CI2Daggett Research Group | Publications

University of Washington - College of Engineering - School of Medicine - Department of Bioengineering
  • Bleem, A., Daggett, V. Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering. Biotechnology and Bioengineering , 2016, in press. [DOI]
  • Bromley, D., Bauer, M., Fersht, A.R., Daggett, V. An in silico algorithm for identifying stabilizing pockets in proteins: Test case the Y220C mutant of the p53 tumor suppressor protein. Protein Engineering Design and Selection 29 : 377-390, 2016. [DOI]
  • Childers, M.C., Towse, C.-L., Daggett, V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: Tools for protein design. Protein Engineering Design and Selection 29 : 271-280, 2016. [DOI]
  • Kellock, J., Hopping, G., Caughey, B., Daggett, V. Peptides composed of alternating L- and D-amino acids inhibit amyloidogenesis in three distinct amyloid systems independent of sequence. Journal of Molecular Biology 428 : 2317-2328, 2016. [DOI]
  • Towse, C.-L., Vymetal, J., Vondrasek, J., Daggett, V. Insights into unfolded proteins from the intrinsic φ/ψ propensities of the AAXAA host-guest series. Biophysical Journal 110 : 348-361, 2016. [DOI]
  • Towse, C.-L., Rysavy, S.J., Vulovic, I.M., Daggett, V. New Dynamic Rotamer Libraries: Data-Driven Analysis of Side Chain Conformational Propensities. Structure 24 : 187-199, 2016. [DOI]
  • Towse, C.-L., Daggett, V. Modeling protein folding pathways. Reviews in Computational Chemistry 28 : 87-135, 2015.
  • Towse, C.-L., Hopping, G., Vulovic, I., Daggett, V. Nature versus design: The conformational propensities of D-amino acids and the importance of side chain chirality. Protein Engineering, Design, and Selection 27 : 447-455, 2014. [DOI]
  • Rysavy, S.J., Beck, D.A.C., Daggett, V. Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction. Protein Science 23 : 1584-1595, 2014. [DOI]
  • Hopping, G., Kellock, J., Barnwal, R.P., Law, P., Bryers, J.D., Varani, G., Caughey, B., Daggett, V. Designed α-Sheet Peptides Inhibit Amyloid Formation by Targeting Toxic Oligomers. eLIFE 3: e01681, 2014. [DOI]
  • Merkley, E.D., Rysavy, S., Kahraman, A., Hafen, R.P., Daggett, V., Adkins, J.N. Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Science 23: 747-759, 2014. [DOI]
  • Cheng, C.J., Daggett, V. Different misfolding mechanisms converge on common conformational changes: Human prion protein pathogenic mutants Y218N and E196K. Prion 8: 1-11, 2014. [DOI][Cover Image]
  • Cheng, C.J., Daggett, V. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH. Biomolecules 4: 181-201, 2014. [DOI]
  • Rysavy, S.J., Bromley, D., Daggett, V. DIVE: A graph-based visual analytics framework for big data. IEEE Computer Graphics and Applications: Visual Analytics for Biological Data , March/April: 26-37, 2014. [DOI]
  • Chen, W., van der Kamp, M.W., Daggett, V. Structural and dynamic properties of the human prion protein. Biophysical Journal 106: 1152-1163, 2014. [DOI]
  • Bromley, D., Rysavy, S.J., Su, R., Toofanny, R.D., Schmidlin, T., Daggett, V. DIVE: A data intensive visualization engine. Bioinformatics , 30: 593-595, 2014. [DOI]
  • Hopping, G., Kellock, J., Caughey, B., Daggett, V. The designed trpzip-3 beta-hairpin inhibits amyloid formation in two different amyloid systems. ACS Medicinal Chemistry Letters , 4: 824-828, 2013. [DOI]
  • Bromley, D., Anderson, P.C., Daggett, V. Structural consequences of mutations to the alpha-tocopherol transfer protein associated with the neurodegenerative diseae ataxia with vitamin E deficiency. Biochemistry , 52: 4264-4273, 2013. [DOI]
  • Schmidlin, T., Ploeger, K., Jonsson, A.L. Daggett, V. Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation. Protein Engineering, Design and Selection, 26: 503-513, 2013. [DOI]
