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Joan-Emma Shea - Publications

Affiliations: 
Chemistry University of California, Santa Barbara, Santa Barbara, CA, United States 
Area:
Physical Chemistry, Theory & Computation, Biochemistry & Biophysics, Biomedical Sciences, Biology-Inspired Chemistry & Physics, Structural Chemistry, Spectroscopy & Advanced Analysis
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134 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Vigers MP, Lobo S, Najafi S, Dubose A, Tsay K, Ganguly P, Longhini AP, Jin Y, Buratto SK, Kosik KS, Shell MS, Shea JE, Han S. Tau P301L mutation promotes core 4R tauopathy fibril fold through near-surface water structuring and conformational rearrangement. Biorxiv : the Preprint Server For Biology. PMID 38077065 DOI: 10.1101/2023.11.28.568818  0.721
2023 Arsiccio A, Liu X, Ganguly P, Buratto SK, Bowers MT, Shea JE. Effect of Cosolutes on the Aggregation of a Tau Fragment: A Combined Experimental and Simulation Approach. The Journal of Physical Chemistry. B. 127: 4022-4031. PMID 37129599 DOI: 10.1021/acs.jpcb.3c00433  0.731
2022 Najafi S, McCarty J, Delaney KT, Fredrickson GH, Shea JE. Field-Theoretic Simulation Method to Study the Liquid-Liquid Phase Separation of Polymers. Methods in Molecular Biology (Clifton, N.J.). 2563: 37-49. PMID 36227467 DOI: 10.1007/978-1-0716-2663-4_2  0.654
2022 Ganguly P, Bubák D, Polák J, Fagan P, Dračínský M, van der Vegt NFA, Heyda J, Shea JE. Cosolvent Exclusion Drives Protein Stability in Trimethylamine -Oxide and Betaine Solutions. The Journal of Physical Chemistry Letters. 7980-7986. PMID 35984361 DOI: 10.1021/acs.jpclett.2c01692  0.714
2022 Liu X, Ganguly P, Jin Y, Jhatro MJ, Shea JE, Buratto SK, Bowers MT. Tachykinin Neuropeptides and Amyloid β (25-35) Assembly: Friend or Foe? Journal of the American Chemical Society. PMID 35917596 DOI: 10.1021/jacs.2c03845  0.72
2022 Arsiccio A, Ganguly P, Shea JE. A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. The Journal of Physical Chemistry. B. PMID 35679169 DOI: 10.1021/acs.jpcb.2c00889  0.723
2021 Laos V, Bishop D, Ganguly P, Schonfeld G, Trapp E, Cantrell KL, Buratto SK, Shea JE, Bowers MT. Catalytic Cross Talk between Key Peptide Fragments That Couple Alzheimer's Disease with Amyotrophic Lateral Sclerosis. Journal of the American Chemical Society. PMID 33621087 DOI: 10.1021/jacs.0c12729  0.742
2021 Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, et al. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chemical Reviews. PMID 33543942 DOI: 10.1021/acs.chemrev.0c01122  0.776
2020 Zhang X, Vigers M, McCarty J, Rauch JN, Fredrickson GH, Wilson MZ, Shea JE, Han S, Kosik KS. The proline-rich domain promotes Tau liquid-liquid phase separation in cells. The Journal of Cell Biology. 219. PMID 32997736 DOI: 10.1083/jcb.202006054  0.679
2020 Peter EK, Shea JE, Schug A. CORE-MD, a path correlated molecular dynamics simulation method. The Journal of Chemical Physics. 153: 084114. PMID 32872878 DOI: 10.1063/5.0015398  0.35
2020 Arya S, Ganguly P, Arsiccio A, Claud SL, Trapp B, Schonfeld GE, Liu X, Lazar Cantrell KL, Shea JE, Bowers MT. Terminal capping of an amyloidogenic Tau fragment modulates its fibrillation propensity. The Journal of Physical Chemistry. B. PMID 32816481 DOI: 10.1021/Acs.Jpcb.0C05768  0.759
2020 Charest N, Tro M, Bowers MT, Shea JE. Latent Models of Molecular Dynamics Data: Automatic Order Parameter Generation for Peptide Fibrillization. The Journal of Physical Chemistry. B. PMID 32790375 DOI: 10.1021/Acs.Jpcb.0C05763  0.344
2020 Arsiccio A, Ganguly P, La Cortiglia L, Shea JE, Pisano R. The ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein-Osmolyte Interaction. The Journal of Physical Chemistry. B. PMID 32790371 DOI: 10.1021/Acs.Jpcb.0C05345  0.724
