 2019 Apr 30; 18(116)8895-8900

Visualizing Protein Folding and Unfolding.

Ferina J, Daggett V.

J Mol Biol. 2019 Apr 5; 8(431)1540-1564

The Role of α-sheet in Amyloid Oligomer Aggregation and Toxicity.

Bi TM, Daggett V.

Yale J Biol Med. 2018 Sep; 3(91)247-255

A Carboxylate to Amide Substitution That Switches Protein Folds.

Gianni S, McCully ME, Malagrinò F, Bonetti D, De Simone A, Brunori M, Daggett V.

Angew Chem Int Ed Engl. 2018 Sep 24; 39(57)12795-12798

De Novo Designed α-Sheet Peptides Inhibit Functional Amyloid Formation of Streptococcus mutans Biofilms.

Paranjapye N, Daggett V.

J Mol Biol. 2018 Oct 12; 20(430)3764-3773

Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.

Childers MC, Towse CL, Daggett V.

Protein Eng Des Sel. 2018 Jun 1; 6(31)191-204

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms.

Bleem A, Christiansen G, Madsen DJ, Maric H, Strømgaard K, Bryers JD, Daggett V, Meyer RL, Otzen DE.

J Mol Biol. 2018 Oct 12; 20(430)3751-3763

Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.

Childers MC, Daggett V.

J Phys Chem B. 2018 Jul 5; 26(122)6673-6689

Chemical and Physical Variability in Structural Isomers of an l/d α-Sheet Peptide Designed To Inhibit Amyloidogenesis.

Maris NL, Shea D, Bleem A, Bryers JD, Daggett V.

Biochemistry. 2018 Feb 6; 5(57)507-510

Designed α-sheet peptides suppress amyloid formation in <i>Staphylococcus aureus</i> biofilms.

Bleem A, Francisco R, Bryers JD, Daggett V.

NPJ Biofilms Microbiomes. 2017; (3)16

Simulations of membrane-bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding.

Cheng CJ, Koldsø H, Van der Kamp MW, Schiøtt B, Daggett V.

J Neurochem. 2017 Jul; 1(142)171-182

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space.

Towse CL, Akke M, Daggett V.

J Phys Chem B. 2017 Apr 27; 16(121)3933-3945

Insights from molecular dynamics simulations for computational protein design.

Childers MC, Daggett V.

Mol Syst Des Eng. 2017 Feb 1; 1(2)9-33

Molecular mechanisms underlying deoxy-ADP.Pi activation of pre-powerstroke myosin.

Nowakowski SG, Regnier M, Daggett V.

Protein Sci. 2017 Apr; 4(26)749-762

An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.

Bromley D, Bauer MR, Fersht AR, Daggett V.

Protein Eng Des Sel. 2016 Sep; 9(29)377-90

Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering.

Bleem A, Daggett V.

Biotechnol Bioeng. 2017 Jan; 1(114)7-20

The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.

Childers MC, Towse CL, Daggett V.

Protein Eng Des Sel. 2016 Jul; 7(29)271-80

Peptides Composed of Alternating L- and D-Amino Acids Inhibit Amyloidogenesis in Three Distinct Amyloid Systems Independent of Sequence.

Kellock J, Hopping G, Caughey B, Daggett V.

J Mol Biol. 2016 Jun 5; 11(428)2317-2328

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.

Towse CL, Vymetal J, Vondrasek J, Daggett V.

Biophys J. 2016 Jan 19; 2(110)348-361

New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.

Towse CL, Rysavy SJ, Vulovic IM, Daggett V.

Structure. 2016 Jan 5; 1(24)187-199

Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality.

Towse CL, Hopping G, Vulovic I, Daggett V.

Protein Eng Des Sel. 2014 Nov; 11(27)447-55

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

Rysavy SJ, Beck DA, Daggett V.

Protein Sci. 2014 Nov; 11(23)1584-95

Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers.

Hopping G, Kellock J, Barnwal RP, Law P, Bryers J, Varani G, Caughey B, Daggett V.

Elife. 2014 Jul 15; (3)e01681

Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH.