  • Wang, D., McCully, M.E., Luo, Z., McMichael, J., Tu, A., Daggett, V., Regnier, M. Structural and function consequences of cardiac tropinin C L57Q and I61Q Ca2+-desensitizing variants. Archives of Biochemistry and Biophysics, 535: 68-75, 2013. [DOI]
  • Rizzuti, B., Daggett V. Using simulations to provide the framework for experimental protein folding studies. Archives of Biochemistry and Biophysics, 531: 128-135, 2013. [DOI]
  • McCully M.E., Beck D.A.C., Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Engineering, Design & Selection, 26:35-45, 2013. [DOI]
  • Towse C.L., Daggett V. When a domain is not a domain, and why it is important to properly filter proteins in databases. BioEssays, 34:1060-1069, 2012. [DOI] [Cover Image]
  • McCully M.E., Beck D.A.C., Daggett V. Multimolecule test-tube simulations of protein unfolding and aggregation. Proceedings of the National Academy of Sciences USA, 109:17851-17856 2012. [DOI]
  • Wang D., Robertson I.M., Li M.X., McCully M.E., Crane M.L., Luo Z., Tu A.Y., Daggett V., Sykes B.D., Regnier M. Structural and functional consequences of the cardiac troponin C L48Q Ca2+-sensitizing mutation. Biochemistry, 51: 4473-4487, 2012. [DOI]
  • Benson N.C. and Daggett V. A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations. Journal of Physical Chemistry B, 116:8722-8731, 2012. [DOI]
  • McCully M.E. and Daggett V. Folding and Dynamics of Engineered Proteins. In Protein Engineering Handbook, vol. III. Eds. Lutz S and Bornscheuer UT. Wiley-VCH, Weinheim. Chapter 5: Folding and Dynamics of Engineered Proteins, 89-114, 2012.
  • Benson N.C. and Daggett V. Wavelet Analysis of Protein Motion. International Journal of Wavelets, Multiresolution and Information Processing, 10:1250040, 2012. [DOI]
  • Towse C.L. and Daggett V. Molecular Dynamics Simulations. In Encyclopedia of Biophysics, Springer, In Press, 2012.
  • Scouras A.D. and Daggett V. Disruption of the X-Loop Turn of the Prion Protein Linked to Scrapie Resistance. Protein Engineering Design & Selection 25: 243-249, 2012. [DOI] [Cover Image]
  • Benson N.C. and Daggett V. A Chemical Group Graph Representation for Efficient High-Throughput Analysis of Atomistic Protein Simulations. Journal of Bioinformatics and Computational Biology 10:1250008-1250024, 2012. [DOI]
  • Toofanny R.D. and Daggett V. Understanding protein unfolding from molecular simulations. WIREs Computational Molecular Science 2:405-423, 2012. [DOI]
  • Merkley E.D., Daggett V., and Parson W.W. A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8. Proteins: Structure, Function, and Bioinformatics 80:546-555, 2012. [DOI]
  • Simms A.M. and Daggett V. Protein simulation data in the relational model. The Journal of Supercomputing, 62:150-173, 2012. [DOI]
  • Morrone A., Giri R., Toofanny R.D., Travaglini-Allocatelli C., Brunori M., Daggett V., and Gianni S. GB1 Is Not a Two-State Folder: Identification and Characterization of an On-Pathway Intermediate. Biophysical Journal 101:2053-2060, 2011. [DOI]
  • Jonsson A.L. and Daggett V. The Effect of Context on the Folding of β-Hairpins. Journal of Structural Biology 176:143-150, 2011. [DOI]
  • Toofanny R.D., Simms A.M., Beck D.A.C., and Daggett V. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics 12:334, 2011. [DOI]
  • Calhoun S. and Daggett V. Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain. Biochemistry 50:5345-5353, 2011. [DOI]
  • Van der Kamp M.W. and Daggett V. Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations. Topics in Current Chemistry 305:169-197, 2011. [DOI]
  • Banachewicz W., Religa T.L., Schaeffer R.D., Daggett V., and Fersht A.R. Malleability of folding intermediates in the homeodomain superfamily. Proceedings of the National Academy of Sciences USA 108:5596-5601, 2011. [DOI]
  • Dar T.A., Schaeffer R.D., Daggett V., and Bowler B.E. Manifestations of Native Topology in the Denatured State Ensemble of Rhodopseudomonas palustris Cytochrome c′. Biochemistry 50:1029-1041, 2011. [DOI]
