Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Computational study of protein folding and dimerization on the ribosome

2019/35/B/ST4/02086

Keywords:

protein folding translation-elongation kinetics protein profiling analysis protein structure protein dimerization hydrophobic interactions molecular dynamics all-atom and coarse-grained force fields

Descriptors:

  • ST4_004:
  • ST4_001:
  • ST4_009:

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Instytut Fizyki Polskiej Akademii Nauk

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Mai Suan Li 

Number of co-investigators in the project: 4

Call: OPUS 18 - announced on 2019-09-16

Amount awarded: 558 000 PLN

Project start date (Y-m-d): 2020-08-26

Project end date (Y-m-d): 2024-02-25

Project duration:: 42 months (the same as in the proposal)

Project status: Project completed

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (34)
  1. Charge-charge interaction in three-layer systems: Classical approach
    Authors:
    A. M. Gabovich , M. S. Li, H. Szymczak , A. I. Voitenko
    Academic press:
    Phys.Rev. B (rok: 2022, tom: 105, strony: 115415), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1103/PhysRevB.105.115415 - link to the publication
  2. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force
    Authors:
    Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch, and Edward P. O'Brien
    Academic press:
    Biochemistry (rok: 2021, tom: 60, strony: 3223–3235), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.biochem.1c00507 - link to the publication
  3. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study
    Authors:
    3. Hoang Linh Nguyen, Huynh Quang Linh, Paolo Matteini, Giovanni La Penna, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2020, tom: 124, strony: 11337–11348), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.0c07312 - link to the publication
  4. Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution
    Authors:
    Hoang Linh Nguyen, Nguyen Quoc Thai, Mai Suan Li
    Academic press:
    J. Chem. Theory Comput. (rok: 2022, tom: 18, strony: 3860–3872), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jctc.1c01158 - link to the publication
  5. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation
    Authors:
    Hoang Linh Nguyen, Nguyen Quoc Thai, Phuong H. Nguyen, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: 126, strony: 4669–4678), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c01048 - link to the publication
  6. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force
    Authors:
    Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch, and Edward P. O'Brien
    Academic press:
    Biochemistry (rok: 2021, tom: 60, strony: 3223–3235), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.biochem.1c00507 - link to the publication
  7. Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study
    Authors:
    Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, and Phuong H. Nguyen
    Academic press:
    Langmuir (rok: 2021, tom: 37, strony: 7945–7954), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.langmuir.1c00555 - link to the publication
  8. Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody
    Authors:
    Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O'Brien, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2021, tom: 125, strony: 7368–7379), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.1c03639 - link to the publication
  9. Dependence of Work on the Pulling speed in Mechanical Ligand Unbinding
    Authors:
    Hong An Pham, Duc Toan Truong, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2021, tom: 125, strony: 8325–8330), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.1c01818 - link to the publication
  10. Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine based compounds on β-amyloid aggregation
    Authors:
    Daniela Marasco, Caterina Vicidomini, Pawel Krupa, Federica Cioffi, Pham Dinh Quoc Huy, Mai Suan Li, Daniele Florio, Kerensa Broersen, Maria Francesca De Pandis, and Giovanni N.Roviello
    Academic press:
    Chemico-Biological Interactions (rok: 2021, tom: 334, strony: 109300), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.cbi.2020.109300 - link to the publication
  11. Molecular mechanism of ultrasound interaction with a blood brain barrier model
    Authors:
    Man Viet Hoang, Mai Suan Li, Philippe Derreumaux, Junmei Wang, Toan T. Nguyen, S. Nangia, and Phuong H. Nguyen
    Academic press:
    J Chem Phys (rok: 2020, tom: 153, strony: 45104), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1063/5.0010667 - link to the publication
  12. Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody
    Authors:
    Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O'Brien, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2021, tom: 125, strony: 7368–7379), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.1c03639 - link to the publication
  13. Protein aggregation rate depends on mechanical stability of fibrillar structure
    Authors:
    Tran Thi Minh Thu and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2022, tom: 157, strony: 55101), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1063/5.0088689 - link to the publication
  14. dentifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases
    Authors:
    Hoang Linh Nguyen, Nguyen Quoc Thai and Mai Suan Li
    Academic press:
    Journal of Biomolecular Structure and Dynamics (rok: 2022, tom: xxx, strony: xxx), Wydawca: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/07391102.2022.2114941 - link to the publication
  15. Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability
    Authors:
    Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O'Brien, and Mai Suan Li.
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: 126, strony: 2812–2823.), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c00708 - link to the publication
  16. Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine based compounds on β-amyloid aggregation
    Authors:
    Daniela Marasco, Caterina Vicidomini, Pawel Krupa, Federica Cioffi, Pham Dinh Quoc Huy, Mai Suan Li, Daniele Florio, Kerensa Broersen, Maria Francesca De Pandis, and Giovanni N.Roviello
    Academic press:
    Chemico-Biological Interactions (rok: 2021, tom: 334, strony: 109300), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.cbi.2020.109300 - link to the publication
  17. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