Cheng CJ, Daggett V.

Biomolecules. 2014 Feb 10; 1(4)181-201

Designed Trpzip-3 β-Hairpin Inhibits Amyloid Formation in Two Different Amyloid Systems.

Hopping G, Kellock J, Caughey B, Daggett V.

ACS Med Chem Lett. 2013 Sep 12; 9(4)824-8

DIVE: a graph-based visual-analytics framework for big data.

Rysavy SJ, Bromley D, Daggett V.

IEEE Comput Graph Appl. 2014 Mar-Apr; 2(34)26-37

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN.

Protein Sci. 2014 Jun; 6(23)747-59

Structural and dynamic properties of the human prion protein.

Chen W, van der Kamp MW, Daggett V.

Biophys J. 2014 Mar 4; 5(106)1152-63

Different misfolding mechanisms converge on common conformational changes: human prion protein pathogenic mutants Y218N and E196K.

Cheng CJ, Daggett V.

Prion. 2014 Jan-Feb; 1(8)125-35

DIVE: a data intensive visualization engine.

Bromley D, Rysavy SJ, Su R, Toofanny RD, Schmidlin T, Daggett V.

Bioinformatics. 2014 Feb 15; 4(30)593-5

Analyzing disease-associated protein structures with visual analytics.

Bromley D, Daggett V.

AMIA Jt Summits Transl Sci Proc. 2013; (2013)33

Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation.

Schmidlin T, Ploeger K, Jonsson AL, Daggett V.

Protein Eng Des Sel. 2013 Aug; 8(26)503-13

Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency.

Bromley D, Anderson PC, Daggett V.

Biochemistry. 2013 Jun 18; 24(52)4264-73

Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca(2+)-desensitizing variants.

Wang D, McCully ME, Luo Z, McMichael J, Tu AY, Daggett V, Regnier M.

Arch Biochem Biophys. 2013 Jul 1; 1(535)68-75

Using simulations to provide the framework for experimental protein folding studies.

Rizzuti B, Daggett V.

Arch Biochem Biophys. 2013 Mar; 1-2(531)128-35

Protein Simulation Data in the Relational Model.

Simms AM, Daggett V.

J Supercomput. 2012 Oct 1; 1(62)150-173

When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative.

Towse CL, Daggett V.

Bioessays. 2012 Dec; 12(34)1060-9

Multimolecule test-tube simulations of protein unfolding and aggregation.

McCully ME, Beck DA, Daggett V.

Proc Natl Acad Sci U S A. 2012 Oct 30; 44(109)17851-6

Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.

McCully ME, Beck DA, Daggett V.

Protein Eng Des Sel. 2013 Jan; 1(26)35-45

A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.

Benson NC, Daggett V.

J Bioinform Comput Biol. 2012 Aug; 4(10)1250008

Wavelet Analysis of Protein Motion.

Benson NC, Daggett V.

Int J Wavelets Multiresolut Inf Process. 2012 Jul; 4(10)

Structural and functional consequences of the cardiac troponin C L48Q Ca(2+)-sensitizing mutation.

Wang D, Robertson IM, Li MX, McCully ME, Crane ML, Luo Z, Tu AY, Daggett V, Sykes BD, Regnier M.

Biochemistry. 2012 Jun 5; 22(51)4473-87

A comparison of multiscale methods for the analysis of molecular dynamics simulations.

Benson NC, Daggett V.

J Phys Chem B. 2012 Jul 26; 29(116)8722-31

Disruption of the X-loop turn of the prion protein linked to scrapie resistance.

Scouras AD, Daggett V.

Protein Eng Des Sel. 2012 May; 5(25)243-9

A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8.

Merkley ED, Daggett V, Parson WW.

Proteins. 2012 Feb; 2(80)546-55

GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate.

Morrone A, Giri R, Toofanny RD, Travaglini-Allocatelli C, Brunori M, Daggett V, Gianni S.

Biophys J. 2011 Oct 19; 8(101)2053-60

The effect of context on the folding of β-hairpins.

Jonsson AL, Daggett V.

