Publications

Publications After Joining UNM

Authors with ## are high school or undergraduate students

2025

  1. Temair Shorty, Amy O. Stevens, Yi He* - Structure ensemble reconstructions of the flexible PICK1 dimer using the SAXS data, Protein Sci., 2025 (Draft)
  2. Emily Hendrix, Tongtong Li,  Yi He* - The reliability of constructing structure ensembles using AI for intrinsically disordered proteins, J. Chem. Theory Comput., 2025 (Draft)
  3. Autumn Arruti+, Shenghan Song+, James Davies, Ryan Davis, Yi He* - Humidity influence on ion-molecule interactions pattern in organic-inorganic aerosol, J. Phys. Chem. Lett, 2025 (Draft)

2024

  1. Mingrui Duan, Shenghan Song, Po-Hsuen Lee, Ke Jian Liu, Yi He, Peng Mao* - High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma, Proc. Natl. Acad. Sci. U.S.A., 121 (4) e2310854121, 2024 DOI:10.1073/pnas.2310854121
  2. Jiayao Chen, Lin Li, Jiancheng Luo, Lingyao Meng, Xiao Zhao, Shenghan Song, Zoriana Demchuk, Pei Li,  Yi He, and Peng-Fei Cao* - Covalent Adaptable Polymer Networks with CO2-Facilitated Recyclability, Nat. Commun., 2024 DOI:10.1038/s41467-024-50738-7
  3. Emily Hendrix, Yi He* - Optimizing Ligand Design for PICK1 PDZ Inhibition: A Benchmark Analysis of AfDesign's Capabilities and Constraints, Curr. Protein Pept. Sci., 2024 DOI:10.2174/0113892037316932240806102854
  4. (Cover) Tongtong Li,  Stefano Motta, Yi He* - Deciphering the Mystery in p300 Taz2-p53 TAD2 Recognition, J. Chem. Theory Comput., 2024 DOI:10.1021/acs.jctc.4c00541
  5. Masroor Ahmad Paddar, Fulong Wang, Einar S Trosdal, Emily Hendrix, Yi He, Michelle Salemi, Michal Mudd, Jingyue Jia, Thabata L A Duque, Ruheena Javed, Brett Phinney, Vojo Deretic* -  Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function, eLife, 2024 DOI:10.7554/eLife.100928.1
  6. Shenghan Song, Yi He* - Deciphering the Role of BAR Domain Proteins in Membrane Curvature Modulation: Insights from All-Atom Molecular Dynamics Simulations, Pathogens, 2024 DOI: 10.3390/pathogens13100902 
  7. Ruheena Javed, Einar Trosdal, Thabata Duque, Masroor Paddar, Lee Allers, Aurore Claude - Taupin, Prithvi Akepati, Emily Hendrix, Michelle Salemi, Yi He,  Brett Phinney, Yasuo Uchiyama, Mauriel Mari, Fulvio Reggiori, and Vojo Deretic - ATG9A facilitates closure of mammalian autophagosomes, J. Cell Biol., 2024 (Accepted)
  8. Xiaosi Li, Qi Li, Xinyu Xia, Edward Deng, Yue Zhao, Yi He, Chao Zhao - Capsaicin-loaded melanin nanoparticles for long-lasting nociceptive-selective nerve blockade, Langmuir, 2024 DOI: 10.1021/acs.langmuir.4c01725
  9. Shenghan Song, Xinyu Xia, Tongtong Li, Amy O. Stevens, Yi He* - Molecular Dynamics Insights into Peptide-based Tetrodotoxin Delivery Nanostructures, Molecules, 2024 (Submitted)

2023

  1. (Cover) Tongtong Li, Emily Hendrix, Yi He* - Simple and effective conformational sampling strategy for intrinsically disordered proteins using UNRES web server, J. Chem. Phys. B, 2023 DOI: 10.1021/acs.jpcb.2c08945
  2. Tongtong Li, Laura I. Gil Pineda, Amy O. Stevens, Yi He* - Key factors regulating the inter-domain dynamics may contribute to the assembly of ASC, Biology, 12(6), 796, 2023 DOI: 10.3390/biology12060796
  3. Ruheena Javed, Ashish Jain, Thabata Duque, Emily Hendrix, Aurore Claude - Taupin, Sajjad Khan, Jingyue Jia, Lee Allers, Graham Timmins, Fulong Wang, Michelle Salemi, Brett Phinney, Keith Lidke, Tor Erik Rusten, Yi He, Fulvio Reggiori, Eeva - Liisa Eskelinen* and Vojo Deretic* - Mammalian ATG8 proteins and ATG9A direct sealing of autophagosomal membranes, EMBO J., e112845, 2023 DOI: 10.15252/embj.2022112845
  4. Catriona Gordon#, Emily Hendrix#, Yi He, Mark Walker*  - A ColabFold-based computational pipeline to accurately predict RiPP complex structures, Biomolecules, 13(8), 1243, 2023 DOI: 10.3390/biom13081243
  5. Tongtong Li, Shenghan Song, Yi He* - Temporary Solution for Investigating γ-AApeptide Packing via Molecular Dynamics, Supramolecular Materials, 2023 DOI:10.1016/j.supmat.2023.100038
  6. Shenghan Song, Tongtong Li, Taha Raad##, Amy O. Stevens, Yi He* - How key residues determine the mechanical responses of BAR dimer to external force, Curr. Protein Pept. Sci., 2023  DOI: 10.2174/1389203724666230522093842
  7. Xiaosi Li, Qi Li, Shenghan Song, Amy O. Stevens, Yi He and Chao Zhao* - Emulsion-induced polymersomes taming tetrodotoxin for prolonged duration local anesthesia, Adv. Ther., 2200199, 2022 DOI:10.1002/adtp.202200199

