Shea Group Publications [ Group Home / 2003 / 2004 / 2005 / 2006 / 2007 / 2008 / 2009 / 2010 / 2011 / 2012 / 2013 / 2014 / 2015 / 2016 / 2017 / 2018 / 2019 / 2020 / 2021 / 2022 ]


  2022

A New Transfer Free Energy Based Implicit Solvation Model for the 2 Description of Disordered and Folded Proteins.

Andrea Arsiccio, Roberto Pisano, Joan-Emma Shea J. Phys. Chem. B. 2022 in press

Field-Theoretic Simulation Method to Study the Liquid-Liquid Phase Separation of Polymers.

Saeed Najafi, James McCarty, Kris T. Delaney, Glenn H. Fredrickson, Joan-Emma Shea In Methods Molecular Biology, Vol. 2563, Huan-Xiang Zhou et al. (Eds): Phase-Separated Biomolecular Condensates. 2022 in press

Tachykinin Neuropeptides and Amyloid β (25-35) Assembly: Friend or Foe?

X Liu, P Ganguly, Y Jin, MJ Jhatro, JE Shea, SK Buratto, MT Bowers J. Am. Chem. Soc. 2022 in press

A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study.

Andrea Arsiccio, Pritam Ganguly, Joan-Emma Shea J. Phys. Chem. B. 2022 126 (24) 4472-4482



  2021

CORE-MD II: A fast, adaptive, and accurate enhanced sampling method.

Emanuel K Peter, Dietmar J Manstein, Joan-Emma Shea, Alexander Schug J. Chem. Phys. 2021 155 104114

Molecular Context of Dopa Influences Adhesion of Mussel-Inspired Peptides.

GD Degen, KC Cunha, ZA Levine, JH Waite, JE Shea J. Phys. Chem. B. 2021 125 (27) 7397-7405

Pressure Unfolding of Proteins: New Insights into the Role of Bound Water.

A Arsiccio, JE Shea J. Phys. Chem. B. 2021 125 (27) 7397-7405

Force Field Parameterization for the Description of the Interactions between Hydroxypropyl-�-Cyclodextrin and Proteins.

Andrea Arsiccio, Marcello Rospiccio, JoanEmma Shea, Robeto Pisano J. Phys. Chem. B. 2021 125 (27) 7397-7405

Liquid-liquid phase separation of Tau by self and complex coacervation.

Saeed Najafi, Yanxian Lin, Andrew P. Longhini, Xuemei Zhang, Kris T. Delaney, Kenneth S. Kosik, Glenn H. Fredrickson, Joan-Emma Shea, Songi Han Proteins 2021 30 (7) 1393-1407

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics
Andrew I Jewett, David Stelter, Jason Lambert, Shyam M Saladi, Otello M Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M Bashusqeh, Tom Keyes, Remus T Dame, Joan-Emma Shea, Grant J Jensen, David S Goodsell 2021 443 (11), 166841
Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach
A Arsiccio, JE Shea The Journal of Physical Chemistry B 2021, in press.
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes and Amyotrophic Lateral Sclerosis.
Nguyen, P. H.; Ramamoorhty, A.; Sahoo, B.; Zheng, J.; Chiricotto, M.; Straub, J. E.; Dominguez, L.; Shea, J.-E.; Dokholyan, N.; De Simone, A.; Ma, B.; Nussinov, R.; Najafi, S.; McCarty, J.; Loquet, A.; Faller, P.; Ganguly, P.; Ngo, S. T.; Li, M. S.; Hall, C.; Wang, Y.; Miller, Y.; Melchionna, S.; Habenstein, B Chem Rev 2021, 121 (4), 2545-2647
Catalytic Cross Talk Between Key Peptide Fragments that Couple Alzheimer's Disease with Amyotrophic Lateral Sclerosis
Laos, V.; Bishop, D., Ganguly; Schonfeld, G.; Trapp, B.; Lazar Cantrell, K.; Buratto, S.; Shea, J.-E.; Bowers, M. J. Am. Chem. Soc. 2021, 143 (9), 3494-3502
Physics Based Computational and Theoretical Approaches to IDPs
Shea, J.-E., Best. R., Mittal, J. Current Opinions in Structural Biology 2021, 67, 219-225