J Struct Biol. 2011 Nov; 2(176)143-50

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

Toofanny RD, Simms AM, Beck DA, Daggett V.

BMC Bioinformatics. 2011 Aug 10; (12)334

Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain.

Calhoun S, Daggett V.

Biochemistry. 2011 Jun 14; 23(50)5345-53

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations.

van der Kamp MW, Daggett V.

Top Curr Chem. 2011; (305)169-97

Malleability of folding intermediates in the homeodomain superfamily.

Banachewicz W, Religa TL, Schaeffer RD, Daggett V, Fersht AR.

Proc Natl Acad Sci U S A. 2011 Apr 5; 14(108)5596-601

The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water.

Scouras AD, Daggett V.

Protein Sci. 2011 Feb; 2(20)341-52

Manifestations of native topology in the denatured state ensemble of Rhodopseudomonas palustris cytochrome c'.

Dar TA, Schaeffer RD, Daggett V, Bowler BE.

Biochemistry. 2011 Feb 15; 6(50)1029-41

Introduction to special issue 'Three decades of protein engineering: impact on structural biology and therapy'.

Daggett V

Protein Eng Des Sel. 2011 Jan; 1-2(24)1

The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function.

Morrone A, McCully ME, Bryan PN, Brunori M, Daggett V, Gianni S, Travaglini-Allocatelli C.

J Biol Chem. 2011 Feb 4; 5(286)3863-72

Dynameomics: protein dynamics and unfolding across fold space.

Jonsson AL, Schaeffer RD, van der Kamp MW, Daggett V.

Biomol Concepts. 2010 Dec 1; 5-6(1)335-44

Generation of a consensus protein domain dictionary.

Schaeffer RD, Jonsson AL, Simms AM, Daggett V.

Bioinformatics. 2011 Jan 1; 1(27)46-54

Protein folds and protein folding.

Schaeffer RD, Daggett V.

Protein Eng Des Sel. 2011 Jan; 1-2(24)11-9

Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations.

Chen W, van der Kamp MW, Daggett V.

Biochemistry. 2010 Nov 16; 45(49)9874-81

Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding.

van der Kamp MW, Daggett V.

J Mol Biol. 2010 Dec 10; 4(404)732-48

Influence of pH on the human prion protein: insights into the early steps of misfolding.

van der Kamp MW, Daggett V.

Biophys J. 2010 Oct 6; 7(99)2289-98

Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.

McCully ME, Beck DA, Fersht AR, Daggett V.

Biophys J. 2010 Sep 8; 5(99)1628-36

A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.

Toofanny RD, Jonsson AL, Daggett V.

Biophys J. 2010 Jun 2; 11(98)2671-81

Dynameomics: a comprehensive database of protein dynamics.

van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD, Benson NC, Anderson PC, Merkley ED, Rysavy S, Bromley D, Beck DA, Daggett V.

Structure. 2010 Mar 14; 4(18)423-35

Polymorphisms and disease: hotspots of inactivation in methyltransferases.

Rutherford K, Daggett V.

Trends Biochem Sci. 2010 Oct; 10(35)531-8

Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.

Merkley ED, Parson WW, Daggett V.

Protein Eng Des Sel. 2010 May; 5(23)327-36

Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B.

Key J, Scheuermann TH, Anderson PC, Daggett V, Gardner KH.

J Am Chem Soc. 2009 Dec 9; 48(131)17647-54

Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds.

Jonsson AL, Scott KA, Daggett V.

Biophys J. 2009 Dec 2; 11(97)2958-66

The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.

Law PB, Daggett V.

Protein Eng Des Sel. 2010 Jan; 1(23)27-33

The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface.

Rutherford K, Daggett V.

Protein Eng Des Sel. 2009 Dec; 12(22)713-21

Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V.

Schmidlin T, Kennedy BK, Daggett V.

Biophys J. 2009 Sep 16; 6(97)1709-18

Shedding light on amyloidosis with protein engineering.

Daggett V

Protein Eng Des Sel. 2009 Aug; 8(22)445

The consequences of pathogenic mutations to the human prion protein.

van der Kamp MW, Daggett V.