  • Scouras A.D. and Daggett V. The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Science 20:341-352, 2011. [DOI]
  • Morrone A., McCully M.E., Bryan P.N., Brunori M., Daggett V., Gianni S., Travaglini-Allocatelli C. The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function. The Journal of Biological Chemistry 286:3863-3872, 2011. [DOI]
  • Schaeffer R.D, Jonsson A.L., Simms A.M., and Daggett V. Generation of a Consensus Protein Domain Dictionary. Bioinformatics 27:46-54, 2011. [DOI]
  • Schaeffer R.D. and Daggett V. Protein folds and protein folding. Protein Engineering Design & Selection 24:11-19, 2011. [DOI]
  • Jonsson A.L., Schaeffer R.D., van der Kamp M.W., and Daggett V. Dynameomics: protein dynamics and unfolding across fold space. Biomolecular Concepts 1:335-344, 2010. [DOI]
  • Chen W., Van der Kamp M.W., and Daggett V. Diverse Effects on the Native β-Sheet of the Human Prion Protein Due to Disease-Associated Mutations. Biochemistry 49:9874-9881, 2010. [DOI]
  • Van der Kamp M.W. and Daggett V. Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding. Journal of Molecular Biology 404:732-748, 2010. [DOI][HTML]
  • Van der Kamp M.W. and Daggett V. The influence of pH on the human prion protein: Insights into the early steps of misfolding. Biophysical Journal 99:2289-2298, 2010. [DOI]
  • McCully M.E., Beck D.A.C., Fersht A.R., and Daggett V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate. Biophysical Journal 99:1628-1636, 2010. [DOI]
  • Toofanny R.D., Jonsson A.L., and Daggett V. A Comprehensive Multidimensional-Embedded, One-Dimensional Reaction Coordinate for Protein Unfolding/Folding. Biophysical Journal 98:2671-2681, 2010. [DOI]
  • Rutherford K. and Daggett V. Polymorphisms and disease: hotspots of inactivation in methyltransferases. Trends in Biochemical Sciences 35:531-538, 2010. [DOI]
  • Van der Kamp M.W., Schaeffer R.D., Jonsson A.L., Scouras A.D., Simms A.M., Toofanny R.D., Benson N.C., Anderson P.C., Merkley E.D., Rysavy S., Bromley D., Beck D.A.C., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 18:423-435, 2010. [DOI] [Cover Image]
  • Merkley E.D., Parson W.W., and Daggett V. Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. Protein Engineering Design & Selection 23:327-336, 2010. [DOI] [Color Figures]
  • Law P.B. and Daggett V. The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures. Protein Engineering Design & Selection 23: 27-33, 2010. [DOI]
  • Key J., Scheuermann T.H., Anderson P.C., Daggett V., and Gardner K.H. Principles of Ligand Binding within a Completely Buried Cavity in HIF2α PAS-B. Journal of the American Chemical Society 131: 17647-17654, 2009. [DOI] [HTML]
  • Jonsson A.L., Scott K.A., and Daggett V. Dynameomics: A consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal 97: 2958-2966, 2009. [DOI]
  • Rutherford K. and Daggett V. The V119I Polymorphism in Protein L-Isoaspartate O-Methyltransferase Alters the Substrate-Binding Interface. Protein Engineering Design & Selection 22: 713-721, 2009. [DOI] [Color Figures]
  • Daggett V. Shedding light on amyloidosis with protein engineering. Protein Engineering Design & Selection 22: 445, 2009. [DOI]
  • Van der Kamp M.W. and Daggett V. The consequences of pathogenic mutations to the human prion protein. Protein Engineering Design & Selection 22: 461-468, 2009. [DOI] [Color Figures]
  • Schmidlin T., Kennedy B., and Daggett V. Structural changes to monomeric CuZn Superoxide Dismutase caused by the familial Amyotrophic Lateral Sclerosis mutation A4V. Biophysical Journal 97: 1709-1718, 2009. [DOI]
  • Anderson P.C. and Daggett V. The R46Q, R131Q and R154H Polymorphs of Human DNA Glycosylase/β-Lyase hOgg1 Severely Distort the Active Site and DNA Recognition Site but do not Cause Unfolding. Journal of the American Chemical Society 131: 9506-9515, 2009. [DOI]