  2020

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Terminal capping of an amyloidogenic Tau fragment modulates its fibrillation propensity
Arya, S.; Ganguly, P.; Arsiccio, A.; Claud, S. L.; Trapp, B.; Schonfeld, G. E.; Liu, X.; Lazar Cantrell, K. L.; Shea, J.-E.; Bowers, M. T. J. Phys. Chem. B 2020, 124 (40), 8772-8783.
Latent models of molecular dynamics data: Automatic order parameter generation for peptide fibrillization
Charest, N.; Tro, M.; Bowers, M. T.; Shea, J.-E. J. Phys. Chem. B 2020, 124 (37), 8012-8022
CORE-MD, a path correlated Molecular Dynamics simulation method
Peter, E.; Shea, J.-E.; Schug, A. J. Chem. Phys. 2020, Journal of Chemical Physics 2020, 153 084114.
Dueling backbones: Comparing peptoid and peptide analogues of a mussel adhesive protein
Wonderly, W. R.; Cristiani, T. R.; Cunha, K. C.; Degen, G. D.; Shea, J.-E.; Waite, J. H. Macromolecules 2020, 53 (16), 6767-6779.
The ADD force field for sugars and polyols: Predicting the additivity of protein-osmolyte interaction
Arsiccio, A.; Ganguly, P.; La Cortiglia, L.; Shea, J.-E.; Pisano, R. J. Phys. Chem. B 2020, 124 (36), 7779-7790.
Protein stability in TMAO and mixed urea-TMAO solutions
Ganguly; P.; Polak, J.; van der Vegt, N. F. A.; Heyda, J.; Shea, J.-E. J. Phys. Chem. B 2020, 124, 6181-6197.
Dehydration entropy drives liquid-liquid phase separation by molecular crowding
Park, S.; Barnes, R.; Lin, Y.; Jeon, B.-j.; Najafi, S.; Delaney, K. T.; Fredrickson, G. H.; Shea, J.-E.; Hwang, D. S.; Han, S. Chem. Comm. 2020, 3, 83.
Heightened cold-denaturation of proteins at the ice-water interface
Arsiccio, A.; McCarty, J.; Pisano, R.; Shea, J.-E. J. Am. Chem. Soc. 2020, 142, 5722-5730.


  2019

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Distinct and nonadditive effects of urea and guanidinium chloride on peptide solvation
Ganguly, P.; Shea, J.-E. J. Phys. Chem. Lett. 2019, 10, 7406-7413.
The mitochondrial peptide humanin targets but does not denature amyloid oligomers in type II diabetes
Levine, Z. A.; Teranishi, K.; Okada, A. K.; Langen, R.; Shea, J.-E. J. Am. Chem. Soc. 2019, 141, 14168-14179.
Small ion effects on self-coacervation phenomena in block polyampholytes
Danielsen, S. P. O.; McCarty, J.; Shea, J.-E.; Delaney, K. T.; Fredrickson, G. H. J. Chem. Phys. 2019, 151, 034904.
The classifying autoencoder: Gaining insight into amyloid assembly of peptides and proteins
Tro, M. J.; Charest, N.; Taitz, Z.; Shea, J.-E.; Bowers, M. T. J. Phys. Chem. B 2019, 123, 5256-5264.
Molecular design of self-coacervation phenomena in block polyampholytes
Danielsen, S. P. O.; McCarty, J.; Shea, J.-E.; Delaney, K. T.; Fredrickson, G. H. Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 8224-8232.
Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions
Lin, Y.; McCarty, J.; Rauch, J. N.; Delaney, K. T.; Kosik, K. S.; Fredrickson, G. H.; Shea, J.-E.; Han, S. ELife 2019, 8, e42571.
Complete phase diagram for liquid-liquid phase separation of intrinsically disordered proteins
McCarty, J.; Delaney, K. T.; Danielsen, S. P. O.; Fredrickson, G. H.; Shea, J.-E. J. Phys. Chem. Lett. 2019, 10, 1644-1652.


  2018

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Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit
Do, T. D.; Checco, J. W.; Tro, M.; Shea, J.-E.; Bower, M. T.; Sweedler, J. V. Phys. Chem. Chem. Phys. 2018, 20, 22047-22057.
Effect of surfactants on surface-induced denaturation of proteins: Evidence of an orientation-dependent mechanism
Arsiccio, A.; McCarty, J.; Pisano, R.; Shea, J.-E. J. Phys. Chem. B 2018, 122, 11390-11399.
Phospholipid chain interactions with cholesterol drive domain formation in lipid membranes
Bennett, W. F. D.; Shea, J.-E.; Tieleman, D. P. Biophys. J. 2018, 114, 2595-2605.
Trimethylamine N-oxide counteracts urea denaturation by inhibiting protein-urea preferential interaction
Ganguly, P.; Boserman, P.; van der Vegt, N. F. A.; Shea, J.-E. J. Am. Chem. Soc. 2018, 140, 483-492.


