SELECTED PUBLICATIONS

- Ayush Gupta, Heng Ma, Arvind Ramanathan, Gul H Zerze (2024.04. 05.588303). A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop. bioRxiv. doi: 10.1101/2024.04.05.588303

- Atanu Baksi, Hasan Zerze, Aman Agrawal, Alamgir Karim, Gul H Zerze (2024.01. 12.575416). The Molecular Picture of the Local Environment in a Stable Model Coacervate. bioRxiv. doi: 10.1101/2024.01.12.575416

- Kosar Rahimi, Pablo M Piaggi, Gül H Zerze (127 (21), 4722-4732). Comparison of on-the-fly probability enhanced sampling and parallel tempering combined with metadynamics for atomistic simulations of RNA tetraloop folding. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.3c00117

- Gul H Zerze (20 (4), 1646-1655). Optimizing the Martini 3 Force Field Reveals the Effects of the Intricate Balance between Protein–Water Interaction Strength and Salt Concentration on Biomolecular Condensate Formation. Journal of Chemical Theory and Computation. doi: 10.1021/acs.jctc.2c01273

- Gül H Zerze, Pablo M Piaggi, Pablo G Debenedetti (2021/12/10 125 (50), 13685-13695). A computational study of RNA tetraloop thermodynamics, including misfolded states. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.1c08038

- Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (2021/1/12 125 (3), 771-779). Thermodynamics of DNA Hybridization from Atomistic Simulations. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.0c09237

- Pablo G Debenedetti, Francesco Sciortino, Gül H Zerze (369 (6501), 289-292 2020/7/17). Second critical point in two realistic models of water. American Association for the Advancement of Science. doi: 10.1126/science.abb9796

- Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (124 (26), 5362-5369 2020/6/5). The handedness of DNA assembly around carbon nanotubes is determined by the chirality of DNA. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.0c02816

- Alexander E Conicella, Gregory L Dignon, Gül H Zerze, Hermann Broder Schmidt, Alexandra M D’Ordine, Young C Kim, Rajat Rohatgi, Yuna M Ayala, Jeetain Mittal, Nicolas L Fawzi (117 (11), 5883-5894 2020/3/17). TDP-43 α-helical structure tunes liquid–liquid phase separation and function. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1912055117

- Alexander E Conicella, Gregory Dignon, Gül H Zerze, Broder Schmidt, MD Alexandra, Youngchan Kim, Rajat Rohatgi, Yuna M Ayala, Jeetain Mittal, Nicolas L Fawzi (118 (3), 5a-6a 2020/2/7). Alpha-Helical Structure in TDP-43 Tunes Liquid-liquid Phase Separation and Cellular Function. Biophysical Journal. doi: 10.1016/j.bpj.2019.11.223

- Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (594 (1), 104-113 2020/1). Computational investigation of retro-isomer equilibrium structures: Intrinsically disordered, foldable, and cyclic peptides. FEBS letters. doi: 10.1002/1873-3468.13558

- Anastasia C Murthy, Gregory L Dignon, Yelena Kan, Gül H Zerze, Sapun H Parekh, Jeetain Mittal, Nicolas L Fawzi (26 (7), 637-648 2019/7). Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain. Nature structural & molecular biology. doi: 10.1038/s41594-019-0250-x

- Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (87 (7), 569-578 7/1/2019). Effect of heterochiral inversions on the structure of a β-hairpin peptide. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.25680

- Daniel A Heller, Hanan Baker, Januka Budhathoki-Uprety, Christian Cupo, Jackson Harvey, Prakrit Vaibhav Jena, Rachel E Langenbacher, Jeetain Mittal, Daniel Roxbury, Janki Shah, Ryan M Williams, Gul H Zerze, Ming Zheng ( 235, 721-721 2019/5/1). Carbon Nanotube Photoluminescence Solvatochromism in Biomedicine: Spectroscopy, Imaging, and Modulation. Electrochemical Society Meeting Abstracts 235. doi: 10.1149/MA2019-01/9/721

- Gül H Zerze, Wenwei Zheng, Robert B Best, Jeetain Mittal (10 (9), 2227-2234 2019/4/16). Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. The journal of physical chemistry letters. doi: 10.1021/acs.jpclett.9b00850