  • Rutherford K. and Daggett V. A Hotspot of Inactivation: The A22S and V108M Polymorphisms Individually Destabilize the Active Site Structure of Catechol O-Methyltransferase. Biochemistry 48: 6450-6460, 2009. [DOI]
  • Daggett V. and Fersht A.R. Protein folding and binding: moving into unchartered territory. Current Opinion in Structural Biology 19: 1-2, 2009. [DOI]
  • DeMarco M.L. and Daggett V. Characterization of cell-surface prion protein relative to its recombinant analogue: Insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. Journal of Neurochemistry 109: 60-73, 2009. [DOI]
  • Benson N. and Daggett V. Dynameomics: Large-Scale Assessment of Native Protein Flexibility. Protein Science 17: 2038-2050, 2008.[DOI]
  • Anderson P.C. and Daggett V. Molecular Basis for the Structural Instability of Human DJ-1 Induced by the L166P Mutation Associated with Parkinson's Disease. Biochemistry 47: 9380-9393, 2008. [DOI]
  • Beck D.A.C., Alonso D.O.V., Inoyama D., and Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proceedings of the National Academy of Sciences USA 105: 12259-12264, 2008. [DOI]
  • Rutherford K., Alphandéry E., McMillan A., Daggett V., and Parson W.W. The V108M mutation decreases the structural stability of catechol O-methyltransferase. Biochimica et Biophysica Acta 1784: 1098-1105, 2008. [DOI]
  • McCully M.E., Beck D.A.C., and Daggett V. Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain. Biochemistry 47: 7079-7089, 2008. [DOI]
  • Smolin N., Li B., Beck D.A.C., and Daggett V. Side-chain dynamics are critical for water permeation through aquaporin-1. Biophysical Journal 95: 1089-1098, 2008. [DOI]
  • Rutherford K. and Daggett V. Four Human Thiopurine S-Methyltransferase Alleles Severely Affect Protein Structure and Dynamics. Journal of Molecular Biology 379: 803-814, 2008. [DOI] [HTML]
  • Kehl C., Simms A.M., Toofanny R.D., and Daggett V. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. Protein Engineering Design & Selection 21: 379-386, 2008. [DOI]
  • Simms A.M., Toofanny R.D., Kehl C., Benson N.C., and Daggett V. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. Protein Engineering Design & Selection 21: 369-377, 2008. [DOI]
  • Beck D.A.C., Jonsson A.L., Schaeffer R.D., Scott K.A., Day R., Toofanny R.D., Alonso D.O.V., and Daggett V. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering Design & Selection 21: 353-368, 2008. [DOI]
  • Scouras A.D. and Daggett V. Species variation in PrPSc protofibril models. Journal of Materials Science 43: 3625-3637, 2008. [DOI]
  • Smolin N. and Daggett V. Formation of ice-like water structure on the surface of an antifreeze protein. Journal of Physical Chemistry B 112: 6193-6206, 2008. [DOI]
  • Steward R.E., Armen R.S., and Daggett V. Different disease-causing mutations in transthyretin trigger the same conformational conversion. Protein Engineering, Design & Selection 21: 187-195, 2008. [DOI]
  • Schaeffer R.D., Fersht A.R., and Daggett V. Combining experiment and simulation in protein folding: closing the gap for small model systems. Current Opinion in Structural Biology 18: 4-9, 2008. [DOI]
  • Rutherford K., Parson W.W., and Daggett V. The Histamine N-Methyltransferase T105I Polymorphism Affects Active Site Structure and Dynamics. Biochemistry 47: 893-901, 2008. [DOI]
  • Merkley E.D., Bernard B., and Daggett V. Conformational Changes below the Tm: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A. Biochemistry 47: 880-892, 2008. [DOI]
  • Beck D.A.C. and Daggett V. A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent Pfold-Like Calculations. Biophysical Journal 93: 3382-3391, 2007. [DOI]
  • Beck D.A.C., Bennion B.J., Alonso D.O.V., and Daggett V. Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics. Methods in Enzymology 428: 373-396, 2007. [DOI]