Protein Eng Des Sel. 2009 Aug; 8(22)461-8

The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding.

Anderson PC, Daggett V.

J Am Chem Soc. 2009 Jul 15; 27(131)9506-15

A hotspot of inactivation: The A22S and V108M polymorphisms individually destabilize the active site structure of catechol O-methyltransferase.

Rutherford K, Daggett V.

Biochemistry. 2009 Jul 14; 27(48)6450-60

Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein.

DeMarco ML, Daggett V.

J Neurochem. 2009 Apr; 1(109)60-73

Protein folding and binding: moving into unchartered territory.

Daggett V, Fersht AR.

Curr Opin Struct Biol. 2009 Feb; 1(19)1-2

Dynameomics: large-scale assessment of native protein flexibility.

Benson NC, Daggett V.

Protein Sci. 2008 Dec; 12(17)2038-50

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.

Beck DA, Alonso DO, Inoyama D, Daggett V.

Proc Natl Acad Sci U S A. 2008 Aug 26; 34(105)12259-64

Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease.

Anderson PC, Daggett V.

Biochemistry. 2008 Sep 9; 36(47)9380-93

Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.

McCully ME, Beck DA, Daggett V.

Biochemistry. 2008 Jul 8; 27(47)7079-89

Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics.

Rutherford K, Daggett V.

J Mol Biol. 2008 Jun 13; 4(379)803-14

Side-chain dynamics are critical for water permeation through aquaporin-1.

Smolin N, Li B, Beck DA, Daggett V.

Biophys J. 2008 Aug; 3(95)1089-98

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations.

Beck DA, Jonsson AL, Schaeffer RD, Scott KA, Day R, Toofanny RD, Alonso DO, Daggett V.

Protein Eng Des Sel. 2008 Jun; 6(21)353-68

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.

Simms AM, Toofanny RD, Kehl C, Benson NC, Daggett V.

Protein Eng Des Sel. 2008 Jun; 6(21)369-77

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.

Kehl C, Simms AM, Toofanny RD, Daggett V.

Protein Eng Des Sel. 2008 Jun; 6(21)379-86

Formation of ice-like water structure on the surface of an antifreeze protein.

Smolin N, Daggett V.

J Phys Chem B. 2008 May 15; 19(112)6193-202

Different disease-causing mutations in transthyretin trigger the same conformational conversion.

Steward RE, Armen RS, Daggett V.

Protein Eng Des Sel. 2008 Mar; 3(21)187-95

Combining experiment and simulation in protein folding: closing the gap for small model systems.

Schaeffer RD, Fersht A, Daggett V.

Curr Opin Struct Biol. 2008 Feb; 1(18)4-9

Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A.

Merkley ED, Bernard B, Daggett V.

Biochemistry. 2008 Jan 22; 3(47)880-92

The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics.

Rutherford K, Parson WW, Daggett V.

Biochemistry. 2008 Jan 22; 3(47)893-901

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.

Beck DA, Daggett V.

Biophys J. 2007 Nov 15; 10(93)3382-91

Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics.

Beck DA, Bennion BJ, Alonso DO, Daggett V.

Methods Enzymol. 2007; (428)373-96

The role of the turn in beta-hairpin formation during WW domain folding.

Sharpe T, Jonsson AL, Rutherford TJ, Daggett V, Fersht AR.

Protein Sci. 2007 Oct; 10(16)2233-9

Molecular mechanism for low pH triggered misfolding of the human prion protein.

DeMarco ML, Daggett V.

Biochemistry. 2007 Mar 20; 11(46)3045-54

Conformational entropy of alanine versus glycine in protein denatured states.

Scott KA, Alonso DO, Sato S, Fersht AR, Daggett V.

Proc Natl Acad Sci U S A. 2007 Feb 20; 8(104)2661-6

Folding mechanisms of proteins with high sequence identity but different folds.

Scott KA, Daggett V.

Biochemistry. 2007 Feb 13; 6(46)1545-56

Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models.

DeMarco ML, Silveira J, Caughey B, Daggett V.