  2017

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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
de Almeida, N. E. C.; Do, T. D.; LaPointe, N. E.; Tro, M.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. Int. J. Mass Spectrom. 2017, 420, 24-34.
Significant performance enhancement of polymer resins by bioinspired dynamic bonding
Seo, S.; Lee, D. W.; Ahn, J. S.; Cunha, K.; Ju, S. W.; Shin, E.; Kim, B.-S.; Levine, Z. A.; Lins, R. D.; Israelachvili, J. N.; Waite, J. H.; Shea, J.-E.; Ahn, B. K. Adv. Mater. 2017, 29 1703026.
Signature of an aggregation-prone conformation of tau
Eschmann, N. A.; Georgieva, E. R.; Ganguly, P.; Borbat, P. P.; Rappaport, M. D.; Akdogan, Y.; Freed, J. H.; Shea, J.-E.; Han, S. Sci. Rep. 2017, 7, 44739.
An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation
Peter, E. K.; Shea, J.-E. Phys. Chem. Chem. Phys. 2017, 19, 17373-17382.
Systematic derivation of implicit solvent models for the study of polymer collapse
Song, B.; Charest, N.; Morris-Andrews, A.; Molinero, V.; Shea, J.-E. J. Comput. Chem. 2017, 38, 1353-1361.
Festschrift in honor of Charlie Brooks III
Simulations of disordered proteins and systems with conformational heterogeneity
Levine, Z. A.; Shea, J.-E. Curr. Opin. Struct. Biol. 2017, 43, 95-103.


  2016

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Molecularly smooth self-assembled monolayer for high-mobility organic field-effect transistors
Das, S.; Lee, B. H.; Linstadt, R. T. H.; Cunha, K.; Li, Y.; Kaufman, Y.; Levine, Z. A.; Lipshutz, B. H.; Lins, R. D.; Shea, J.-E.; Heeger, A. J.; Ahn, B. K. Nano Lett. 2016, 16, 6709-6715.
Studying the early stages of protein aggregation using replica exchange molecular dynamics simulations
Shea, J.-E.; Levine, Z. A. In Protein Amyloid Aggregation: Methods and Protocols, Eliezer, D., Ed. Springer New York: New York, NY, 2016; pp 225-250.
A canonical replica exchange molecular dynamics implementation with normal pressure in each replica
Peter, E. K.; Pivkin, I. V.; Shea, J.-E. J. Chem. Phys. 2016, 145, 044903.
Hydrophobic association in mixed urea-TMAO solutions
Ganguly, P.; van der Vegt, N. F. A.; Shea, J.-E. J. Phys. Chem. Lett. 2016, 7, 3052-3059.
Aggregation of chameleon peptides: Implications of α-helicity in fibril formation
Kim, B.; Do, T. D.; Hayden, E. Y.; Teplow, D. B.; Bowers, M. T.; Shea, J.-E. J. Phys. Chem. B 2016, 120, 5874-5883.
Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent
Peter, E. K.; Shea, J.-E.; Pivkin, I. V. Phys. Chem. Chem. Phys. 2016, 18, 13052-13065.
Human islet amyloid polypeptide N-terminus fragment self-assembly: Effect of conserved disulfide bond on aggregation propensity
Ilitchev, A. I.; Giammona, M. J.; Do, T. D.; Wong, A. G.; Buratto, S. K.; Shea, J.-E.; Raleigh, D. P.; Bowers, M. T. J. Am. Soc. Mass Spectrom. 2016, 27 1010-1018.
Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces
Levine, Z. A.; Rapp, M. V.; Wei, W.; Mullen, R. G.; Wu, C.; Zerze, G. H.; Mittal, J.; Waite, J. H.; Israelachvili, J. N.; Shea, J.-E. Proc. Natl. Acad. Sci. U.S.A. 2016, 113 4332-4337.
Amyloid β-protein C-terminal fragments: Formation of cylindrins and β-barrels
Do, T. D.; LaPointe, N. E.; Nelson, R.; Krotee, P.; Hayden, E. Y.; Ulrich, B.; Quan, S.; Feinstein, S. C.; Teplow, D. B.; Eisenberg, D.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc. 2016, 138, 549�557.
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
Wong, A. G.; Wu, C.; Hannaberry, E.; Watson, M. D.; Shea, J.-E.; Raleigh, D. P. Biochemistry 2016, 55, 510�518.
Opposing effects of cucurbit[7]uril and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose on amyloid β25�35 assembly
de Almeida, N. E. C.; Do, T. D.; Tro, M.; LaPointe, N. E.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. ACS Chem. Neurosci. 2016, 7, 218�226.
Mechanism of C-terminal fragments of amyloid β-protein as Aβ inhibitors: Do C-terminal interactions play a key role in their inhibitory activity?
Zheng, X.; Wu, C.; Liu, D.; Li, H.; Bitan, G.; Shea, J-E.; Bowers, M. T. J. Phys. Chem. B 2016, 120, 1615�1623.