2020 Ganguly P, Polak J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea-TMAO Solutions. The Journal of Physical Chemistry. B. PMID 32495623 DOI: 10.1021/Acs.Jpcb.0C04357  0.721
2020 Arsiccio A, McCarty J, Pisano R, Shea JE. Heightened Cold-Denaturation of Proteins at the Ice-Water Interface. Journal of the American Chemical Society. PMID 32122128 DOI: 10.1021/Jacs.9B13454  0.711
2020 Wonderly WR, Cristiani TR, Cunha KC, Degen GD, Shea J, Waite JH. Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein Macromolecules. 53: 6767-6779. DOI: 10.1021/Acs.Macromol.9B02715  0.37
2019 Ganguly P, Shea JE. Distinct and Non-additive Effects of Urea and Guanidinium Chloride on Peptide-Solvation. The Journal of Physical Chemistry Letters. PMID 31721587 DOI: 10.1021/Acs.Jpclett.9B03004  0.746
2019 Levine ZA, Teranishi K, Okada AK, Langen R, Shea JE. The Mitochondrial Peptide Humanin Targets, but does not Denature Amyloid Oligomers in Type II Diabetes. Journal of the American Chemical Society. PMID 31456396 DOI: 10.1021/Jacs.9B04995  0.423
2019 Danielsen SPO, McCarty J, Shea JE, Delaney KT, Fredrickson GH. Small ion effects on self-coacervation phenomena in block polyampholytes. The Journal of Chemical Physics. 151: 034904. PMID 31325933 DOI: 10.1063/1.5109045  0.702
2019 Tro MJ, Charest N, Taitz Z, Shea JE, Bowers MT. The Classifying Autoencoder: Gaining Insight into Amyloid Assembly of Peptides and Proteins. The Journal of Physical Chemistry. B. PMID 31150250 DOI: 10.1021/Acs.Jpcb.9B03415  0.368
2019 Lin Y, McCarty J, Rauch JN, Delaney KT, Kosik KS, Fredrickson GH, Shea JE, Han S. Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions. Elife. 8. PMID 30950394 DOI: 10.7554/Elife.42571  0.71
2019 Danielsen SPO, McCarty J, Shea JE, Delaney KT, Fredrickson GH. Molecular design of self-coacervation phenomena in block polyampholytes. Proceedings of the National Academy of Sciences of the United States of America. PMID 30948640 DOI: 10.1073/Pnas.1900435116  0.708
2019 McCarty JJ, Delaney KT, Danielsen SPO, Fredrickson GH, Shea JE. Complete Phase Diagram for Liquid-liquid Phase Separation of Intrinsically Disordered Proteins. The Journal of Physical Chemistry Letters. PMID 30873835 DOI: 10.1021/Acs.Jpclett.9B00099  0.702
2019 Lin Y, McCarty J, Rauch JN, Delaney KT, Kosik KS, Fredrickson GH, Shea J, Han S. Author response: Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions Elife. DOI: 10.7554/Elife.42571.028  0.663
2018 Arsiccio A, McCarty JJ, Pisano R, Shea JE. The Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism. The Journal of Physical Chemistry. B. PMID 30118226 DOI: 10.1021/Acs.Jpcb.8B07368  0.722
2018 Shea J. Aggregation of the TAU Protein: Insights from Atomistic and Mesoscale Simulations Biophysical Journal. 114: 185a. DOI: 10.1016/J.Bpj.2017.11.1032  0.404
2017 Ganguly P, Boserman P, van der Vegt NFA, Shea JE. Trimethylamine N-oxide Counteracts Urea Denaturation by Inhibiting Protein-Urea Preferential Interaction. Journal of the American Chemical Society. PMID 29214802 DOI: 10.1021/Jacs.7B11695  0.743
2017 de Almeida NEC, Do TD, LaPointe NE, Tro M, Feinstein SC, Shea JE, Bowers MT. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid β-protein Oligomer and Fibril Formation. International Journal of Mass Spectrometry. 420: 24-34. PMID 29056865 DOI: 10.1016/J.Ijms.2016.09.018  0.389
2017 Peter EK, Shea JE. An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation. Physical Chemistry Chemical Physics : Pccp. PMID 28650060 DOI: 10.1039/C7Cp03035E  0.383
2017 Eschmann NA, Georgieva ER, Ganguly P, Borbat PP, Rappaport MD, Akdogan Y, Freed JH, Shea JE, Han S. Signature of an aggregation-prone conformation of tau. Scientific Reports. 7: 44739. PMID 28303942 DOI: 10.1038/Srep44739  0.733