  • Sharpe T., Jonsson A.L., Rutherford T.J., Daggett V., and Fersht A.R. The role of the turn in β-hairpin formation during WW domain folding. Protein Science 16: 2233-2239, 2007. [DOI]
  • Beck D.A.C., White G.W.N., and Daggett V. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Journal of Structural Biology 157: 514-523, 2007. [DOI]
  • Fersht A.R. and Daggett V. Folding and binding: implementing the game plan. Current Opinion in Structural Biology 17: 1-2, 2007. [DOI]
  • Day R. and Daggett V. Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding. Journal of Molecular Biology 366: 677-686, 2007. [DOI] [HTML]
  • Scott K.A. and Daggett V. Folding mechanisms of proteins with high sequence identity but different folds. Biochemistry 46: 1545-1556, 2007. [DOI]
  • Scott K.A., Alonso D.O.V., Sato S., Fersht A.R., and Daggett V. Conformational Entropy of Alanine versus Glycine in Protein Denatured States. Proceedings of the National Academy of Sciences USA 104: 2661-2666, 2007. [DOI]
  • DeMarco M.L. and Daggett V. Molecular Mechanism for Low pH-Triggered Misfolding of the Human Prion Protein. Biochemistry46: 3045-3054, 2007. [DOI]
  • DeMarco M.L., Silveira J., Caughey B., and Daggett V. Structural Properties of Prion Protein Protofibrils and Fibrils: An Experimental Assessment of Atomic Models. Biochemistry 45: 15573-15582, 2006. [DOI]
  • Petrovich M., Jonsson A.L., Ferguson N., Daggett V., and Fersht A.R. Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation. Journal of Molecular Biology 360: 865-881, 2006. [DOI] [HTML]
  • Daggett V. α-Sheet: The toxic conformer in amyloid diseases? Accounts of Chemical Research 39: 594-602, 2006. [DOI]
  • Daggett V. Protein Folding-Simulation. Chemical Reviews 106: 1898-1916, 2006. [DOI]
  • Scott K.A., Randles L.G., Moran S.J., Daggett V., and Clarke J. The Folding Pathway of Spectrin R17 from Experiment and Simulations: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment. Journal of Molecular Biology 359: 159-173, 2006. [DOI] [HTML]
  • Scott K.A., Alonso D.O.V., Pan Y., and Daggett V. Importance of Context in Protein Folding: Secondary Structural Propensities versus Tertiary Contact-Assisted Secondary Structure Formation. Biochemistry 45: 4153-4163, 2006. [DOI]
  • Rutherford K., Bennion B.J., Parson W.W., and Daggett V. The 108M Polymorph of Human Catechol O-Methyltransferase Is Prone to Deformation at Physiological Temperatures. Biochemistry 45: 2178-2188, 2006. [DOI]
  • Armen R.S. and Daggett V. Characterization of Two Distinct β2-Microglobulin Unfolding Intermediates that May Lead to Amyloid Fibrils of Different Morphology. Biochemistry 44: 16098-16107, 2005. [DOI]
  • Armen R.S., Bernard B.M., Day R, Alonso D.O.V., and Daggett V. Characterization of a possible amyloidogenic precursor in glutamine-repeat diseases. Proceedings of the National Academy of Sciences USA 102: 13433-13438, 2005. [DOI]
  • Day R. and Daggett V. Ensemble versus single-molecule protein unfolding. Proceedings of the National Academy of Sciences USA 102: 13445-13450, 2005. [DOI]
  • DeMarco M.L. and Daggett V. Local environmental effects on the structure of the prion protein. Comptes Rendus Biologies 238: 847-862, 2005. [DOI]
  • Beck D.A.C., Armen R.S., and Daggett V. Cutoff size need not strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 44: 609-616, 2005. [DOI]
  • Esposito L. and Daggett V. Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations. Biochemistry 44: 3358-3368, 2005. [DOI]
  • Jemth P., Day R., Gianni S., Khan F., Allen M., Daggett V., and Fersht A.R. The structure of the major transition state for folding of an FF domain from experiment and simulation. Journal of Molecular Biology 350: 363-378, 2005. [DOI] [HTML]
  • Ferguson N., Day R., Johnson C.M., Allen M.D., Daggett V., and Fersht A.R. Simulation and experiment at high temperatures: Ultrafast folding of a thermophilic protein by nucleation-condensation. Journal of Molecular Biology 347: 855-870, 2005. [DOI] [HTML]