  2015

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Elucidation of the aggregation pathways of helix-turn-helix peptides: Stabilization at the turn region is critical for fibril formation
Do, T. D.; Chamas, A.; Zheng, X.; Barnes, A.; Chang, D. Veldstra, T.; Takhar, H.; Dressler, N.; Trapp, B.; Miller, K.; McMahon, A.; Meredith, S. C.; Shea, J.-E.; Cantrell, K. L.; Bowers, M. T. Biochemistry 2015, 54, 4050-4062.
Tau aggregation propensity engrained in its solution state
Eschmann, N. A.; Do, T. D.; LaPointe, N. E.; Shea, J.-E.; Feinstein, S. C.; Bowers, M. T.; Han, S. J. Phys. Chem. B 2015, 119, 14421-14432.
To what extent does surface hydrophobicity dictate peptide folding and stability near surfaces?
Zerze, G. H.; Mullen, R. G.; Levine, Z. A.; Shea, J.-E.; Mittal, J. Langmuir 2015, 31, 12223-12230.
Trp-cage folding on organic surfaces
Levine, Z. A.; Fischer, S. A.; Shea, J.-E.; Pfaendtner, J. J. Phys. Chem. B 2015, 119, 10417�10425.
Catechol and HCl desorption on TiO2(110) in vacuum and at the water�TiO2 interface
Kristoffersen, H. H.; Shea, J.-E.; Metiu, H. J. Phys. Chem. Lett. 2015, 6, 2277�2281.
Easy transition path sampling methods: Flexible-length aimless shooting and permutation shooting
Mullen, R. G.; Shea, J.-E.; Peters, B. J. Chem. Theory Comput. 2015, 11, 2421�2428.
Tau assembly: The dominant role of PHF6 (VQIVYK) in microtubule binding region repeat R3
Ganguly, P.; Do, T. D.; Larini, L.; LaPointe, N. E.; Sercel, A. J.; Shade, M. F.; Feinstein, S. C.; Bowers, M. T.; Shea, J.-E. J. Phys. Chem. B 2015, 119, 4582-4593.
A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides
Peter, E. K.; Pivkin, I. V.; Shea, J.-E. J. Chem. Phys. 2015, 142, 144903.
Regulation and aggregation of intrinsically disordered peptides
Levine, Z.; Larini, L.; Lapointe, N.; Feinstein, S.; Shea, J.-E. Proc. Natl. Acad. Sci. U.S.A. 2015, 112, 2758�2763.
Computational studies of protein aggregation: Methods and applications
Morriss-Andrews, A.; Shea, J.-E. Ann. Rev. Phys. Chem. 2015, 66, 643-666.
Mutual exclusion of urea and trimethylamine N-oxide from amino acids in mixed solvent environment
Ganguly, P.; Hajari, T.; Shea, J.-E.; van der Vegt, N. F. A. J. Phys. Chem. Lett. 2015, 6, 581�585.


  2014

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How water layers on graphene affect folding and adsorption of trpzip2
Shea, J.-E.; Peter, E. K.; Agarwal, M.; Kim, B.-K.; Pivkin, I. J. Chem. Phys. 2014, 141, 22D511.
Determination of biomembrane bending moduli in fully atomistic simulations
Levine, Z. A.; Venable, R. M.; Watson, M. C.; Lerner, M. G.; Shea, J.-E.; Pastor, R. W.; Brown, F. L. H. J. Am. Chem. Soc. 2014, 136, 13582�13585.
Interactions between amyloid-β and tau fragments promote aberrant aggregates: Implications for amyloid toxicity
Do; T. D.; Economou, N. J.; Chamas, A.; Buratto, S. K.; Shea, J.-E.; Bowers, M. T. J. Phys. Chem. B 2014, 118, 11220�11230.
Defining the molecular basis of amyloid inhibitors: Human islet amyloid polypeptide-insulin interactions
Susa, A. C.; Wu, C.; Bernstein; S. L.; Dupuis; N. F.; Wang, H.; Raleigh, D. P.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc. 2014, 136, 12912�12919.
A coarse-grained model for peptide aggregation on a membrane surface
Morriss-Andrews, A.; Brown, F. L. H.; Shea, J.-E. J. Phys. Chem. B 2014, 118, 8420�8432.
Simulations of protein aggregation: Insights from atomistic and coarse-grained models
Morriss-Andrews, A.; Shea J.-E. J. Phys. Chem. Lett. 2014, 5, 1899�1908.
Amyloid peptide aggregation: Computational techniques to deal with multiple time and length scales
Larini, L.; Shea, J.-E.
In Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology; Zhou, R.; Ed.; Series in Computational Biophysics; CRC Press: Boca Raton, FL. 2014; pp 165-190.
An existence test for dividing surfaces without recrossing
Mullen, R. G.; Shea, J.-E.; Peters, P. J. Chem. Phys. 2014, 140, 041104.
A hybrid MD-kMC algorithm for folding proteins in explicit solvent
Peter, E. K.; Shea, J.-E. Phys. Chem. Chem. Phys. 2014, 16, 6430-6440.
The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity
Wang, X.; Vallurupalli, P.; Vu, A.; Lee, K.; Sun, S.; Bai, W.-J.; Wu, C.; Zhou, H.; Shea, J.-E.; Kay, L. E.; Dahlquist, F. W. Biochemistry 2014, 53, 855-861.
Transmission coefficients, committors, and solvent coordinates in ion-pair dissociation
Mullen, R. G.; Shea, J.-E.; Peters, P. J. Chem. Theory Comput. 2014, 10, 659�667.