2017 Bennett WD, Shea J, Brown FL. Surfactant pK a Calculations using Molecular Dynamics Simulations Biophysical Journal. 112: 522a. DOI: 10.1016/J.Bpj.2016.11.2821  0.326
2016 Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5  0.714
2016 Levine ZA, Shea JE. Simulations of disordered proteins and systems with conformational heterogeneity. Current Opinion in Structural Biology. 43: 95-103. PMID 27988422 DOI: 10.1016/J.Sbi.2016.11.006  0.376
2016 Peter EK, Pivkin IV, Shea JE. A canonical replica exchange molecular dynamics implementation with normal pressure in each replica. The Journal of Chemical Physics. 145: 044903. PMID 27475393 DOI: 10.1063/1.4958325  0.326
2016 Ganguly P, van der Vegt NF, Shea JE. Hydrophobic Association in Mixed Urea-TMAO Solutions. The Journal of Physical Chemistry Letters. PMID 27440555 DOI: 10.1021/Acs.Jpclett.6B01344  0.795
2016 Peter EK, Shea JE, Pivkin IV. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent. Physical Chemistry Chemical Physics : Pccp. PMID 27111190 DOI: 10.1039/C5Cp06867C  0.367
2016 Levine ZA, Rapp MV, Wei W, Mullen RG, Wu C, Zerze GH, Mittal J, Waite JH, Israelachvili JN, Shea JE. Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings of the National Academy of Sciences of the United States of America. PMID 27036002 DOI: 10.1073/Pnas.1603065113  0.788
2016 Kim B, Do TD, Hayden EY, Teplow DB, Bowers MT, Shea JE. Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation. The Journal of Physical Chemistry. B. PMID 27001160 DOI: 10.1021/Acs.Jpcb.6B00830  0.361
2016 Ilitchev AI, Giammona MJ, Do TD, Wong AG, Buratto SK, Shea JE, Raleigh DP, Bowers MT. Human Islet Amyloid Polypeptide N-Terminus Fragment Self-Assembly: Effect of Conserved Disulfide Bond on Aggregation Propensity. Journal of the American Society For Mass Spectrometry. PMID 26894887 DOI: 10.1007/S13361-016-1347-7  0.393
2016 Shea JE, Levine ZA. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations. Methods in Molecular Biology (Clifton, N.J.). 1345: 225-50. PMID 26453216 DOI: 10.1007/978-1-4939-2978-8_15  0.42
2016 Levine ZA, Okada A, Teranishi K, Langen R, Shea J. Reducing IAPP Aggregation with Mitochondrial Humanin Peptides; Results from Simulations and Experiments Biophysical Journal. 110: 177a. DOI: 10.1016/J.Bpj.2015.11.990  0.451
2015 Do TD, LaPointe NE, Nelson R, Krotee P, Hayden EY, Ulrich B, Quan S, Feinstein SC, Teplow DB, Eisenberg D, Shea JE, Bowers MT. Amyloid β-Protein C-terminal Fragments: Formation of Cylindrins and β-barrels. Journal of the American Chemical Society. PMID 26700445 DOI: 10.1021/Jacs.5B09536  0.375
2015 Wong AG, Wu C, Hannaberry E, Watson MD, Shea JE, Raleigh DP. Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity. Biochemistry. PMID 26694855 DOI: 10.1021/Acs.Biochem.5B01107  0.348
2015 de Almeida NE, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea JE, Bowers MT. Opposing Effects of Cucurbit[7]uril and 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose on Amyloid β25-35 Assembly. Acs Chemical Neuroscience. PMID 26629788 DOI: 10.1021/Acschemneuro.5B00280  0.382
2015 Mullen RG, Shea JE, Peters B. Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting. Journal of Chemical Theory and Computation. 11: 2421-8. PMID 26575542 DOI: 10.1021/Acs.Jctc.5B00032  0.748
2015 Ganguly P, Hajari T, Shea JE, van der Vegt NF. Correction to "Mutual Exclusion of Urea and Trimethylamine N-Oxide from Amino Acids in Mixed Solvent Environment". The Journal of Physical Chemistry Letters. 4728-4729. PMID 26570993 DOI: 10.1021/Acs.Jpclett.5B02536  0.755
2015 Zerze GH, Mullen RG, Levine ZA, Shea JE, Mittal J. To What Extent Does Surface Hydrophobicity Dictate Peptide Folding and Stability near Surfaces? Langmuir : the Acs Journal of Surfaces and Colloids. 31: 12223-30. PMID 26484800 DOI: 10.1021/Acs.Langmuir.5B03814  0.78