  • White G.W.N., Gianni S., Grossman J.G., Jemth P., Fersht A.R., and Daggett V. Simulation and Experiment Conspire to reveal Cryptic Intermediates and the Slide from the Nucleation-Condensation to Framework Mechanism of Folding. Journal of Molecular Biology 350: 757-775, 2005. [DOI] [HTML]
  • Day R. and Daggett v. Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent. Protein Science 14: 1242-1252, 2005. [DOI]
  • Armen R.S., DeMarco M.L., Alonso D.O.V., and Daggett V. Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease. Proceedings of the National Academy of Sciences USA 101: 11622-11627, 2004. [DOI]
  • Armen R.S., Alonso D.O.V., and Daggett V. Anatomy of an amyloidogenic intermediate: Conversion of β-sheet to α-pleated sheet structure in transthyretin at acidic pH. Structure 12: 1847-1863, 2004. [DOI]
  • Rizzuti B., Daggett V., Guzzi R., and Sportelli L. The early steps in the unfolding of azurin. Biochemistry 43: 15604-15609. [DOI]
  • Bennion B.J., DeMarco M.L., and Daggett V. Preventing misfolding of the prion protein by Trimethylamine N-oxide. Biochemistry 41, 12955-12963, 2004. [DOI]
  • DeMarco M.L., Alonso D.O.V., and Daggett V. Diffusing and colliding: The atomic level folding/unfolding pathway of a small helical protein. Journal of Molecular Biology 341: 1109-1124, 2004. [DOI] [HTML]
  • Beck D.A.C. and Daggett V. Methods for Molecular Dynamics Simulations of Protein Folding/Unfolding in Solution. Methods 34: 112-120, 2004. [DOI]
  • Bennion B.J. and Daggett V. Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: A chemical chaperone at atomic resolution. Proceedings of the National Academy of Sciences USA 101: 6433-6438, 2004. [DOI]
  • Sato S., Religa T., Daggett V., and Fersht A.R. Testing protein-folding simulations by experiment: B domain of protein A. Proceedings of the National Academy of Sciences USA 101, 6952-6956, 2004. [DOI]
  • Jemth P., Gianni S., Day R., Li B., Johnson C.M., Daggett V., and Fersht A.R. Demonstration of a low energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proceedings of the National Academy of Sciences USA 101: 6450-6455, 2004. [DOI]
  • DeMarco M.L. and Daggett V. From Conversion to Aggregation: Protofibril Formation of the Prion Protein. Proceedings of the National Academy of Sciences USA 101: 2293-2298, 2004. [DOI]
  • Zhu Y., Alonso D.O.V., Maki K., Huang C.-Y., Lahr S.J., Daggett V., Roder H., DeGrado W.F., and Gai F. Ultrafast folding of α3D, A de novo designed three-helix bundle protein. Proceedings of the National Academy of Sciences USA 100:15486-15491, 2003. [DOI]
  • Gianni S., Guydosh N.R., Khan F., Caldas T.D. Mayor U., White G.W.N., DeMarco M.L., Daggett V., and Fersht A.R. Unifying features in protein folding mechanisms. Proceedings of the National Academy of Sciences USA 100: 13286-13291, 2003. [DOI]
  • Day R., Beck D.A.C., Armen R. and Daggett V. A Consensus View of Fold Space: Combining SCOP, CATH, and the Dali Domain Dictionary. Protein Science 12: 2150-2160, 2003. [DOI]
  • Daggett V. and Fersht A.R. The present view of the mechanism of protein folding. Nature Reviews: Molecular Cell Biology 4: 497-502, 2003. [DOI]
  • Mayor M., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M.V., Alonso D.O.V., Daggett V. and Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421: 863-867, 2003. [DOI]
  • Day R. and Daggett V. All-atom simulations of protein folding and unfolding. In "Protein Simulations," V. Daggett, Editor. Advances in Protein Chemistry 66: 373-403, 2003. [DOI]
  • Beck D.A.C., Alonso D.O.V., and Daggett V. A microscopic view of peptide and protein solvation. Biophysical Chemistry 100: 221-237, 2003. [DOI]