- Gül H Zerze, Pablo Debenedetti, Frank Stillinger (116 (3), 46a 2019/2/15). Computational Investigation of the Effect of Backbone Chiral Inversions on Polypeptide Structure. Biophysical Journal. doi: 10.1016/j.bpj.2018.11.292

- Jackson D Harvey, Gül H Zerze, Kathryn M Tully, Jeetain Mittal, Daniel A Heller (122 (19), 10592-10599 2018/5/7). Electrostatic Screening Modulates Analyte Binding and Emission of Carbon Nanotubes. The Journal of Physical Chemistry C. doi: 10.1021/acs.jpcc.8b01239

- Fanjie Meng, Mathias MJ Bellaiche, Jae-Yeol Kim, Gül H Zerze, Robert B Best, Hoi Sung Chung (114 (4), 870-884 2018/2/27). Highly disordered amyloid-β monomer probed by single-molecule FRET and MD simulation. Biophysical journal. doi: 10.1016/j.bpj.2017.12.025

- Brandon G Horan, Gül H Zerze, Young C Kim, Dimitrios Vavylonis, Jeetain Mittal (263566 2018/2/11). Computational modeling highlights disordered Formin Homology 1 domain’s role in profilin-actin transfer. bioRxiv. doi: 10.1101/263566

- Wenwei Zheng, Gül Zerze, Alessandro Borgia, Jeetain Mittal, Benjamin Schuler, Robert B Best (114 (3), 367a 2018/2/2). Inferring Properties of Disordered Chains From FRET Transfer Efficiencies. Biophysical Journal. doi: 10.1016/j.bpj.2017.11.2036

- Brandon G Horan, Gül Zerze, Gregory L Dignon, Young C Kim, Dimitrios Vavylonis, Jeetain Mittal (114 (3), 144a 2018/2/2). Multiscale Model of the Formin Homology 1 Domain Illustrates its Role in Regulation of Actin Polymerization. Biophysical Journal. doi: /10.1016/j.bpj.2017.11.810

- Veronica H Ryan, Gregory L Dignon, Gül H Zerze, Charlene V Chabata, Rute Silva, Alexander E Conicella, Joshua Amaya, Kathleen A Burke, Jeetain Mittal, Nicolas L Fawzi (69 (3), 465-479. e7 2018/2/1). Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation. Molecular cell. doi: 10.1016/j.molcel.2017.12.022

- Zachary Monahan, Veronica H Ryan, Abigail M Janke, Kathleen A Burke, Shannon N Rhoads, Gül H Zerze, Robert OMeally, Gregory L Dignon, Alexander E Conicella, Wenwei Zheng, Robert B Best, Robert N Cole, Jeetain Mittal, Frank Shewmaker, Nicolas L Fawzi (36 (20), 2951-2967 2017/10/16). Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity'. The EMBO journal. doi: 10.15252/embj.201696394

- Gregory L Dignon, Gül H Zerze, Jeetain Mittal (121 (37), 8661-8668 2017/9/21). Interplay between membrane composition and structural stability of membrane-bound hIAPP. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.7b05689

- Daniel A Heller, Jackson D Harvey, Prakrit V Jena, Ryan M Williams, Thomas V Galassi, Hanan A Baker, Daniel Roxbury, Gül Zerze, Jeetain Mittal (77 (13_Supplement), LB-222-LB-222 2017/7/1). Abstract LB-222: A nanoscale optical reporter implant for miRNA biomarkers in vivo. Cancer Research. doi: 10.1158/1538-7445.AM2017-LB-222

- Jackson D Harvey, Prakrit V Jena, Hanan A Baker, Gül H Zerze, Ryan M Williams, Thomas V Galassi, Daniel Roxbury, Jeetain Mittal, Daniel A Heller (1 (4), 0041 2017/3/13). A carbon nanotube reporter of microRNA hybridization events in vivo. Nature biomedical engineering. doi: 10.1038/s41551-017-0041

- Tushar Modi, Gül H Zerze, Jeetain Mittal, Sara M Vaiana, S Banu Ozkan (112 (3), 208a-209a 2017/2/3). Intrinsically Disordered Protein Dynamics Uncovered through Dynamic Flexibility Index (DFI) Analysis. Biophysical Journal. doi: 10.1016/j.bpj.2016.11.1152

- Alexander E Conicella, Gül H Zerze, Jeetain Mittal, Nicolas L Fawzi (24 (9), 1537-1549 2016/9/6). ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain. Structure. doi: 10.1016/j.str.2016.07.007