2015 Eschmann NA, Do TD, LaPointe NE, Shea JE, Feinstein SC, Bowers MT, Han S. Tau Aggregation Propensity Engrained in Its Solution State. The Journal of Physical Chemistry. B. PMID 26484390 DOI: 10.1021/Acs.Jpcb.5B08092  0.438
2015 Zheng X, Wu C, Liu D, Li H, Bitan G, Shea JE, Bowers MT. Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? The Journal of Physical Chemistry. B. PMID 26439281 DOI: 10.1021/Acs.Jpcb.5B08177  0.36
2015 Ganguly P, Hajari T, Shea JE, van der Vegt NF. Mutual Exclusion of Urea and Trimethylamine N-Oxide from Amino Acids in Mixed Solvent Environment. The Journal of Physical Chemistry Letters. 6: 581-5. PMID 26262470 DOI: 10.1021/Jz502634K  0.791
2015 Levine ZA, Fischer SA, Shea JE, Pfaendtner J. Trp-Cage Folding on Organic Surfaces. The Journal of Physical Chemistry. B. 119: 10417-25. PMID 26207727 DOI: 10.1021/Acs.Jpcb.5B04213  0.359
2015 Do TD, Chamas A, Zheng X, Barnes A, Chang D, Veldstra T, Takhar H, Dressler N, Trapp B, Miller K, McMahon A, Meredith SC, Shea JE, Lazar Cantrell K, Bowers MT. Elucidation of the Aggregation Pathways of Helix-Turn-Helix Peptides: Stabilization at the Turn Region Is Critical for Fibril Formation. Biochemistry. PMID 26070092 DOI: 10.1021/Acs.Biochem.5B00414  0.435
2015 Peter EK, Pivkin IV, Shea JE. A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. The Journal of Chemical Physics. 142: 144903. PMID 25877593 DOI: 10.1063/1.4915919  0.394
2015 Ganguly P, Do TD, Larini L, LaPointe NE, Sercel AJ, Shade MF, Feinstein SC, Bowers MT, Shea JE. Tau assembly: the dominant role of PHF6 (VQIVYK) in microtubule binding region repeat R3. The Journal of Physical Chemistry. B. 119: 4582-93. PMID 25775228 DOI: 10.1021/Acs.Jpcb.5B00175  0.683
2015 Levine ZA, Larini L, LaPointe NE, Feinstein SC, Shea JE. Regulation and aggregation of intrinsically disordered peptides. Proceedings of the National Academy of Sciences of the United States of America. 112: 2758-63. PMID 25691742 DOI: 10.1073/Pnas.1418155112  0.328
2015 Morriss-Andrews A, Shea JE. Computational studies of protein aggregation: methods and applications. Annual Review of Physical Chemistry. 66: 643-66. PMID 25648485 DOI: 10.1146/Annurev-Physchem-040513-103738  0.401
2014 Mullen RG, Shea JE, Peters B. Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation. Journal of Chemical Theory and Computation. 10: 659-67. PMID 26580043 DOI: 10.1021/Ct4009798  0.747
2014 Morriss-Andrews A, Shea JE. Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models. The Journal of Physical Chemistry Letters. 5: 1899-908. PMID 26273871 DOI: 10.1021/Jz5006847  0.37
2014 Mullen RG, Shea JE, Peters B. Communication: an existence test for dividing surfaces without recrossing. The Journal of Chemical Physics. 140: 041104. PMID 25669495 DOI: 10.1063/1.4862504  0.737
2014 Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE. How water layers on graphene affect folding and adsorption of TrpZip2. The Journal of Chemical Physics. 141: 22D511. PMID 25494782 DOI: 10.1063/1.4896984  0.307
2014 Do TD, Economou NJ, Chamas A, Buratto SK, Shea JE, Bowers MT. Interactions between amyloid-β and Tau fragments promote aberrant aggregates: implications for amyloid toxicity. The Journal of Physical Chemistry. B. 118: 11220-30. PMID 25153942 DOI: 10.1021/Jp506258G  0.41
2014 Susa AC, Wu C, Bernstein SL, Dupuis NF, Wang H, Raleigh DP, Shea JE, Bowers MT. Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions. Journal of the American Chemical Society. 136: 12912-9. PMID 25144879 DOI: 10.1021/Ja504031D  0.309
2014 Morriss-Andrews A, Brown FL, Shea JE. A coarse-grained model for peptide aggregation on a membrane surface. The Journal of Physical Chemistry. B. 118: 8420-32. PMID 24791936 DOI: 10.1021/Jp502871M  0.382