  • Armen R., Alonso D.O.V., and Daggett V. The Role of α-, 310-, and π-helix in Helix → Coil Transitions. Protein Science 12: 1145-1157, 2003. [DOI]
  • Bennion B.J. and Daggett V. The molecular basis for the chemical denaturation of proteins by urea. Proceedings of the National Academy of Sciences USA 100: 5142-5147, 2003. [DOI]
  • Walsh S.T.R., Cheng R.P., Alonso D.O.V., Daggett V., Vanderkooi J., and DeGrado W.F. The Hydration of Amides in Helices; A Comprehensive Picture from Molecular Dynamics, IR and NMR. Protein Science 12: 520-531, 2003. [DOI] [HTML]
  • Li B. and Daggett V. The Molecular Basis for the Extensibility of Elastin. Journal of Muscle Research and Cell Motility 23: 561-573, 2003. [DOI]
  • Daggett V. and Fersht A.R. Is There a Unifying Mechanism for Protein Folding? Trends in Biochemical Sciences 28: 18-25, 2003. [DOI]
  • Li B. and Daggett V. The molecular basis for temperature- and pH-induced conformational transitions in elastin-based peptides. Biopolymers 68: 121-129. [DOI]
  • Bennion B.J. and Daggett V. Protein Conformation and Diagnostic Tests: The Prion Protein. Clinical Chemistry 48: 2105-2114, 2002. [PDF] [HTML]
  • Day R., Bennion B., Ham S., and Daggett V. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. Journal of Molecular Biology 322: 189-203, 2002. [DOI] [HTML]
  • Li B., Alonso D.O.V., and Daggett V. Stabilization of globular proteins via introduction of temperature-activated elastin-based switches. Structure 10: 989-998, 2002. [DOI]
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  • Zou Q., Bennion B.J., Daggett V., and Murphy K.P. The Molecular Mechanism of Stabilization of Proteins by TMAO and its Ability to Counteract the Effects of Urea. Journal of the American Chemical Society 125: 1192-1202, 2002. [DOI]
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  • Li B., Alonso D.O.V., Bennion B.J., and Daggett V. Hydrophobic Hydration is an Important Source of Elasticity in Elastin-Based Biopolymers. Journal of the American Chemical Society 123: 11991-11998, 2001. [DOI]
  • Ferguson N., Pires J.R., Toepert F., Johnson C.J., Pan Y.P., Volkmer-Engert R., Schneider-Mergener J., Daggett V., Oschkinat H., and Fersht A.R. Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions. Proceedings of the National Academy of Sciences USA 98: 13008-13013, 2001. [DOI]
  • Best R.B., Li B., Steward A., Daggett V., and Clarke J. Can non-mechanical proteins withstand force? Stretching barnase by AFM and MD simulation. Biophysical Journal 81: 2344-2356, 2001. [DOI]
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  • Kazmirski S.L., Wong K.B., Freund S.M.V., Tan Y.J., Fersht A.R., and Daggett V. Protein Folding from a Highly Disordered Denatured State: The Folding Pathway of Chymotrypsin Inhibitor 2 at Atomic Resolution. Proceedings of the National Academy of Sciences USA 98: 4349-4354, 2001. [DOI]
  • Pan Y. and Daggett V. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. Biochemistry 40: 2723-2731, 2001. [DOI]
  • Li B., Alonso D.O.V. and Daggett V. The Molecular Basis for the Inverse Temperature Transition of Elastin. Journal of Molecular Biology 305: 581-592, 2001. [DOI] [HTML]
  • Clarke J., Hounslow A.M., Bond C.J., Fersht A.R. and Daggett V. The Effect of Disulfide Bonds on the Denatured State of Barnase. Protein Science 9: 2394-2404, 2000. [DOI]
  • Mayor U., Johnson C.M., Daggett V., and Fersht A.R. Protein Folding and Unfolding in Microseconds to Nanoseconds by Experiment and Simulation. Proceedings of the National Academy of Sciences USA 97: 13518-13522, 2000. [DOI]
  • Hom K., Wolfe G., Ma Q.-F., Zhang H., Storch E.M., Daggett V., Basus V.J., Waskell L. NMR Studies of the Association of Cytochrome b5 with Cytochrome c: Biochemistry 39, 14025-14039, 2000. [DOI]