  2013

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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
Bleiholder, C.; Do, T. D.; Wu, C.; Economou, N. J.; Sivas Bernstein, S.; Buratto, S. K.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc. 2013, 135, 16926�16937.
Effects of pH and charge state on peptide assembly: The YVIFL model system
Do, T. D.; LaPointe, N. E.; Economou, N. J.; Buratto, S. K.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. J. Phys. Chem. B 2013, 117, 10759�10768.
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
Wu, C.; Shea, J.-E. PLoS Comput. Biol. 2013, 9, e1003211.
Double resolution model for studying TMAO/water effective interactions
Larini, L.; Shea, J.-E. J. Phys. Chem. B 2013, 117, 13268�13277.
Initiation of assembly of Tau(273-284) and its ΔK280 mutant: An experimental and computational study
Larini, L.; Gessel, M. M.; LaPointe, N. E.; Do, T. D.; Bowers, M. T.; Feinstein, S. C.; Shea, J.-E. Phys. Chem. Chem. Phys. 2013, 15, 8916-8928.
The GA-minor submotif as a case study of RNA modularity, prediction, and design
Grabow, W. W.; Zhuang, Z.; Shea, J.-E.; Jaeger, L. WIREs RNA 2013, 4, 181-203.
Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency
Peters, B.; Bolhuis, P. G.; Mullen, R. G.; Shea, J.-E. J. Chem. Phys. 2013, 138, 054106.
Inhibiting peptide and protein self aggregation: What can simulations tell us?
Shea, J.-E.; Colombo, G.
In Alzheimer's Disease: Insights into Low Molecular Weight and Cytotoxic Aggregates from In Vitro and Computer Experiments - Molecular Basis of Amyloid-β Protein Aggregation and Fibril Formation; Derreumaux, P.; Ed.; Molecular Medicine and Medicinal Chemistry; Imperial College Press: London, UK, 2013; Vol 7. pp 401-437.


  2012

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Insights into Aβ aggregation: A molecular dynamics perspective
Shea, J.-E.; Urbanc, B. Curr. Top. Med. Chem. 2012, 12, 2596-2610.
Computational and experimental analyses reveal the essential roles of inter-domain linkers in the biological function of chemotaxis histidine kinase CheA
Wang, X.; Wu, C.; Vu, A.; Shea, J.-E.; Dahlquist, F. J. Am. Chem. Soc. 2012, 134, 16107-16110.
The right angle (RA) motif: A prevalent ribosomal RNA structural pattern found in group I introns
Grabow, W. W.; Zhuang, Z.; Swank, Z. N.; Shea, J.-E.; Jaeger, L. J. Mol. Biol. 2012, 424, 54-67.
β-Sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation
Morriss-Andrews, A.; Bellesia, G.; Shea, J.-E. J. Chem. Phys. 2012, 137, 145104.
Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ9-40 peptide probed by molecular dynamics simulations
Wu, Chun; Scott, J.; Shea, J.-E. Biophys. J. 2012, 103, 550�557.
Role of β-hairpin formation in aggregation: The self-assembly of the amyloid-β(25-35) peptide
Larini, L.; Shea, J.-E. Biophys. J. 2012, 103, 576�586.
Coarse-grained modeling of simple molecules at different resolutions in the absence of good sampling
Larini, L.; Shea, J.-E. J. Phys. Chem. B 2012, 116, 8337�8349.
Aβ(39�42) modulates Aβ oligomerization but not fibril formation
Gessel, M. M.; Wu, Chun; Li, H.; Bitan, G.; Shea, J.-E.; Bowers, M. T. Biochemistry 2012, 51, 108�117.
Kinetic pathways to peptide aggregation on surfaces: The effects of β-sheet propensity and surface attraction
Morriss-Andrews, A.; Shea, J.-E. J. Chem. Phys. 2012, 136, 065103.
The structure of intrinsically disordered peptides implicated in amyloid diseases: Insights from fully atomistic simulations
Wu, C.; Shea, J.-E.
In Computational Modeling of Biological Systems: From Molecules to Pathways; Dokholyan, N.; Ed.; Biological and Medical Physics, Biomedical Engineering; Springer: Berlin, 2012; Part 2, pp 215-227.


