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Inhibitors, protein aggregation and carbon nanotube

2011/01/B/NZ1/01622

Keywords

Descriptors

  • NZ1_3: Biofizyka
  • NZ1_1: Biologia molekularna
  • ST4_15: Chemia teoretyczna i obliczeniowa

Panel

NZ1 – Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution

Instytut Fizyki PAN

Voivodeship: mazowieckie

Other projects carried out by the institution »

Principal investigator (from the host institution)

dr hab. Mai Suan Li

Number of co-investigators in the project: 5

Call

OPUS 1 – announced on 2011-03-15

Amount awarded
214 500 PLN
Project start date
2011-12-06
Project end date
2014-12-05
Project duration
36 months (the same as in the proposal)
Project status
Project settled

Equipment purchased [PL]

  1. Notebook. Cost: 3 000 PLN
  2. Oprogramowanie (5 pcs). Cost: 3 298 PLN
  3. Serwer obliczeniowy. Cost: 60 000 PLN

Information in the final report

Publication in academic press/journals (23)

  1. A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

    Authors:
    M. Kouza, C-K. Hu, Mai Suan Li, and A. Kolinski
    Academic press:
    J. Chem. Phys. (year: 2013, volume: 139, pages: 65103), Publisher: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4817773 – link to the publication

  2. Curcumin Binds to Ab40 Peptides and Fibrils Stronger Than Ibuprofen and Naproxen

    Authors:
    Son Tung Ngo and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (year: 2012, volume: 116, pages: 10165-10175), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/jp302506a – link to the publication

  3. Oligomerization of peptides LVEALYL and RGFFYT and their binding affinity to insulin

    Authors:
    H. -L. Chiang, S. T. Ngo, C. -J. Chen, C.-K. Hu, and M. S. Li
    Academic press:
    Plos One (year: 2013, volume: 8, pages: e65358), Publisher: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0065358 – link to the publication

  4. Binding of fullerenes to amyloid beta fibrils: Size matters

    Authors:
    Pham Dinh Quoc Huy and Mai Suan Li
    Academic press:
    Phys. Chem. Chem. Phys (year: 2014, volume: 16, pages: 20030), Publisher: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/c4cp02348j – link to the publication

  5. Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models

    Authors:
    Nguyen Truong Co, Chin-Kun Hu, and Mai Suan Li
    Academic press:
    J. Chem. Phys. (year: 2013, volume: 138, pages: 185101), Publisher: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4804299 – link to the publication

  6. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Ab40 and Ab42

    Authors:
    M.H. Viet, P.H. Nguyen, S.T. Ngo, Mai Suan Li, and P. Derreumaux
    Academic press:
    ACS Chemical Neuroscience (year: 2013, volume: 4, pages: 1446), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cn400110d – link to the publication

  7. Amyloid peptide Ab40 inhibits aggregation of Ab42: evidence from molecular dynamics simulations

    Authors:
    Man Hoang Viet and Mai Suan Li
    Academic press:
    J. Chem. Phys. (year: 2012, volume: 136, pages: 245105), Publisher: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4817773 – link to the publication

  8. New method for determining size of critical nucleus of fibril formation of polypeptide chains

    Authors:
    Nguyen Truong Co and Mai Suan Li
    Academic press:
    J. Chem. Phys. (year: 2012, volume: 137, pages: 95101), Publisher: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4749257 – link to the publication

  9. Amyloid oligomer structure characterization from simulations: A general method

    Authors:
    Phuong Hoang Nguyen, Philippe Derreumaux, and Mai Suan Li
    Academic press:
    J. Chem. Phys. (year: 2014, volume: 140, pages: 94105), Publisher: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4866902 – link to the publication

  10. Discovery of Dihydrochalcone as potential lead for Alzheimer's disease: in silico and in vitro study

    Authors:
    M. H. Viet, C-Y. Chen, C-K. Hu, Y-R. Chen, and Mai Suan Li
    Academic press:
    Plose One (year: 2013, volume: 8, pages: e79151), Publisher: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0079151 – link to the publication

  11. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    Authors:
    Trang Truc Nguyen, Man Hoang Viet, and Mai Suan Li
    Academic press:
    The Scientific World Journal (year: 2014, volume: 2014, pages: Article number 536084), Publisher: Hindawi
    Status:
    Published
    DOI:
    10.1155/2014/536084 – link to the publication

  12. Binding of glyco-acridine derivatives to lysozyme leads to inhibition of amyloid fibrillization, Biomacromolecules

    Authors:
    V.Q. Vuong, K. Siposova,T.T. Nguyen, A. Antosova, L. Balogova, L. Drajna,J. Imrich, M. S. Li, and Z. Gazova
    Academic press:
    Biomacromolecules (year: 2013, volume: 14, pages: 1035-1043), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/bm301891q – link to the publication