2014 Peter EK, Shea JE. A hybrid MD-kMC algorithm for folding proteins in explicit solvent. Physical Chemistry Chemical Physics : Pccp. 16: 6430-40. PMID 24499973 DOI: 10.1039/C3Cp55251A  0.349
2014 Morriss-Andrews A, Shea J. Coarse-Grained Simulations of Peptide Aggregation on Surfaces Biophysical Journal. 106: 100a. DOI: 10.1016/J.Bpj.2013.11.624  0.418
2014 Levine ZA, Larini L, Shea J. Tau(273-284): A Molecular Dynamics Study of Intrinsically Disordered Protein Conformations in the Presence of Osmolytes Biophysical Journal. 106: 483a. DOI: 10.1016/J.Bpj.2013.11.2729  0.408
2013 Bleiholder C, Do TD, Wu C, Economou NJ, Bernstein SS, Buratto SK, Shea JE, Bowers MT. Ion mobility spectrometry reveals the mechanism of amyloid formation of Aβ(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol. Journal of the American Chemical Society. 135: 16926-37. PMID 24131107 DOI: 10.1021/Ja406197F  0.402
2013 Wu C, Shea JE. Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides. Plos Computational Biology. 9: e1003211. PMID 24009497 DOI: 10.1371/Journal.Pcbi.1003211  0.422
2013 Do TD, LaPointe NE, Economou NJ, Buratto SK, Feinstein SC, Shea JE, Bowers MT. Effects of pH and charge state on peptide assembly: the YVIFL model system. The Journal of Physical Chemistry. B. 117: 10759-68. PMID 23937333 DOI: 10.1021/Jp406066D  0.417
2013 Larini L, Shea JE. Double resolution model for studying TMAO/water effective interactions. The Journal of Physical Chemistry. B. 117: 13268-77. PMID 23786631 DOI: 10.1021/Jp403635G  0.354
2013 Larini L, Gessel MM, LaPointe NE, Do TD, Bowers MT, Feinstein SC, Shea JE. Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study. Physical Chemistry Chemical Physics : Pccp. 15: 8916-28. PMID 23515417 DOI: 10.1039/C3Cp00063J  0.328
2013 Peters B, Bolhuis PG, Mullen RG, Shea JE. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency. The Journal of Chemical Physics. 138: 054106. PMID 23406097 DOI: 10.1063/1.4775807  0.748
2013 Peters B, Bolhuis PG, Mullen RG, Shea JE. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency Journal of Chemical Physics. 138. DOI: 10.1063/1.4775807  0.727
2013 Jewett AI, Zhuang Z, Shea J. Moltemplate a Coarse-Grained Model Assembly Tool Biophysical Journal. 104: 169a. DOI: 10.1016/J.Bpj.2012.11.953  0.328
2013 Shea J. Simulations of Protein Aggregation Biophysical Journal. 104: 45a. DOI: 10.1016/J.Bpj.2012.11.288  0.453
2012 Shea JE, Urbanc B. Insights into Aβ aggregation: a molecular dynamics perspective. Current Topics in Medicinal Chemistry. 12: 2596-610. PMID 23339310 DOI: 10.2174/1568026611212220012  0.416
2012 Morriss-Andrews A, Bellesia G, Shea JE. β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation. The Journal of Chemical Physics. 137: 145104. PMID 23061868 DOI: 10.1063/1.4755748  0.36
2012 Larini L, Shea JE. Role of β-hairpin formation in aggregation: the self-assembly of the amyloid-β(25-35) peptide. Biophysical Journal. 103: 576-86. PMID 22947874 DOI: 10.1016/J.Bpj.2012.06.027  0.392
2012 Wu C, Scott J, Shea JE. Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ(9-40) peptide probed by molecular dynamics simulations. Biophysical Journal. 103: 550-7. PMID 22947871 DOI: 10.1016/J.Bpj.2012.07.008  0.338
2012 Morriss-Andrews A, Shea JE. Kinetic pathways to peptide aggregation on surfaces: the effects of β-sheet propensity and surface attraction. The Journal of Chemical Physics. 136: 065103. PMID 22360223 DOI: 10.1063/1.3682986  0.401
2012 Gessel MM, Wu C, Li H, Bitan G, Shea JE, Bowers MT. Aβ(39-42) modulates Aβ oligomerization but not fibril formation. Biochemistry. 51: 108-17. PMID 22129303 DOI: 10.1021/Bi201520B  0.367
2011 Morriss-Andrews A, Bellesia G, Shea JE. Effects of surface interactions on peptide aggregate morphology. The Journal of Chemical Physics. 135: 085102. PMID 21895220 DOI: 10.1063/1.3624929  0.396