Biochemistry. 2006 Dec 26; 51(45)15573-82

Direct observation of microscopic reversibility in single-molecule protein folding.

Day R, Daggett V.

J Mol Biol. 2007 Feb 16; 2(366)677-86

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.

Beck DA, White GW, Daggett V.

J Struct Biol. 2007 Mar; 3(157)514-23

Alpha-sheet: The toxic conformer in amyloid diseases?

Daggett V

Acc Chem Res. 2006 Sep; 9(39)594-602

Phi-analysis at the experimental limits: mechanism of beta-hairpin formation.

Petrovich M, Jonsson AL, Ferguson N, Daggett V, Fersht AR.

J Mol Biol. 2006 Jul 21; 4(360)865-81

Protein folding-simulation.

Daggett V

Chem Rev. 2006 May; 5(106)1898-916

The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment.

Scott KA, Randles LG, Moran SJ, Daggett V, Clarke J.

J Mol Biol. 2006 May 26; 1(359)159-73

Importance of context in protein folding: secondary structural propensities versus tertiary contact-assisted secondary structure formation.

Scott KA, Alonso DO, Pan Y, Daggett V.

Biochemistry. 2006 Apr 4; 13(45)4153-63

The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures.

Rutherford K, Bennion BJ, Parson WW, Daggett V.

Biochemistry. 2006 Feb 21; 7(45)2178-88

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

Armen RS, Daggett V.

Biochemistry. 2005 Dec 13; 49(44)16098-107

Local environmental effects on the structure of the prion protein.

DeMarco ML, Daggett V.

C R Biol. 2005 Oct-Nov; 10-11(328)847-62

Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases.

Armen RS, Bernard BM, Day R, Alonso DO, Daggett V.

Proc Natl Acad Sci U S A. 2005 Sep 20; 38(102)13433-8

Ensemble versus single-molecule protein unfolding.

Day R, Daggett V.

Proc Natl Acad Sci U S A. 2005 Sep 20; 38(102)13445-50

Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding.

White GW, Gianni S, Grossmann JG, Jemth P, Fersht AR, Daggett V.

J Mol Biol. 2005 Jul 22; 4(350)757-75

The structure of the major transition state for folding of an FF domain from experiment and simulation.

Jemth P, Day R, Gianni S, Khan F, Allen M, Daggett V, Fersht AR.

J Mol Biol. 2005 Jul 8; 2(350)363-78

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent.

Day R, Daggett V.

Protein Sci. 2005 May; 5(14)1242-52

Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation.

Ferguson N, Day R, Johnson CM, Allen MD, Daggett V, Fersht AR.

J Mol Biol. 2005 Apr 8; 4(347)855-70

Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations.

Esposito L, Daggett V.

Biochemistry. 2005 Mar 8; 9(44)3358-68

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.

Beck DA, Armen RS, Daggett V.

Biochemistry. 2005 Jan 18; 2(44)609-16

The early steps in the unfolding of azurin.

Rizzuti B, Daggett V, Guzzi R, Sportelli L.

Biochemistry. 2004 Dec 14; 49(43)15604-9

Preventing misfolding of the prion protein by trimethylamine N-oxide.

Bennion BJ, DeMarco ML, Daggett V.

Biochemistry. 2004 Oct 19; 41(43)12955-63

Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH.

Armen RS, Alonso DO, Daggett V.

Structure. 2004 Oct; 10(12)1847-63

Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

DeMarco ML, Alonso DO, Daggett V.

J Mol Biol. 2004 Aug 20; 4(341)1109-24

Methods for molecular dynamics simulations of protein folding/unfolding in solution.

Beck DA, Daggett V.

Methods. 2004 Sep; 1(34)112-20

Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.

Armen RS, DeMarco ML, Alonso DO, Daggett V.

Proc Natl Acad Sci U S A. 2004 Aug 10; 32(101)11622-7

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation.

Jemth P, Gianni S, Day R, Li B, Johnson CM, Daggett V, Fersht AR.

Proc Natl Acad Sci U S A. 2004 Apr 27; 17(101)6450-5

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.

Bennion BJ, Daggett V.

