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Biomolecular Modeling Group
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Biomolecular Modeling Group |
Publications "Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator", Samanta R., Zhuang X., Varney K.M., Weber D., Matysiak S., J. Chem. Inf. Model., DOI:10.1021/acs.jcim.4c00116 (2024). pdf "Opposing roles of organic salts on mini-protein structure", Lee P.-Y., Singh O., Nanajkar N., Bermudez H., Matysiak S., Phys. Chem. Chem. Phys., DOI:10.1039/d3cp05607d (2024). pdf "Modulation of Abeta 16–22 aggregation by glucose", Jain M., Sahoo A., Matysiak S., Phys. Chem. Chem. Phys., 26, 5038-5044 (2024). pdf "Decoupling epistasis mechanims in biomacromolecules", Samanta R., Matysiak S., Biophys. J., 122, 1574-1576 (2023). pdf "Folding and modulation of the helical conformation of Glycophorin A by point mutations", Pei-Yin L., Sahoo A., Matysiak S., Phys. Chem. Chem. Phys., 25, 10885-10893 (2023).pdf "Mechanistic insights into the inhibition of amyloid-β aggregation by chitosan", Gotla S., Matysiak S., Phys. Chem. Chem. Phys., 25, 10113-10120 (2023). pdf "Emergence of Allostery through Reorganization of Protein Residue Network Architecture", Samanta R., Sanghvi N., Beckett D., Matysiak S., J. Chem. Phys., 158, 085104 (2023). pdf "Discovery and Characterization of a Functional scFv for CCR2 Inhibition via an Extracellular Loop", Jasiewicz N. E. , Brown A. D., Deci M., Matysiak S., Earp S., Nguyen J., Int. J. Pharm., 632, 122547 (2023) .pdf "Opinion: Protein folds vs. protein folding: Differing questions, different challenges", Chen S.-J., Hassan M. , Jernigan R.L., Jia K.,Kihara D. ,Kloczkowski A., Kotelnikov S., Kozakov D. , Liang J. , Liwo A., Matysiak S., Meller J., Micheletti C., Mitchell J. C., Mondal S., Nussinov R., Okazaki K., Padhorny D., Skolnick J., Sosnick T. S., Stan G. , Vakser I., Zou X., and Rose G. D., Proc. Natl. Acad. Sci., 120, e2214423119 (2022). pdf "Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery", Young B. D., Cook M. E., Costabile B. K., Samanta R., Zhuang X., Sevdalis S. E., Varney K. M., Flippo M., Matysiak S., Lattman E., Weber D. J., J. Mol. Biol., 434, 1678772 (2022). pdf "Transferable and Polarizable Coarse Grained Model for Proteins -ProMPT", Sahoo A., Lee P.-Y., Matysiak S., J. Chem. Theory Comput., DOI:10.1021/acs.jctc.2c00269 (2022). pdf "Load-Bearing Nanostructures in Composites of Chitosan with Anionic Surfactants: Implications for Programmable Mechanomaterials", Gotla S., Tong C., Matysiak S., ACS Appl. Nano Mater., 5, 6463-6473 (2022). pdf "Recovery of enzyme structure and activity following rehydration from ionic liquid", Lee P.-Y, Singh O., Bermudez H., Matysiak S., Phys. Chem. Chem. Phys., 34, 10365-10372 (2022). pdf "Effects of applied surface-tension on membrane-assisted Ab aggregation", Sahoo A., Matysiak S., Phys. Chem. Chem. Phys., 23, 20627-20633 (2021). pdf "Dual mechanism of ionic liquid-induced protein unfolding", Singh O., Lee P.-Y., Matysiak S., Bermudez H., Phys. Chem. Chem. Phys., 22, 19779-19786 (2020). pdf "Microscopic picture of Calcium-assisted lipid demixing and membrane remodeling using multiscale simulations", Sahoo A., Matysiak S., J. Phys. Chem. B, 124, 7327-7335 (2020). pdf "Tuning allostery through integration of disorder-to-order with a residue network", Wang J., Samanta R., Custer G.S., Look C., Matysiak S., Beckett D., Biochemistry, 59, 790-801 (2020). pdf "Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration", Sahoo A., Matysiak S., Phys. Chem. Chem. Phys. , 21, 22679-22694 (2019) .pdf "Pathways of amyloid-beta absorption and aggregation in membranous environments", Sahoo A., Xu H., Matysiak S., Phys. Chem. Chem. Phys. , 21, 8559-8568 (2019). pdf "Mesoporous Encapsulated Chiral Nanogold for Use in Enantioselective Reactions", Zhou Y., Sun H., Xu H., Matysiak S., Ren J., Qu X., Angew. Chem., 57, 16791-16795 (2018). pdf "How hydrophobic hydration destabilizes surfactant micelle at low temperature: A coarse-grained simulation study", Custer G.S., Xu H., Matysiak S., Das P., Langmuir, 34, 12590-12599 (2018). pdf "Looking at the disordered proteins through the computational microscope", Das P., Matysiak S., Mittal J., ACS Cent. Sci., 4, 534-542 (2018). pdf "Superrepression through Altered Corepressor-Activated Protein:Protein Interactions", He, C., Custer, G., Wang, J., Matysiak, S., Beckett, D., Biochemistry, 57, 1119-1129 (2018) .pdf "Long Distance Modulation of Disorder-to-Order in Protein Allostery", Wang J., Custer G.S., Beckett D., Matysiak S., Biochemistry, 56, 4478-4488 (2017). pdf "Effect of pH on Chitosan Hydrogel Polymer Network Structure", Xu H., Matysiak S., Chem. Commun., 13, 7373-7376 (2017). pdf "Interplay between Conformational Heterogeneity and Hydration in the Folding Landscape of a Designed 3-Helix Bundle", Custer G., Das P., Matysiak S., J. Phys. Chem. B, 121, 2731-2738 (2017). pdf "Influence of Monovalent Cation Size on Nanodomain Formation in Anionic-Zwitterionic Mixed Bilayers", Ganesan S.J., Xu H., Matysiak S., J. Phys. Chem. B, 121, 787-799 (2017). pdf "Acetylation within the first 17 amino acids of huntingtin exon 1 alters aggregation and binding to lipid membranes", Chaibva M., Jawahery S., Pilkington IV A. W. , Arndt J. R. , Sarver O., Valentine S., Matysiak S., and Legleiter J., Biophys. J., 111, 349-362 (2016). pdf "Effect of Lipid Head Group Interactions in Membrane Properties and Membrane-Induced Cationic beta-Hairpin Folding", Ganesan, S. J., Xu, H., Matysiak, S., Phys. Chem. Chem. Phys., 18, 17836-17850 (2016).pdf "Interplay Between Hydrophobic Effect and Dipole Interactions in Peptide Aggregation at Interfaces", Ganesan, S. J., Matysiak, S., Phys. Chem. Chem. Phys., 18, 2449-2458 (2016). pdf "The Interplay of Dynamical Properties Between Ionic Liquids and Ionic Surfactants: Mechanism and Aggregation", McCutchen M., Chen L.G., Bermudez H., Matysiak S., J. Phys. Chem. B, 119, 9925-9932 (2015). pdf "The Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins", Ganesan S. J., Matysiak S., J. Chem. Theory and Comput., 10, 2569-2576 (2014). pdf "The Effects of Flanking Sequences in the Interaction of Polyglutamine Peptides with a Membrane Bilayer", Nagarajan, A., Jawahery, S., Matysiak, S., J. Phys. Chem. B, 118, 6368-6379 (2014). pdf "Multiscale simulation of liquid water using a four-to-one mapping for coarse-graining", Nagarajan, A., Junghans, C., Matysiak, S., J. Chem. Theory and Comput., 9, 5168-5175 (2013). pdf "Effects of Sequence and Solvation on the Temperature-Pressure Conformational Landscape of Proteinlike Heteropolymers", Matysiak, S, Das, P., Phys. Rev. Lett., 111, 058103 (2013). pdf "Thermal Stability of Hydrophobic Helical Oligomers", Romero-Vargas Castrillón, S., Matysiak, S., Stillinger, F., Rossky, P. J., Debenedetti, P., J. Phys. Chem. B, J. Phys. Chem. B, 116, 9963-9970 (2012) . pdf "Phase Behavior of a Lattice Hydrophobic Oligomer in Explicit Water", Romero-Vargas Castrillón, S., Matysiak, S., Stillinger, F., Rossky, P. J., Debenedetti, P., J. Phys. Chem. B, 116, 9540-9548 (2012). pdf "The Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation", Matysiak, S., Debenedetti, P. G., Rossky, P. J., J. Phys. Chem. B, 116, 8095-8104 (2012). pdf "Direct Characterization of Hydrophobic Hydration during Cold and Pressure Denaturation", Das, P., Matysiak, S., J. Phys. Chem. B, 116, 5342-5348 (2012). pdf "Dissecting the Energetics of Hydrophobic Hydration of Polypeptides", Matysiak, S., Debenedetti, P. G., Rossky, P. J., J. Phys. Chem. B, 115, 14859-65 (2011). pdf "Mapping folding energy landscapes with theory and experiment", Matysiak S., Clementi C., Arch. Biochem. Biophys., 468, 29-33 (2008). pdf "Modeling diffusive dynamics in adaptive simulation of liquid water", Matysiak S., Clementi C., Praprotnik M., Delle Site, L., Kremer, K., J. Chem. Phys. 128,1 (2008). pdf "Adaptive resolution simulation of liquid water", Praprotnik, M., Matysiak S., Delle Site, L., Kremer, K., Clementi, C., J. Phys: Cond. Matter, 19, 292201 (2007). pdf "Minimalist protein model as a diagnostic tool for misfolding and aggregation", Matysiak S., Clementi C., J. Mol. Biol. 363, 297-308 (2006). pdf "Dynamics of polymer translocation through nanopore: Theory meet experiments", Matysiak S., Montesi A., Kolomeisky, A. B., Pasquali, M., Clementi C., Phys. Rev. Lett., 96, 118103 (2006). pdf "Balancing energy and entropy: A new minimalist model for the characterization of protein folding landscapes", Das P., Matysiak S., Clementi C., PNAS, 102, 10141-10146 (2005). pdf "Optimal combination of theory and experiments for the characterization of the protein folding landscape of S6", Matysiak S., Clementi C., J. Mol. Biol. 343, 235 (2004). pdf Books and Chapters "Simulation studies on the influence of cations on nano-domain formation in mixed lipid bilayers”, Ganesan S.J., Xu H, Matysiak S., Biomembrane simulations: Computational Studies of Biological Membranes, Berkowitz M.L. editor, Taylor and Francis/CRC press, Chapter 11 (2019) “Biomolecular Modeling in Biomaterials”, Ganesan S.J., Matysiak S. in Biomaterial Mechanics, Hayenga H., Aranda-Espinoza H. editors, Taylor and Francis/CRC press, Chapter 8 (2017) "Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental Data", Matysiak S., Clementi C., Coarse-Graining of Condensed Phase and Biomolecular Systems, G. A. Voth Ed, Taylor & Francis/CRC press, Chapter 11 (2009). |