  • Wong K., Clarke J., Bond C.J., Neira J.L., Freund S.M.V., Fersht A.R., and Daggett V. Towards Complete Characterization of the Structural and Dynamic Properties of the Denatured State of Barnase and the Role of Residual Structure in Folding. Journal of Molecular Biology 296: 1257-1285, 2000. [DOI] [HTML]
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  • DeArmond S., Qiu Y., Sanchez H., Spilman P.R., Ninchak-Casey A., Alonso, D.O.V., and Daggett V. PrPC Glycoform Heterogeneity as a Function of Brain Region: Implications for Selective Targeting of Neurons by Prion Strains. Journal of Neuropathology & Experimental Neurology 58: 1000-1009, 1999. [HTML] [PDF]
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  • Kazmirski S., Li A., and Daggett V. Analysis Methods for Comparison of Molecular Dynamics Trajectories: Applications to Protein Unfolding Pathways and Denatured Ensembles. Journal of Molecular Biology 290: 283-304, 1999. [DOI] [HTML]
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  • Storch E.M., Grinstead J.S., Campbell A.P., Daggett V., and Atkins W.M. Engineering Out Motion: A Surface Disulfide Bond Alters the Mobility of Trp 22 in Cytochrome b5 as Probed by Time-Resolved Fluorescence and 1H-NMR Experiments. Biochemistry 38: 5065-5075, 1999. [DOI]
  • Ladurner A.G., Itzhaki L.S., Daggett V., and Fersht A.R. Synergy Between Simulation and Experiment in Describing the Energy Landscape of Protein Folding. Proceedings of the National Academy of Sciences USA 95: 8473-8478, 1998. [PDF] [HTML]
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  • Laidig K.E., Gainer J.L., and Daggett V. Altering Diffusivity in Biological Solutions Through Modification of Solution Structure and Dynamics. Journal of the American Chemical Society 120: 9394-9395, 1998. [DOI]
  • Kazmirski S. and Daggett V. Non-Native Interactions in Protein Folding Intermediates: Molecular Dynamics Simulation of Hen Lysozyme. Journal of Molecular Biology 284: 793-806, 1998. [DOI] [HTML]
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  • Storch E.A. and Daggett V. Structural Consequences of Heme Removal: Molecular Dynamics Simulations of Rat and Bovine Apocytochrome b5. Biochemistry 35: 11596-11604, 1996. [DOI]
  • Laidig K.E. and Daggett V. Molecular Dynamics Simulations of Apocytochrome b562 – The Highly Ordered Limit of Molten Globules. Folding & Design 1: 335-346, 1996. [DOI]
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  • Laidig K.E. and Daggett V. Testing the Modified Hydration-Shell Hydrogen-Bond Model of Hydrophobic Effects using Molecular Dynamics Simulation. Journal of Physical Chemistry 100: 5616-5619, 1996. [DOI]
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  • Alonso D.O.V. and V. Daggett V. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Water. Journal of Molecular Biology 247: 501-520, 1995. [DOI] [HTML]
  • Kazmirski S., Alonso D.O.V, Cohen F.E., Prusiner S., and Daggett V. Theoretical Studies of Sequence Effects on the Conformational Properties of a Fragment of the Prion Protein: Implications for Scrapie Formation. Chemistry & Biology 2: 305-315, 1995. [DOI]
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  • Kirshenbaum K. and Daggett V. pH-Dependent Conformations of the Amyloid β(1-28) Peptide Fragment Explored Using Molecular Dynamics. Biochemistry 34: 7629-7639, 1995. [DOI]
  • Kirshenbaum K. and Daggett V. Sequence Effects on the Conformational Properties of the Amyloid β(1-28) Peptide: Testing a Proposed Mechanism for the α → β Transition. Biochemistry 34: 7640-7647, 1995. [DOI]
  • Levitt M., Hirshberg M., Sharon R., and Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Computer Physics Communications 91: 215-231, 1995. [DOI]
  • Li A. and Daggett V. Characterization of the Transition State of Protein Unfolding Using Molecular Dynamics: Chymotrypsin Inhibitor 2. Proceedings of the National Academy of Sciences USA 91: 10430-10434, 1994. [PDF] [HTML]
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