Proc Natl Acad Sci U S A. 2004 Apr 27; 17(101)6433-8

Testing protein-folding simulations by experiment: B domain of protein A.

Sato S, Religa TL, Daggett V, Fersht AR.

Proc Natl Acad Sci U S A. 2004 May 4; 18(101)6952-6

From conversion to aggregation: protofibril formation of the prion protein.

DeMarco ML, Daggett V.

Proc Natl Acad Sci U S A. 2004 Feb 24; 8(101)2293-8

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

Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F.

Proc Natl Acad Sci U S A. 2003 Dec 23; 26(100)15486-91

All-atom simulations of protein folding and unfolding.

Day R, Daggett V.

Adv Protein Chem. 2003; (66)373-403

Unifying features in protein-folding mechanisms.

Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor U, White GW, DeMarco ML, Daggett V, Fersht AR.

Proc Natl Acad Sci U S A. 2003 Nov 11; 23(100)13286-91

A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

Day R, Beck DA, Armen RS, Daggett V.

Protein Sci. 2003 Oct; 10(12)2150-60

Simulations of biomolecules: Characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein.

Alonso DO, An C, Daggett V.

Philos Trans A Math Phys Eng Sci. 2002 Jun 15; 1795(360)1165-78

Molecular basis for the extensibility of elastin.

Li B, Daggett V.

J Muscle Res Cell Motil. 2002; 5-6(23)561-73

The present view of the mechanism of protein folding.

Daggett V, Fersht A.

Nat Rev Mol Cell Biol. 2003 Jun; 6(4)497-502

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions.

Armen R, Alonso DO, Daggett V.

Protein Sci. 2003 Jun; 6(12)1145-57

The molecular basis for the chemical denaturation of proteins by urea.

Bennion BJ, Daggett V.

Proc Natl Acad Sci U S A. 2003 Apr 29; 9(100)5142-7

A microscopic view of peptide and protein solvation.

Beck DA, Alonso DO, Daggett V.

Biophys Chem. 2003; 1-3(100)221-37

The complete folding pathway of a protein from nanoseconds to microseconds.

Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SM, Alonso DO, Daggett V, Fersht AR.

Nature. 2003 Feb 20; 6925(421)863-7

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

Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF.

Protein Sci. 2003 Mar; 3(12)520-31

The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides.

Li B, Daggett V.

Biopolymers. 2003 Jan; 1(68)121-9

Is there a unifying mechanism for protein folding?

Daggett V, Fersht AR.

Trends Biochem Sci. 2003 Jan; 1(28)18-25

Protein conformation and diagnostic tests: the prion protein.

Bennion BJ, Daggett V.

Clin Chem. 2002 Dec; 12(48)2105-14

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding.

Day R, Bennion BJ, Ham S, Daggett V.

J Mol Biol. 2002 Sep 6; 1(322)189-203

Stabilization of globular proteins via introduction of temperature-activated elastin-based switches.

Li B, Alonso DO, Daggett V.

Structure. 2002 Jul; 7(10)989-98

Molecular dynamics simulations of the protein unfolding/folding reaction.

Daggett V

Acc Chem Res. 2002 Jun; 6(35)422-9

Probing the energy landscape of protein folding/unfolding transition states.

De Jong D, Riley R, Alonso DO, Daggett V.

J Mol Biol. 2002 May 24; 1(319)229-42

Protein folding and unfolding at atomic resolution.

Fersht AR, Daggett V.

Cell. 2002 Feb 22; 4(108)573-82

The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea.

Zou Q, Bennion BJ, Daggett V, Murphy KP.

J Am Chem Soc. 2002 Feb 20; 7(124)1192-202

Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.

Kazmirski SL, Isaacson RL, An C, Buckle A, Johnson CM, Daggett V, Fersht AR.

Nat Struct Biol. 2002 Feb; 2(9)112-6

Courses

Introduction to Structural Biology

Research Summary

My lab uses both experimental and computational simulation methods to explore protein dynamics, unfolding and the effects of disease-associated mutations. Many of our current projects focus on amyloid diseases.