Computational exploration of the self-aggregation mechanisms of phenol-soluble modulins β1 and β2 in Staphylococcus aureus biofilms

Authors: Xu, Huan ^a, Zhang, Xiaohan ^a, Lv, Zhongyue ^b, Huang, Fengjuan ^c, Zou, Yu ^d, Wang, Chuang ^{e, ⁎}, Ding, Feng ^{f, ⁎}, Sun, Yunxiang ^{a, f, ⁎⁎}

Source: In Colloids and Surfaces B: Biointerfaces April 2025 248

Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations

Authors: Wang, Bo^{aff1, aff2}, Sun, Yunxiang^aff1, Davis, Thomas P.^aff3, Ke, Pu Chun^aff3, Wu, Yinghao^aff2, Ding, Feng^aff1

Source: ACS Sustainable Chemistry & Engineering. 6(9):11704-11715

Availability: https://pubs.acs.org/doi/10.1021/acssuschemeng.8b01959

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Authors: Chen, Jiaxing ^{1, 6}, Zaer, Sofia ^{2, 6}, Drori, Paz ², Zamel, Joanna ², Joron, Khalil ², Kalisman, Nir ², Lerner, Eitan ^{2, 3, ∗}, Dokholyan, Nikolay V. ^{1, 4, 5, 7, ∗∗}

Source: In Structure 2 September 2021 29(9):1048-1064

Fuzzy supertertiary interactions within PSD-95 enable ligand binding

Authors: George L Hamilton, Nabanita Saikia, Sujit Basak, Franceine S Welcome, Fang Wu, Jakub Kubiak, Changcheng Zhang, Yan Hao, Claus AM Seidel, Feng Ding, Hugo Sanabria, Mark E Bowen

Source: eLife, Vol 11 (2022)

Subject Terms: protein dynamics, single molecule fluorescence, postsynaptic density, FRET, discrete molecular dynamics simulations, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/77242; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/253718a2b64044b084b1faac60a77f9a

Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide

Authors: Pu Chun Ke, Aleksandr Kakinen, Yanting Xing, Feng Ding, Thomas P. Davis, Yunxiang Sun, Emily H. Pilkington

Source: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 1865:434-444

Subject Terms: 0301 basic medicine, 0303 health sciences, Entropy, Type 2 diabetes, Molecular Dynamics Simulation, Protein Structure, Secondary, Islet Amyloid Polypeptide, β-Barrel oligomer, Protein Aggregates, 03 medical and health sciences, 1313 Molecular Medicine, Nucleation, 1312 Molecular Biology, Oligomerization, Humans, Thermodynamics, Protein Multimerization, Amyloid aggregation, Discrete molecular dynamics simulations

Access URL: https://pubmed.ncbi.nlm.nih.gov/30502402
https://pubmed.ncbi.nlm.nih.gov/30502402/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310638
https://www.sciencedirect.com/science/article/abs/pii/S0925443918304836
https://wrap.warwick.ac.uk/120483/
https://findanexpert.unimelb.edu.au/scholarlywork/1436317-nucleation-of-beta-rich-oligomers-and-beta-barrels-in-the-early-aggregation-of-human-islet-amyloid-polypeptide
https://www.sciencedirect.com/science/article/pii/S0925443918304836

Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-Cell Toxicity by OH-Terminated PAMAM Dendrimer

Authors: Gurzov, EN, Wang, B, Pilkington, EH, Chen, P, Kakinen, A, Stanley, WJ, Litwak, SA, Hanssen, EG, Davis, TP, Ding, F, Ke, PC

Source: Small. 12:1615-1626

Subject Terms: Models, Molecular, 0301 basic medicine, Engineering, high-throughput dynamic light scattering, Materials Science and Engineering, Models, Dendrimers -- toxicity, Insulin-Secreting Cells, Insulin, Diabetes-Mellitus, Alzheimers-Disease, Oil Dispersants, 2. Zero hunger, 0303 health sciences, Cell Death, Physics, Amyloid -- metabolism, Sciences bio-médicales et agricoles, Islet Amyloid Polypeptide, 3. Good health, Cytoprotection -- drug effects, Iapp, cytotoxicity, Islet, Amyloid, Dendrimers, human islet amyloid polypeptide, amyloid fibrillation, Science, hydroxyl-terminated polyamidoamine dendrimer, Hydroxylation, Protein Multimerization -- drug effects, protein aggregation, Protein Aggregates -- drug effects, Protein Aggregates, 03 medical and health sciences, Thiazoles -- metabolism, Islet Amyloid Polypeptide -- metabolism, Humans, Cell Death -- drug effects, Benzothiazoles, discrete molecular dynamics simulations, hydroxyl‐terminated polyamidoamine dendrimer, Polypeptide Fibril Formation, Molecular, Discrete Molecular-Dynamics, Insulin-Secreting Cells -- drug effects -- pathology, Thiazoles, high‐throughput dynamic light scattering, In-Vitro, Cytoprotection, Branched Polyamines, Protein Multimerization