    Authors:
    Phuong H. Nguyen, Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, Joan-Emma Shea, Nikolay V. Dokholyan, Alfonso De Simone, Buyong MaBuyong Ma Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China More by Buyong Ma Orcidhttp://orcid.org/0000-0002-7383-719X , Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, and Philippe Derreumaux
    Academic press:
    Chem Rev (rok: 2021, tom: 121, strony: 2545–2647), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.chemrev.0c01122 - link to the publication
  18. The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering
    Authors:
    Quyen V Vu, Yang Jiang, Mai Suan Li, Edward O'Brien
    Academic press:
    Chemical Science (rok: 2021, tom: 12, strony: 11851-11857), Wydawca: RSC
    Status:
    Published
    DOI:
    10.1039/D1SC01008E - link to the publication
  19. Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution
    Authors:
    Hoang Linh Nguyen, Nguyen Quoc Thai, Mai Suan Li
    Academic press:
    J. Chem. Theory Comput. (rok: 2022, tom: 18, strony: 3860–3872), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jctc.1c01158 - link to the publication
  20. Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse
    Authors:
    Nguyen Hoang Linh, Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux, Thi Ly Mai, and Phuong H. Nguyen
    Academic press:
    J. Chem. Phys. (rok: 2022, tom: 157, strony: 225102), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1063/5.0105675 - link to the publication
  21. The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering
    Authors:
    Quyen V Vu, Yang Jiang, Mai Suan Li, Edward O'Brien
    Academic press:
    Chemical Science (rok: 2021, tom: 12, strony: 11851-11857), Wydawca: RSC
    Status:
    Published
    DOI:
    10.1039/D1SC01008E - link to the publication
  22. Antibody–nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants
    Authors:
    Hung Nguyen & Mai Suan Li
    Academic press:
    Scientific Reports (rok: 2022, tom: 12, strony: Article number: 9701), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41598-022-14263-1 - link to the publication
  23. Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity
    Authors:
    Hoang Linh Nguyen, Huynh Quang Linh, Pawel Krupa, Giovanni La Penna, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: 126, strony: 3659–3672), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c01769 - link to the publication
  24. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study
    Authors:
    3. Hoang Linh Nguyen, Huynh Quang Linh, Paolo Matteini, Giovanni La Penna, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2020, tom: 124, strony: 11337–11348), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.0c07312 - link to the publication
  25. Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study
    Authors:
    Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, and Phuong H. Nguyen
    Academic press:
    Langmuir (rok: 2021, tom: 37, strony: 7945–7954), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.langmuir.1c00555 - link to the publication
  26. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
    Authors:
    Phuong H. Nguyen, Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, Joan-Emma Shea, Nikolay V. Dokholyan, Alfonso De Simone, Buyong MaBuyong Ma Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China More by Buyong Ma Orcidhttp://orcid.org/0000-0002-7383-719X , Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, and Philippe Derreumaux
    Academic press:
    Chem Rev (rok: 2021, tom: 121, strony: 2545–2647), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.chemrev.0c01122 - link to the publication
  27. Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling
    Authors:
    Martina Banchelli, Roberta Cascella, Cristiano D'Andrea, Giovanni La Penna, Mai Suan Li, Fabrizio Machetti, Paolo Matteini, and Silvia Pizzanelli
    Academic press:
    ACS Chem. Neurosci (rok: 2021, tom: 12, strony: 1150–1161), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acschemneuro.0c00714 - link to the publication
  28. Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
    Authors:
    Adolfo B. Poma, Tran Thi Minh Thu, Lam Tang Minh Tri, Hoang Linh Nguyen, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2021, tom: 125, strony: 7628–7637), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.1c02322 - link to the publication
  29. Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling
    Authors:
    Martina Banchelli, Roberta Cascella, Cristiano D'Andrea, Giovanni La Penna, Mai Suan Li, Fabrizio Machetti, Paolo Matteini, and Silvia Pizzanelli
    Academic press:
    ACS Chem. Neurosci (rok: 2021, tom: 12, strony: 1150–1161), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acschemneuro.0c00714 - link to the publication
  30. Remdesivir Strongly Binds to both RNA-dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations
    Authors:
    Hoang Linh Nguyen, Thai Nguyen, Duc Toan Truong, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2020, tom: 124, strony: 7336–7347), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.0c04511 - link to the publication
  31. Protein aggregation rate depends on mechanical stability of fibrillar structure
    Authors:
    Tran Thi Minh Thu and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2022, tom: 157, strony: 55101), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1063/5.0088689 - link to the publication
  32. Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
    Authors:
    Adolfo B. Poma, Tran Thi Minh Thu, Lam Tang Minh Tri, Hoang Linh Nguyen, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2021, tom: 125, strony: 7628–7637), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.1c02322 - link to the publication
  33. Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity
    Authors:
    Hoang Linh Nguyen, Huynh Quang Linh, Pawel Krupa, Giovanni La Penna, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: 126, strony: 3659–3672), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c01769 - link to the publication
  34. Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability
    Authors:
    Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O'Brien, and Mai Suan Li.
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: 126, strony: 2812–2823.), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c00708 - link to the publication

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