2011 Dupuis NF, Wu C, Shea JE, Bowers MT. The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces. Journal of the American Chemical Society. 133: 7240-3. PMID 21517093 DOI: 10.1021/Ja1081537  0.367
2011 Jiang P, Li W, Shea JE, Mu Y. Resveratrol inhibits the formation of multiple-layered β-sheet oligomers of the human islet amyloid polypeptide segment 22-27. Biophysical Journal. 100: 1550-8. PMID 21402038 DOI: 10.1016/J.Bpj.2011.02.010  0.411
2011 Wu C, Shea JE. Coarse-grained models for protein aggregation. Current Opinion in Structural Biology. 21: 209-20. PMID 21371882 DOI: 10.1016/J.Sbi.2011.02.002  0.386
2011 Wu C, Bowers MT, Shea JE. On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study. Biophysical Journal. 100: 1316-24. PMID 21354405 DOI: 10.1016/J.Bpj.2011.01.058  0.382
2011 Zhuang Z, Jewett AI, Kuttimalai S, Bellesia G, Gnanakaran S, Shea JE. Assisted peptide folding by surface pattern recognition. Biophysical Journal. 100: 1306-15. PMID 21354404 DOI: 10.1016/J.Bpj.2010.12.3735  0.37
2011 Bellesia G, Jewett AI, Shea JE. Relative stability of de novo four-helix bundle proteins: insights from coarse grained molecular simulations. Protein Science : a Publication of the Protein Society. 20: 818-26. PMID 21344535 DOI: 10.1002/Pro.605  0.373
2010 Wu C, Shea JE. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1. Plos Computational Biology. 6: e1000998. PMID 21124953 DOI: 10.1371/Journal.Pcbi.1000998  0.378
2010 Wei G, Jewett AI, Shea JE. Structural diversity of dimers of the Alzheimer amyloid-beta(25-35) peptide and polymorphism of the resulting fibrils. Physical Chemistry Chemical Physics : Pccp. 12: 3622-9. PMID 20336261 DOI: 10.1039/C000755M  0.408
2010 Wu C, Bowers MT, Shea JE. Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid abeta9-40 peptide: a comparison to agitated fibrils. Plos Computational Biology. 6: e1000693. PMID 20221247 DOI: 10.1371/Journal.Pcbi.1000693  0.402
2010 Bellesia G, Jewett AI, Shea JE. Sequence periodicity and secondary structure propensity in model proteins. Protein Science : a Publication of the Protein Society. 19: 141-54. PMID 19937649 DOI: 10.1002/Pro.288  0.349
2010 Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cellular and Molecular Life Sciences : Cmls. 67: 255-76. PMID 19851829 DOI: 10.1007/S00018-009-0164-6  0.353
2010 Shea J. Simulations of Protein Aggregation in the Cellular Milieu Biophysical Journal. 98: 5a. DOI: 10.1016/J.Bpj.2009.12.030  0.457
2009 Dupuis NF, Wu C, Shea JE, Bowers MT. Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor. Journal of the American Chemical Society. 131: 18283-92. PMID 19950949 DOI: 10.1021/Ja903814Q  0.372
2009 Wu C, Biancalana M, Koide S, Shea JE. Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics. Journal of Molecular Biology. 394: 627-33. PMID 19799914 DOI: 10.1016/J.Jmb.2009.09.056  0.393
2009 Bellesia G, Shea JE. Diversity of kinetic pathways in amyloid fibril formation. The Journal of Chemical Physics. 131: 111102. PMID 19778093 DOI: 10.1063/1.3216103  0.402
2009 Bellesia G, Shea JE. Effect of beta-sheet propensity on peptide aggregation. The Journal of Chemical Physics. 130: 145103. PMID 19368476 DOI: 10.1063/1.3108461  0.379
2009 Wu C, Murray MM, Bernstein SL, Condron MM, Bitan G, Shea JE, Bowers MT. The structure of Abeta42 C-terminal fragments probed by a combined experimental and theoretical study. Journal of Molecular Biology. 387: 492-501. PMID 19356595 DOI: 10.1016/J.Jmb.2009.01.029  0.392
2009 Murray MM, Krone MG, Bernstein SL, Baumketner A, Condron MM, Lazo ND, Teplow DB, Wyttenbach T, Shea JE, Bowers MT. Amyloid beta-protein: experiment and theory on the 21-30 fragment. The Journal of Physical Chemistry. B. 113: 6041-6. PMID 19341254 DOI: 10.1021/Jp808384X  0.786