  13. Stationary Josephson current in junctions involving d-wave superconductors with charge density waves: the temperature dependence and deviations from the law of corresponding states

    Authors:
    Alexander M. Gabovich, Mai Suan Li, Henryk Szymczak, and Alexander I. Voitenko
    Academic press:
    EUROPEAN PHYSICAL JOURNAL B (year: 2014, volume: 87, pages: 115), Publisher: Springer
    Status:
    Published
    DOI:
    10.1140/epjb/e2014-41063-0 – link to the publication

  14. In silico and in vitro study of binding affinity oftripeptides to amyloid beta fibrils: Implications for Alzheimer's disease

    Authors:
    Man Hoang Viet, Katarina Siposova, Zuzana Bednarikova, Andrea Antosova, Truc Trang Nguyen, Zuzana Gazova, and Mai Suan Li
    Academic press:
    J Phys Chem B (year: 2015, volume: 119, pages: 5145), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.5b00006 – link to the publication

  15. Amyloid β-protein and Alzheimer's disease: when computer simulations complement experimental studies

    Authors:
    J. Nasica-Labouze, Phuong Nguyen, F. Sterpone, O. Bertomieu, N-V. Buchete, S. Cote, A. De Simone, A. Doig, P. Fallen, A. Garcia, A. Laio, Mai Suan Li, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D. Resenman, B. Strodel, B. Tarus, J. Viles, T. Zang, C. Wang, and P. Derreumaux
    Academic press:
    Chemical Reviews (year: 2015, volume: 115, pages: 3518-3563), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cr500638n – link to the publication

  16. Streered molecular dynamics – a promising tool for drug design

    Authors:
    Mai Suan Li and Binh Khanh Mai
    Academic press:
    Current Bioinformatics (year: 2012, volume: 7, pages: 342-351), Publisher: Bentham Science Publisher LTD
    Status:
    Published
    DOI:
    10.2174/1574893611207040342 – link to the publication

  17. Estimation of the binding free energy of AC1NX476 to HIV-1 protease wild-type and mutations using free energy perturbation method

    Authors:
    Son Tung Ngo, Binh Khanh Mai, Dinh Minh Hiep, and Mai Suan Li
    Academic press:
    Chem Biol Drug Design (year: 2015, volume: 86, pages: 546–558), Publisher: Wiley
    Status:
    Published
    DOI:
    10.1111/cbdd.12518 – link to the publication

  18. Inhibition of insulin amyloid fibrillization by glyco-acridines: anin vitro andin silico study

    Authors:
    Quan Van Vuong, Zuzana Bednarikova, Andrea Antosova, Pham Dinh Quoc Huy, Katarina Siposova, Nguyen Anh Tuan, Mai Suan Li and Zuzana Gazova
    Academic press:
    Med Chem Commun (year: 2015, volume: 6, pages: 810), Publisher: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/C5MD00004A – link to the publication

  19. Effect of Taiwan Mutation (D7H) on Structures of Amyloid Beta Peptides: Replica Exchange Molecular Dynamics Study

    Authors:
    Phan Minh Truong, Man Hoang Viet, Phuong H. Nguyen, C. K. Hu, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (year: 2014, volume: 118, pages: 8972), Publisher: ACS Publishing
    Status:
    Published
    DOI:
    10.1021/jp503652s – link to the publication

  20. Exploring the potent inhibitors against NS3/4A protease of hepatitis C virus using steered molecular dynamics technique

    Authors:
    Arthitaya Meeprasert, Thanyada Rungrotmongkol, Mai Suan Li, Supot Hannongbua
    Academic press:
    Current Pharmaceutical Design (year: 2014, volume: 20, pages: 3465), Publisher: BENTHAM SCIENCE PUBL LTD
    Status:
    Published

  21. In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease

    Authors:
    P.D.Q. Huy, Y-C. Yu, Son Tung Ngo, Tran Van Thao, C-P Chen, M. S. Li, and Y-C Chen
    Academic press:
    Biochimica et Biophysica Acta-General Subjects (year: 2013, volume: 1380, pages: 2960-2969), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbagen.2012.12.026 – link to the publication

  22. Top-leads from natural products for treatment of Alzheimer's disease: Docking and molecular dynamics study

    Authors:
    Son Tung Ngo and Mai Suan Li
    Academic press:
    Molecular Simulation (year: 2013, volume: 39, pages: 279-291), Publisher: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/08927022.2012.718769 – link to the publication

  23. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Abeta and Abeta42

    Authors:
    Man Hoang Viet, Phuong H. Nguyen, P. Derreumaux, and Mai Suan Li
    Academic press:
    ACS Chem Neurosci. (year: 2014, volume: 5, pages: 646), Publisher: ACS Publishing
    Status:
    Published
    DOI:
    10.1021/cn500007j – link to the publication

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