- Zachary A Levine, Michael V Rapp, Wei Wei, Ryan Gotchy Mullen, Chun Wu, Gul H Zerze, Jeetain Mittal, J Herbert Waite, Jacob N Israelachvili, Joan-Emma Shea (113 (16), 4332-4337 2016/4/19). Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1603065113

- Hande Güneş, Erdem Boy, Özge Ata, Gül H Zerze, Pınar Çalık, Tunçer H Özdamar (91 (3), 664-671 2016/3). Methanol feeding strategy design enhances recombinant human growth hormone production by Pichia pastoris. Journal of Chemical Technology & Biotechnology. doi: 10.1002/jctb.4619

- Gül H Zerze, Robert B Best, Jeetain Mittal (110 (3), 557a 2016/2/16). Dynamics of Contact Formation in Disordered Polypeptides. Biophysical Journal. doi: 10.1016/j.bpj.2015.11.2979

- Gül H Zerze, Jeetain Mittal, Robert B Best (116 (6), 068102 2016/2/12). Diffusive Dynamics of Contact Formation in Disordered Polypeptides. Physical review letters. doi: 10.1103/PhysRevLett.116.068102

- Gul H Zerze, Jeetain Mittal (119 (51), 15583-15592 2015/12/24). Effect of O-Linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.5b10022

- Gül H Zerze, Robert B Best, Jeetain Mittal (119 (46), 14622-14630 2015/11/19). Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.5b08619

- Gül H Zerze, Ryan G Mullen, Zachary A Levine, Joan-Emma Shea, Jeetain Mittal (31 (44), 12223-12230 2015/11/10). To What Extent Does Surface Hydrophobicity Dictate Peptide Folding and Stability near Surfaces?. Langmuir. doi: 10.1021/acs.langmuir.5b03814

- Gül H Zerze, Bilge Uz, Jeetain Mittal (83 (7), 1307-1315 2015/7). Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.24827

- Gül H Zerze, Cayla M Miller, Daniele Granata, Jeetain Mittal (11 (6), 2776-2782 2015/6/9). Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics. Journal of chemical theory and computation. doi: 10.1021/acs.jctc.5b00047

- Pınar Çalık, Özge Ata, Hande Güneş, Aslan Massahi, Erdem Boy, Abdullah Keskin, Sibel Öztürk, Gül H Zerze, Tunçer H Özdamar (95, 20-36 2015/3/15). Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters. Biochemical engineering journal. doi: 10.1016/j.bej.2014.12.003

- Sara M Sizemore, Gül H Zerze, Stephanie M Cope, Jeetain Mittal, Sara M Vaiana (108 (2), 388a-389a 2015/1/27). Comparing Solution Structures of Amylin and CGRP by Nanosecond Laser-Pump Spectroscopy and Atomistic Simulations. Biophysical Journal. doi: 10.1016/j.bpj.2014.11.2129

- Gül H Zerze, Robert B Best, Jeetain Mittal (108 (2), 194a 2015/1/27). Molecular Simulations of Unfolded and Intrinsically Disordered Proteins. Biophysical Journal. doi: 10.1016/j.bpj.2014.11.1072

- Gül H Zerze, Robert B Best, Jeetain Mittal (107 (7), 1654-1660 2014/10/7). Modest Influence of FRET Chromophores on the Properties of Unfolded Proteins. Biophysical Journal. doi: 10.1016/j.bpj.2014.07.071

- Gül H Zerze, Cayla Miller, Jeetain Mittal (106 (2), 483a 2014/1/28). Correlation of Helical Propensity in Amylin Sequences with Known Aggregation Propensity. Biophysical Journal. doi: 10.1016/j.bpj.2013.11.2728

- Cayla Miller, Gul H Zerze, Jeetain Mittal (117 (50), 16066-16075 2013/12/19). Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity. The Journal of Physical Chemistry B. doi: 10.1021/jp409755y

- Pınar Çalık, Bahar Bozkurt, Gül H Zerze, Bahar İnankur, Eda Bayraktar, Erdem Boy, Mehmet Ali Orman, Eda Açık, Tunçer H Özdamar (88 (9), 1631-1640 2013/9). Effect of co-substrate sorbitol different feeding strategies on human growth hormone production by recombinant Pichia pastoris. Journal of Chemical Technology & Biotechnology. doi: 10.1002/jctb.4011