  2011

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Effects of surfaces on peptide aggregate morphology
Morriss-Andrews, A.; Bellesia, G; Shea, J.-E. J. Chem. Phys. 2011, 135, 085102.
The amyloid formation mechanism in human IAPP: Dimers have β-strand monomer-monomer interfaces
Dupuis, N. F.; Wu, C.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc. 2011, 133, 7240-7243.
Relative stability of de novo four-helix bundle proteins: Insights from coarse grained molecular simulations
Bellesia, G.; Jewett, A. I.; Shea. J.-E. Prot. Sci. 2011, 20, 818-826.
Coarse-grained models for protein aggregation
Wu, C.; Shea, J.-E. Curr. Opin. Struct. Biol. 2011, 21, 209-220.
Resveratrol inhibits the formation of multiple-layered β-sheet oligomers of the human islet amyloid polypeptide segment 22-27
Jiang, P.; Li, W.; Shea, J.-E.; Mu, Y. Biophys. J. 2011, 100, 1550-1558.
On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: A molecular dynamics study
Wu, C.; Bowers, M. T.; Shea, J.-E. Biophys. J. 2011, 100, 1316-1324.
Assisted peptide folding by surface pattern recognition
Zhuang, Z.; Jewett, A. I.; Kuttimalai, S.; Bellesia, G.; Gnanakaran, S.; Shea, J.-E. Biophys. J. 2011, 100, 1306-1315.


  2010

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On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1
Wu, C.; Shea. J.-E. PLoS Comput. Biol. 2010, 6, e1000998.
Structural diversity of dimers of the Alzheimer Amyloid-β(25-35) peptide and polymorphism of the resulting fibrils
Wei, G; Jewett, A. I.; Shea. J.-E. Phys. Chem. Chem. Phys. 2010, 12, 3622-3629.
Molecular structures of quiescently-grown and brain-derived polymorphic fibrils of the Alzheimer amyloid Aβ9-40 peptide: A comparison to agitated fibrils
Wu, C.; Bowers, M. T.; Shea, J.-E. PLoS Comput. Biol. 2010, 6, e1000693.
Sequence periodicity and secondary structure propensity in model proteins
Bellesia, G.; Jewett, A. I.; Shea, J.-E. Protein Sci. 2010, 19, 141-154.
Oligomers of the prion protein fragment 106-126 are likely assembled from β-hairpins in solution, and methionine oxidation inhibits assembly without altering the peptide's monomeric conformation
Grabenauer, M.; Wu, C.; Soto, P.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc. 2010, 132, 532-539.
Reconciling theories of chaperonin accelerated folding with experimental evidence
Jewett, A. I.; Shea, J.-E. Cell. Mol. Life Sci. 2010, 67, 255�276.


  2009

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Human islet amyloid polypeptide monomers form ordered β-hairpins: A possible direct amyloidogenic precursor
Dupuis, N. F.; Wu, C.; Shea, J.-E.; Bowers, M. T. J. Am. Chem. Soc., 2009, 131, 18283-18292.
Binding modes of thioflavin-T to the single-layer β-sheet of the peptide self-assembly mimics
Wu, C.; Biancalana, M.; Koide, S.; Shea, J.-E. J. Mol. Biol. 2009, 394, 627-633.
Diversity of kinetic pathways in amyloid fibril formation
Bellesia, G.; Shea, J.-E. J. Chem. Phys. 2009, 131, 111102.
Overhauser dynamic nuclear polarization and molecular dynamics simulations using pyrroline and piperidine ring nitroxide radicals
Armstrong, B. D.; Soto, P.; Shea, J.-E.; Han, S. J. Magn. Reson. 2009, 200, 137-141.
TiReX: Replica-exchange molecular dynamics using TINKER
Penev, E. S.; Lampoudi, S.; Shea, J.-E. Comput. Phys. Commun. 2009, 180, 2013-2019.
Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease
Bernstein, S. L.; Dupuis, N. F.; Lazo, N. D.; Wyttenbach, T.; Condron, M. M.; Bitan, G.; Teplow, D. B.; Shea, J.-E.; Ruotolo, B. T.; Robinson, C. V.; Bowers, M. T. Nat. Chem. 2009, 1, 326-331.
Amyloid-β protein: Experiment and theory on the 21-30 fragment
Murray, M. M.; Krone, M. G.; Bernstein, S. L.; Baumketner, A.; Condron, M. M.; Lazo, N. D.; Teplow, D. B.; Wyttenbach, T.; Shea, J.-E.; Bowers, M. T. J. Phys. Chem. B 2009, 113, 6041-6046.
Effect of β-sheet propensity on peptide aggregation
Bellesia, G.; Shea, J.-E. J. Chem. Phys. 2009, 130, 145103.
What determines the structure and stability of KFFE monomers, dimers, and protofibrils?
Bellesia, G.; Shea, J.-E. Biophys. J. 2009, 96, 875-886.
The structure of Aβ42 C-terminal fragments probed by a combined experimental and theoretical study
Wu, C.; Murray, M. M.; Bernstein, S. L.; Condron, M. M.; Bitan, G.; Shea, J.-E.; Bowers, M. T. J. Mol. Biol. 2009, 387, 492-501.
The effect of surface tethering on the folding of the src-SH3 protein domain
Zhuang, Z.; Jewett, A. I.; Soto, P.; Shea, J.-E. Phys. Biol. 2009, 6, 015004.