2022

  1. Amy O. Stevens, Yi He* - Allosterism in the PDZ family, Int. J. Mol. Sci., 23(3):1454, 2022, DOI: 10.3390/ijms23031454
  2. Jessica L. Binder, Joel Berendzen, Amy O. Stevens, Jian Wang, Yi He, Nikolay V. Dokholyan, & Tudor I. Oprea* - AlphaFold Models Illuminate Half of Dark Human Proteins, 74:102372, Curr. Opin. Struct. Biol., 2022, DOI:10.1101/2021.11.04.467322
  3. Amy O. Stevens, Yi He* - Evaluation of loop structures in AlphaFold 2 predictions, Biomolecules, 12(7), 985, 2022 DOI:10.3390/biom12070985
  4. Tongtong Li, Stefano Motta*, Amy O. Stevens, Shenghan Song, Emily Hendrix, Alessandro Pandini, Yi He* -  Recognizing the binding pattern and dissociation pathways of p300 Taz2 - p53 TAD2 complex, J. Am. Chem. Soc. Au, 2(8) 1935–1945, 2022 DOI: 10.1021/jacsau.2c00358
  5. Amy O. Stevens, Samuel Luo##, Yi He* -Three binding conformations of BIO124 in the pocket of the PICK1 PDZ domain, Cells, 11(15), 2451, 2022 DOI: 10.3390/cells11152451
  6. Emily Hendrix, Stefano Motta, Robert Gahl*, Yi He* - Insight into the initial stages of the folding process in Onconase revealed by UNRES, J. Chem. Phys. B, 126(40), 7934–7942, 2022 DOI:10.1021/acs.jpcb.2c04770
  7. Amy O. Stevens, John Kazan, Banu Ozkan*, Yi He* - Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations, Protein Sci., e4474, 2022 DOI: 10.1002/pro.4474
  8. Xinyuan Shan, Madison Morey, Zhenxi Li, Sheng Zhao, Shenghan Song, Zhenxue Xiao, Hao Feng, Shilun Gao, Guoran Li, Alexei Sokolov, Emily Ryan, Kang Xu, Ming Tian, Yi He, Huabin Yang, Pengfei Cao - A Polymer Electrolyte with High Cationic Transport Number for Safe and Stable Solid Li-metal Batteries, ACS Energy Lett., 7, 4342–4351, 2022 DOI: 10.1021/acsenergylett.2c02349

2021

  1. Amy O. Stevens, Yi He* - Residue-level contact reveals modular domain interactions of PICK1 are driven by both electrostatic and hydrophobic forces, Front. Mol. Biosci., 7:6161352020, 2021, DOI: 10.3389/fmolb.2020.616135 
  2. Sheng Zhao, Shenghan Song, Yingqi Wang,  Jong Keum,  Jiadeng Zhu, Yi He, Alexei Sokolov*, Peng-Fei Cao* - Unraveling the Role of Neutral Units for Single-Ion Conducting Polymer Electrolytes,  ACS Appl. Mater. Interfaces, 13(43):51525–51534, 2021, DOI: 10.1021/acsami.1c15641

2020

  1. Laura I. Gil##, Laurie N. Milko##, Yi He* - Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: A case study, Biophysics Reports, 1, 2020, DOI:10.1007/s41048-020-00107-w
  2. Tongtong Li, Amy O. Stevens, Laura I. Gil Pineda, Shenghan Song, Christabel A. Ameyaw Baah, Yi He* - Changes in structure and flexibility of p53 TAD2 upon binding to p300 Taz2, J. Theor. Comput. Chem., 2040007, 2020 DOI: 10.1142/S0219633620400076

Selected Publications Before Joining UNM 

  1. Y He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor Muñoz – Glutton: A tool for generating structural ensembles of partly disordered proteins from chemical shifts, Bioinformatics, bty755 (2018)
  2. Y He, GG Maisuradze, Y Yin, K Kachlishvili, S Rackovsky, HA Scheraga – Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins,Proc. Natl. Acad. Sci., U.S.A., 114 (7):1578-1583 (2017)
  3. Y He, A Liwo, HA Scheraga – Optimization of a Nucleic Acids united-RESidue 2-Point Model (NARES-2P) Force Field with a Maximum-Likelihood Approach, J. Chem. Phys., 143, 243111 (2015)
  4. Y He, S Rackovsky, Y Yin, HA Scheraga – Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proc. Natl. Acad. Sci., U.S.A., 112, 5029-5032 (2015).(F1000Prime - Article Recommendations ) 
  5. Y He, M Maciejczyk, S Ołdziej, HA Scheraga, A Liwo – Mean-field interactions between nucleic acid base dipoles drive formation of the double helix, Phys. Rev. Lett., 110, 098101 (2013)
  6. Y He, MA Mozolewska, P Krupa, AK Sieradzan, TK Wirecki, A Liwo, K Kachlishvili, S Rackovsky, D Jagieła, R Ślusarz, C Czaplewski, S Ołdziej and HA Scheraga – Lessons from application of the UNRES force field to predictions of structures of CASP10 targets,Proc. Natl. Acad. Sci., U.S.A., 110, 14936-14941 (2013) (F1000Prime - Article Recommendations )
  7. A Liwo, Y He, HA Scheraga – Coarse-grained force field: general folding theory, Phys. Chem. Chem. Phys., 13 (38), 16890-16901 (2011)
  8. Y He, A Liwo, H Weinstein, HA Scheraga – PDZ Binding to the BAR domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics, J. Mol. Biol., 405, 298-314 (2011)