2009 Bellesia G, Shea JE. What determines the structure and stability of KFFE monomers, dimers, and protofibrils? Biophysical Journal. 96: 875-86. PMID 19186127 DOI: 10.1016/J.Bpj.2008.10.040  0.363
2008 Bellesia G, Lampoudi S, Shea JE. Computational methods in nanostructure design: replica exchange simulations of self-assembling peptides. Methods in Molecular Biology (Clifton, N.J.). 474: 133-51. PMID 19031065 DOI: 10.1007/978-1-59745-480-3_9  0.404
2008 Wu C, Wang Z, Lei H, Duan Y, Bowers MT, Shea JE. The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations. Journal of Molecular Biology. 384: 718-29. PMID 18851978 DOI: 10.1016/J.Jmb.2008.09.062  0.369
2008 Krone MG, Hua L, Soto P, Zhou R, Berne BJ, Shea JE. Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments. Journal of the American Chemical Society. 130: 11066-72. PMID 18661994 DOI: 10.1021/Ja8017303  0.79
2008 Krone MG, Baumketner A, Bernstein SL, Wyttenbach T, Lazo ND, Teplow DB, Bowers MT, Shea JE. Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid beta-protein. Journal of Molecular Biology. 381: 221-8. PMID 18597778 DOI: 10.1016/J.Jmb.2008.05.069  0.786
2008 Bellesia G, Shea JE. Structure and stability of amyloid fibrils formed from synthetic beta-peptides. Frontiers in Bioscience : a Journal and Virtual Library. 13: 6957-65. PMID 18508708 DOI: 10.2741/3202  0.394
2008 Penev E, Ireta J, Shea JE. Energetics of infinite homopolypeptide chains: a new look at commonly used force fields. The Journal of Physical Chemistry. B. 112: 6872-7. PMID 18476737 DOI: 10.1021/Jp800058F  0.316
2008 Baumketner A, Krone MG, Shea JE. Role of the familial Dutch mutation E22Q in the folding and aggregation of the 15-28 fragment of the Alzheimer amyloid-beta protein. Proceedings of the National Academy of Sciences of the United States of America. 105: 6027-32. PMID 18408165 DOI: 10.1073/Pnas.0708193105  0.79
2007 Bellesia G, Shea JE. Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates. The Journal of Chemical Physics. 126: 245104. PMID 17614592 DOI: 10.1063/1.2739547  0.412
2007 Kamiya N, Mitomo D, Shea JE, Higo J. Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one. The Journal of Physical Chemistry. B. 111: 5351-6. PMID 17439167 DOI: 10.1021/Jp067075V  0.415
2007 Friedel M, Baumketner A, Shea JE. Stability of a protein tethered to a surface. The Journal of Chemical Physics. 126: 095101. PMID 17362129 DOI: 10.1063/1.2464114  0.384
2007 Baumketner A, Shea JE. The structure of the Alzheimer amyloid beta 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent. Journal of Molecular Biology. 366: 275-85. PMID 17166516 DOI: 10.1016/J.Jmb.2006.11.015  0.432
2006 Teplow DB, Lazo ND, Bitan G, Bernstein S, Wyttenbach T, Bowers MT, Baumketner A, Shea JE, Urbanc B, Cruz L, Borreguero J, Stanley HE. Elucidating amyloid beta-protein folding and assembly: A multidisciplinary approach. Accounts of Chemical Research. 39: 635-45. PMID 16981680 DOI: 10.1021/Ar050063S  0.392
2006 Baumketner A, Shea JE. Folding landscapes of the Alzheimer amyloid-beta(12-28) peptide. Journal of Molecular Biology. 362: 567-79. PMID 16930617 DOI: 10.1016/J.Jmb.2006.07.032  0.417
2006 Wei G, Shea JE. Effects of solvent on the structure of the Alzheimer amyloid-beta(25-35) peptide. Biophysical Journal. 91: 1638-47. PMID 16766615 DOI: 10.1529/Biophysj.105.079186  0.402
2006 Baumketner A, Bernstein SL, Wyttenbach T, Lazo ND, Teplow DB, Bowers MT, Shea JE. Structure of the 21-30 fragment of amyloid beta-protein. Protein Science : a Publication of the Protein Society. 15: 1239-47. PMID 16731963 DOI: 10.1110/Ps.062076806  0.444
2006 Friedel M, Baumketner A, Shea JE. Effects of surface tethering on protein folding mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 103: 8396-401. PMID 16709672 DOI: 10.1073/Pnas.0601210103  0.398