  2008

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The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Aß16-22 peptide probed by molecular dynamics simulations
Wu, C.; Wang, Z. X.; Lei, H. X.; Duan, Y.; Bowers, M. T.; Shea, J.-E. J. Mol. Biol. 2008, 384, 718-729.
Role of water in mediating the assembly of Alzheimer amyloid-ß Aß16-22 protofilaments
Krone, M. G.; Hua, L.; Soto, P.; Zhou, R. H.; Berne, B. J.; Shea, J.-E. J. Am. Chem. Soc. 2008, 130, 11066-11072.
Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid-ß protein
Krone, M. G.; Baumketner, A.; Bernstein, S. L.; Wyttenbach, T.; Lazo, N. D.; Teplow, D. B.; Bowers, M. T.; Shea, J.-E. J. Mol. Biol. 2008, 381, 221-228.
Computational methods in nanostructure design: Replica exchange simulations of self-assembling peptides
Bellesia, G.; Lampoudi, S.; Shea, J.-E. In Nanostructure Design: Methods and Protocols; Gazit, E., Nussinov, R., Eds.; Methods in Molecular Biology; Humana Press: Totowa, NJ, 2008; Vol. 474, pp 133-152.
Energetics of infinite homopolypeptide chains: A new look at commonly used force fields
Penev, E.; Ireta, J.; Shea, J.-E. J. Phys. Chem. B 2008, 112, 6872-6877.
Role of the familial Dutch mutation E22Q in the folding and aggregation of the 15-28 fragment of the Alzheimer amyloid-ß protein
Baumketner, A.; Krone, M. G.; Shea, J.-E. Proc. Natl. Acad. Sci. USA 2008, 105, 6027-6032.
Do chaperonins boost protein yields by accelerating folding or preventing aggregation?
Jewett, A. I.; Shea, J.-E. Biophys. J. 2008, 94, 2987-2993.
Structure and stability of amyloid fibrils formed from synthetic ß-peptides
Bellesia, G.; Shea, J.-E. Front. Biosci. 2008, 13, 6957-6965.


  2007

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Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
Zhuang, Z. Y.; Jaeger, L.; Shea, J.-E. Nucleic Acids Res. 2007, 35, 6995-7002.
New insights into the mechanism of Alzheimer amyloid-ß fibrillogenesis inhibition by N-methylated peptides
Soto, P.; Griffin, M. A.; Shea, J.-E. Biophys. J. 2007, 93, 3015-3025.
Self-assembly of ß-sheet forming peptides into chiral fibrillar aggregates
Bellesia, G.; Shea, J.-E. J. Chem. Phys. 2007, 126, 245104.
Folding of the 25 residue Aß(12-36) peptide in TFE/water: Temperature-dependent transition from a funneled free-energy landscape to a rugged one
Kamiya, N.; Mitomo, D.; Shea, J.-E.; Higo, J. J. Phys. Chem. B 2007, 111, 5351-5356.
Stability of a protein tethered to a surface
Friedel, M.; Baumketner, A.; Shea, J.-E. J. Chem. Phys. 2007, 126, 095101.
The structure of the Alzheimer amyloid ß 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent
Baumketner, A.; Shea, J.-E. J. Mol. Biol. 2007, 366, 275-285.