File Description: No full-text files; application/pdf

Access URL: http://minerva-access.unimelb.edu.au/bitstream/11343/290861/1/smll.201502317.pdf
https://pubmed.ncbi.nlm.nih.gov/26808649
http://europepmc.org/abstract/MED/26808649
https://www.ncbi.nlm.nih.gov/pubmed/26808649
https://difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/260224/Details
https://onlinelibrary.wiley.com/doi/full/10.1002/smll.201502317
https://research.monash.edu/en/publications/inhibition-of-hiapp-amyloid-aggregation-and-pancreatic-%CE%B2-cell-tox
https://onlinelibrary.wiley.com/doi/10.1002/smll.201502317/full

Discrete Molecular Dynamics Study of Aβ16-22 Folding and Aggregation

Authors: S. Peng, B. Urbanc, S. V. Buldyrev, L. Cruz, S. Yun, D. B. Teplow, H. E. Stanley

Contributors: The Pennsylvania State University CiteSeerX Archives

Source: http://cps-www.bu.edu/hes/articles/pubcyts05.pdf.

Subject Terms: Alzheimer’s disease, amyloid β-protein, discrete molecular dynamics simulations, cross-β

File Description: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.379.699

Availability: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.379.699
http://cps-www.bu.edu/hes/articles/pubcyts05.pdf

Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide

Authors: Sun, Yunxiang, Kakinen, Aleksandr, Xing, Yanting, Pilkington, Emily H., Davis, Thomas P., Ke, Pu Chun, Ding, Feng

Subject Terms: Amyloid aggregation, Discrete molecular dynamics simulations, Nucleation, Oligomerization, Type 2 diabetes, β-Barrel oligomer, 1312 Molecular Biology, 1313 Molecular Medicine

Relation: orcid:0000-0003-1547-2855; CBET-1553945; CE140100036; R35GM119691

Availability: https://espace.library.uq.edu.au/view/UQ:816516f

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

Authors: Brodie, Nicholas I., Popov, Konstantin I., Petrotchenko, Evgeniy V., Dokholyan, Nikolay V., Borchers, Christoph H.

Source: Science Advances, 3(7)

Subject Terms: structural proteomics, surface modification, protein structure, hydrogen/deuterium exchange, DMD, HDX, crosslinking, crosslinking distance constraints, discrete molecular dynamics simulations

Relation: https://cdr.lib.unc.edu/downloads/ff365b62d?file=thumbnail; https://cdr.lib.unc.edu/downloads/ff365b62d

Availability: https://doi.org/10.17615/49hd-1e89
https://cdr.lib.unc.edu/downloads/ff365b62d?file=thumbnail
https://cdr.lib.unc.edu/downloads/ff365b62d

Inhibition of hIAPP Amyloid Aggregation and Pancreatic Beta-Cell Toxicity by OH-Terminated PAMAM Dendrimer.

Authors: Gurzov, Esteban Nicolas, Wang, Bo, Pilkington, Emily H, Chen, Pengyu, Kakinen, Aleksandr, Stanley, William J, Litwak, Sara A, Hanssen, Eric G, Davis, Thomas P, Ding, Feng, Ke, Pu Chun

Source: Small, 12 (12

Subject Terms: Sciences bio-médicales et agricoles, Amyloid -- metabolism, Cell Death -- drug effects, Cytoprotection -- drug effects, Dendrimers -- toxicity, Humans, Hydroxylation, Insulin-Secreting Cells -- drug effects -- pathology, Islet Amyloid Polypeptide -- metabolism, Models, Molecular, Protein Aggregates -- drug effects, Protein Multimerization -- drug effects, Thiazoles -- metabolism, amyloid fibrillation, cytotoxicity, discrete molecular dynamics simulations, high-throughput dynamic light scattering, human islet amyloid polypeptide, hydroxyl-terminated polyamidoamine dendrimer, protein aggregation

File Description: No full-text files

Relation: uri/info:doi/10.1002/smll.201502317; uri/info:pmid/26808649

Availability: http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/260224