2006 Baumketner A, Bernstein SL, Wyttenbach T, Bitan G, Teplow DB, Bowers MT, Shea JE. Amyloid beta-protein monomer structure: a computational and experimental study. Protein Science : a Publication of the Protein Society. 15: 420-8. PMID 16501222 DOI: 10.1110/Ps.051762406  0.417
2006 Baumketner A, Shea JE. The thermodynamics of folding of a β hairpin peptide probed through replica exchange molecular dynamics simulations Theoretical Chemistry Accounts. 116: 262-273. DOI: 10.1007/S00214-005-0041-9  0.429
2005 Baumketner A, Shea JE. The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides. The Journal of Physical Chemistry. B. 109: 21322-8. PMID 16853765 DOI: 10.1021/Jp051325A  0.419
2005 Guo W, Shea JE, Berry RS. The physics of the interactions governing folding and association of proteins. Annals of the New York Academy of Sciences. 1066: 34-53. PMID 16533917 DOI: 10.1196/Annals.1363.025  0.386
2005 Griffin MA, Friedel M, Shea JE. Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein. The Journal of Chemical Physics. 123: 174707. PMID 16375557 DOI: 10.1063/1.2101458  0.401
2005 Bernstein SL, Wyttenbach T, Baumketner A, Shea JE, Bitan G, Teplow DB, Bowers MT. Amyloid beta-protein: monomer structure and early aggregation states of Abeta42 and its Pro19 alloform. Journal of the American Chemical Society. 127: 2075-84. PMID 15713083 DOI: 10.1021/Ja044531P  0.388
2004 Friedel M, Shea JE. Self-assembly of peptides into a beta-barrel motif. The Journal of Chemical Physics. 120: 5809-23. PMID 15267461 DOI: 10.1063/1.1649934  0.406
2004 Guo W, Lampoudi S, Shea JE. Temperature dependence of the free energy landscape of the src-SH3 protein domain. Proteins. 55: 395-406. PMID 15048830 DOI: 10.1002/Prot.20053  0.372
2003 Guo W, Lampoudi S, Shea JE. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. Biophysical Journal. 85: 61-9. PMID 12829464 DOI: 10.1016/S0006-3495(03)74454-3  0.393
2003 Friedel M, Sheeler DJ, Shea JE. Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein Journal of Chemical Physics. 118: 8106-8113. DOI: 10.1063/1.1564048  0.342
2002 Shea JE, Onuchic JN, Brooks CL. Probing the folding free energy landscape of the Src-SH3 protein domain. Proceedings of the National Academy of Sciences of the United States of America. 99: 16064-8. PMID 12446834 DOI: 10.1073/Pnas.242293099  0.657
2001 Shea JE, Brooks CL. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding Annual Review of Physical Chemistry. 52: 499-535. PMID 11326073 DOI: 10.1146/Annurev.Physchem.52.1.499  0.536
2000 Shea JE, Onuchic JN, Brooks CL. Energetic frustration and the nature of the transition state in protein folding Journal of Chemical Physics. 113: 7663-7671. DOI: 10.1063/1.1313792  0.617
1999 Shea JE, Onuchic JN, Brooks CL. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A Proceedings of the National Academy of Sciences of the United States of America. 96: 12512-12517. PMID 10535953 DOI: 10.1073/Pnas.96.22.12512  0.624
1998 Shea JE, Nochomovitz YD, Guo Z, Brooks CL. Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model Journal of Chemical Physics. 109: 2895-2903. DOI: 10.1063/1.476842  0.545
1998 Shea J, Oppenheim I. Fokker–Planck and non-linear hydrodynamic equations of an inelastic system of several Brownian particles in a non-equilibrium bath Physica a: Statistical Mechanics and Its Applications. 250: 265-294. DOI: 10.1016/S0378-4371(97)00536-0  0.374
1997 Shea J, Oppenheim I. Fokker-Planck equation and non-linear hydrodynamic equations of a system of several Brownian particles in a non-equilibrium bath Physica a: Statistical Mechanics and Its Applications. 247: 417-443. DOI: 10.1016/S0378-4371(97)00407-X  0.369
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