  2006

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Folding on the chaperone: Yield enhancement through loose binding
Jewett, A. I.; Shea, J.-E. J. Mol. Biol. 2006, 363, 945-957.
Elucidation Amyloid-ß protein folding and assembly: A multidisciplinary approach.
D.B. Teplow, N. D. Lazo, G. Bitan, S. Bernstein, T. Wyttenbach, M. T. Bowers, A. Baumketner, J.-E. Shea, B. Urbanc, L. Cruz and H. E. Stanley. Acc. Chem. Res. (2006) vol 39, pages 635-645.
Folding landscapes of the Alzheimer amyloid-ß(12-28) peptide
Baumketner, A.; Shea, J.-E. J. Mol. Biol. 2006, 362, 567-579.
Effects of solvent on the structure of the Alzheimer amyloid-ß(25-35) peptide
Wei, G. H.; Shea, J.-E. Biophys. J. 2006, 91, 1638-1647.
The thermodynamics of folding of a ß-hairpin peptide probed through replica exchange molecular dynamics simulations
Baumketner, A.; Shea, J.-E. Theor. Chem. Acc. 2006, 116, 262-273.
Effects of surface tethering on protein folding mechanisms
Friedel, M.; Baumketner, A.; Shea, J.-E. Proc. Natl. Acad. Sci. USA 2006, 103, 8396-8401.
Structure of the 21-30 fragment of amyloid ß-protein
Baumketner, A.; Bernstein, S. L.; Wyttenbach, T.; Lazo, N. D.; Teplow, D. B.; Bowers, M. T.; Shea, J.-E. Protein Sci. 2006, 15, 1239-1247.
Simulations of protein folding
Shea, J.-E.; Friedel, M. R.; Baumketner, A. In Reviews in Computational Chemistry; Lipkowitz, K. B., Cundari, T. R., Gillet, V. J., Eds.; Wiley-VCH: Hoboken, NJ, 2006; Vol. 22, pp 169-228.
Amyloid ß-protein monomer structure: A computational and experimental study
Baumketner, A.; Bernstein, S. L.; Wyttenbach, T.; Bitan, G.; Teplow, D. B.; Bowers, M. T.; Shea, J.-E. Protein Sci. 2006, 15, 420-428.
Aggregation of polyalanine in a hydrophobic environment
Soto, P.; Baumketner, A.; Shea, J.-E. J. Chem. Phys. 2006, 124, 134904.


  2005

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The physics of the interactions governing folding and association of proteins
Guo, W.; Shea, J.-E.; Berry, R. S. In Cell Injury: Mechanisms, Responses, and Repair; Lee, R. C., Despa, F., Hamann, K. J., Eds.; Annals of the New York Academy of Sciences; New York Academy of Sciences: New York, NY, 2005; Vol. 1066, pp 34-53.
Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice ß-barrel protein
Griffin, M. A.; Friedel, M.; Shea, J.-E. J. Chem. Phys. 2005, 123, 174707.
Amyloid ß-protein: Monomer structure and early aggregation states of Aß42 and its Pro19 alloform
Bernstein, S. L.; Wyttenbach, T.; Baumketner, A.; Shea, J.-E.; Bitan, G.; Teplow, D. B.; Bowers, M. T. J. Am. Chem. Soc. 2005, 127, 2075-2084.
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
Ding, F.; Guo, W. H.; Dokholyan, N. V.; Shakhnovich, E. I.; Shea, J.-E. J. Mol. Biol. 2005, 350, 1035-1050.
Free energy landscapes for amyloidogenic tetrapeptides dimerization
Baumketner, A.; Shea, J.-E. Biophys. J. 2005, 89, 1493-1503.
The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides
Baumketner, A.; Shea, J.-E. J. Phys. Chem. B 2005, 109, 21322-21328.


  2004

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Effects of frustration on the kinetics of helix formation in alanine polypeptides
Baumketner, A.; Shea, J.-E. Conden. Matter Physics 2004, 7, 421-434.
Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: Creation of an alternate fast folding pathway
Jewett, A. I.; Baumketner, A.; Shea, J.-E. Proc. Natl. Acad. Sci. USA 2004, 101, 13192-13197.
Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters
Baumketner, A.; Shea, J.-E.; Hiwatari, Y. J. Chem. Phys. 2004, 121, 1114-1120.
Temperature dependence of the free energy landscape of the src-SH3 protein domain
Guo, W. H.; Lampoudi, S.; Shea, J.-E. Proteins 2004, 55, 395-406.
Self-assembly of peptides into a ß-barrel motif
Friedel, M.; Shea, J.-E. J. Chem. Phys. 2004, 120, 5809-5823.



  2003

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Post-transition state desolvation of the hydrophobic core of the src-SH3 protein domain
Guo, W. H.; Lampoudi, S.; Shea, J.-E. Biophys. J. 2003, 85, 61-69.
Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist ß-barrel protein
Friedel, M.; Sheeler, D. J.; Shea, J.-E. J. Chem. Phys. 2003, 118, 8106-8113.
Glass transition in an off-lattice protein model studied by molecular dynamics simulations
Baumketner, A.; Shea, J.-E.; Hiwatari, Y. Phys. Rev. E 2003, 67, 011912.
Effects of confinement in chaperonin assisted protein folding: Rate enhancement by decreasing the roughness of the folding energy landscape
Baumketner, A.; Jewett, A.; Shea, J.-E. J. Mol. Biol. 2003, 332, 701-713.
Kinetics of the coil-to-helix transition on a rough energy landscape
Baumketner, A.; Shea, J.-E. Phys. Rev. E 2003, 68, 051901.