January 3, 2025, Filed Under: 2009, PublicationsStructures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. Citation: Miyashita, N. ; Straub, J. E. ; Thirumalai, D. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 131, 17843-52. Download Citation PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsThermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. Citation: O’Brien, E. P. ; Okamoto, Y. ; Straub, J. E. ; Brooks, B. R. ; Thirumalai, D. Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. J Phys Chem B 113, 14421-30. Download thermodynamic-perspective-on-the-docklock-growth-mechanism-of-amyloid-fibrils.pdf3.27 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsUrea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. Citation: Priyakumar, D. U. ; Hyeon, C. ; Thirumalai, D. ; MacKerell, A. D. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. J Am Chem Soc 131, 17759-61. Download urea-destabilizes-rna-by-forming-stacking-interactions-and-multiple-hydrogen-bonds-with-nucleic-acid-bases.pdf1.6 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsDissecting contact potentials for proteins: relative contributions of individual amino acids. Citation: Buchete, N. – V. ; Straub, J. E. ; Thirumalai, D. Dissecting contact potentials for proteins: relative contributions of individual amino acids. Proteins 70, 119-30. Download dissecting-contact-potentials-for-proteins-relative-contributions-of-individual-amino-acids.pdf707 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsEffects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. Citation: Pincus, D. L. ; Hyeon, C. ; Thirumalai, D. Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. J Am Chem Soc 130, 7364-72. Download effects-of-trimethylamine-n-oxide-tmao-and-crowding-agents-on-the-stability-of-rna-hairpins.pdf1.57 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsKinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. Citation: Tehver, R. ; Thirumalai, D. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. J Mol Biol 377, 1279-95. Download kinetic-model-for-the-coupling-between-allosteric-transitions-in-groel-and-substrate-protein-folding-and-aggregation.pdf1.09 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsKinetics of loop formation in polymer chains. Citation: Toan, N. M. ; Morrison, G. ; Hyeon, C. ; Thirumalai, D. Kinetics of loop formation in polymer chains. J Phys Chem B 112, 6094-106. Download kinetics-of-loop-formation-in-polymer-chains.pdf525 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsMultiple probes are required to explore and control the rugged energy landscape of RNA hairpins. Citation: Hyeon, C. ; Thirumalai, D. Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc 130, 1538-9. Download multiple-probes-are-required-to-explore-and-control-the-rugged-energy-landscape-of-rna-hairpins.pdf204 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsStructures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. Citation: Tarus, B. ; Straub, J. E. ; Thirumalai, D. Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol 379, 815-29. Download structures-and-free-energy-landscapes-of-the-wild-type-and-mutants-of-the-ab21-30-peptide-are-determined-by-an-interplay-between-intrapeptide-electrostatic-and-hydrophobic-interactions.pdf1.57 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2008, PublicationsCompression and stretching of a self-avoiding chain in cylindrical nanopores. Citation: Jun, S. ; Thirumalai, D. ; Ha, B. – Y. Compression and stretching of a self-avoiding chain in cylindrical nanopores. Phys Rev Lett 101, 138101. Download compression-and-stretching-of-a-self-avoiding-chain-in-cylindrical-nanopores.pdf371 KB Last updated on 08/18/2017 PubMed DOI
