Citations (69)
Keep up to date with the latest research on this topic with citation updates for this article.
Read on this site (7)
Kingsley Y. Wu, David Doan, Marco Medrano & Chia-en A. Chang. (2022) Modeling structural interconversion in Alzheimers’ amyloid beta peptide with classical and intrinsically disordered protein force fields. Journal of Biomolecular Structure and Dynamics 40:20, pages 10005-10022.
Read now
Read now
Gianvito Grasso & Andrea Danani. (2020) Molecular simulations of amyloid beta assemblies. Advances in Physics: X 5:1.
Read now
Read now
Rajneet Kaur Saini, Suniba Shuaib, Deepti Goyal & Bhupesh Goyal. (2019) Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics 37:12, pages 3183-3197.
Read now
Read now
Suniba Shuaib & Bhupesh Goyal. (2018) Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 36:3, pages 663-678.
Read now
Read now
Sangeeta Kundu. (2018) Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35–56) in aqueous environment. Journal of Biomolecular Structure and Dynamics 36:2, pages 302-317.
Read now
Read now
Orkid Coskuner Weber & Vladimir N. Uversky. (2017) How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42 in water. Intrinsically Disordered Proteins 5:1.
Read now
Read now
Shelly DeForte, Krishna D. Reddy & Vladimir N. Uversky. (2016) Quarterly intrinsic disorder digest (January-February-March, 2014). Intrinsically Disordered Proteins 4:1.
Read now
Read now
Articles from other publishers (62)
Ian Cook & Thomas S. Leyh. (2023) Sterol-activated amyloid beta fibril formation. Journal of Biological Chemistry 299:12, pages 105445.
Crossref
Crossref
N. Salehi, A. Lohrasebi & A.K. Bordbar. (2023) Preventing the amyloid-beta peptides accumulation on the cell membrane by applying GHz electric fields: A molecular dynamic simulation. Journal of Molecular Graphics and Modelling 123, pages 108516.
Crossref
Crossref
Mei Fang, Kehe Su, Xin Wang, Ping Guan & Xiaoling Hu. (2023) Study on molecular mechanisms of destabilizing Aβ(1–42) protofibrils by licochalcone A and licochalcone B using molecular dynamics simulations. Journal of Molecular Graphics and Modelling 122, pages 108500.
Crossref
Crossref
Samal Kaumbekova, Mehdi Amouei Torkmahalleh, Masakazu Umezawa, Yanwei Wang & Dhawal Shah. (2023) Effect of carbonaceous ultrafine particles on the structure and oligomerization of Aβ42 peptide. Environmental Pollution 323, pages 121273.
Crossref
Crossref
Samal Kaumbekova, Mehdi Amouei Torkmahalleh, Naoya Sakaguchi, Masakazu Umezawa & Dhawal Shah. (2022) Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ42 protein. Frontiers of Environmental Science & Engineering 17:2.
Crossref
Crossref
Samal Kaumbekova, Mehdi Amouei Torkmahalleh & Dhawal Shah. (2022) Ambient Benzo[a]pyrene’s Effect on Kinetic Modulation of Amyloid Beta Peptide Aggregation: A Tentative Association between Ultrafine Particulate Matter and Alzheimer’s Disease. Toxics 10:12, pages 786.
Crossref
Crossref
Mei Fang, Quan Zhang, Ping Guan, Kehe Su, Xin Wang & Xiaoling Hu. (2022) Insights into Molecular Mechanisms of EGCG and Apigenin on Disrupting Amyloid-Beta Protofibrils Based on Molecular Dynamics Simulations. The Journal of Physical Chemistry B 126:41, pages 8155-8165.
Crossref
Crossref
Mei Fang, Quan Zhang, Xin Wang, Kehe Su, Ping Guan & Xiaoling Hu. (2022) Inhibition Mechanisms of (−)-Epigallocatechin-3-gallate and Genistein on Amyloid-beta 42 Peptide of Alzheimer’s Disease via Molecular Simulations. ACS Omega 7:23, pages 19665-19675.
Crossref
Crossref
Kelsie M. King, Amanda K. Sharp, Darcy S. Davidson, Anne M. Brown & Justin A. Lemkul. (2021) Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers. Journal of Computational Biophysics and Chemistry 21:04, pages 449-460.
Crossref
Crossref
Kelsie M. King, David R. Bevan & Anne M. Brown. (2022)
Molecular Dynamics Simulations Indicate Aromaticity as a Key Factor in the Inhibition of IAPP
(20–29)
Aggregation
. ACS Chemical Neuroscience 13:11, pages 1615-1626.
Crossref
Crossref
Grant E. Kawecki, Kelsie M. King, Nicholas A. Cramer, David R. Bevan & Anne M. Brown. (2022) Simulations of cross-amyloid aggregation of amyloid-β and islet amyloid polypeptide fragments. Biophysical Journal 121:11, pages 2002-2013.
Crossref
Crossref
Min Zhou, Huilin Wen, Huimin Lei & Tao Zhang. (2021) Molecular dynamics study of conformation transition from helix to sheet of Aβ42 peptide. Journal of Molecular Graphics and Modelling 109, pages 108027.
Crossref
Crossref
Samal Kaumbekova & Dhawal Shah. (2021)
Early Aggregation Kinetics of Alzheimer’s Aβ
16–21
in the Presence of Ultrafine Fullerene Particles and Ammonium Nitrate
. ACS Chemical Health & Safety 28:5, pages 369-375.
Crossref
Crossref
Pandurangan Kalipillai & Ethayaraja Mani. (2021) Adsorption of the amyloid β40 monomer on charged gold nanoparticles and slabs: a molecular dynamics study. Physical Chemistry Chemical Physics 23:34, pages 18618-18627.
Crossref
Crossref
Samal Kaumbekova, Mehdi Amouei Torkmahalleh & Dhawal Shah. (2021) Impact of ultrafine particles and secondary inorganic ions on early onset and progression of amyloid aggregation: Insights from molecular simulations. Environmental Pollution 284, pages 117147.
Crossref
Crossref
Ehsan Alimohammadi, Arash Nikzad, Mohammad Khedri, Sepehr Shafiee, Ahmad Miri Jahromi, Reza Maleki & Nima Rezaei. (2021) Molecular Tuning of the Nano–Bio Interface: Alpha-Synuclein’s Surface Targeting with Doped Carbon Nanostructures. ACS Applied Bio Materials 4:8, pages 6073-6083.
Crossref
Crossref
Ashim Paul, Guru KrishnaKumar Viswanathan, Adi Huber, Elad Arad, Hamutal Engel, Raz Jelinek, Ehud Gazit & Daniel Segal. (2021) Inhibition of tau amyloid formation and disruption of its preformed fibrils by Naphthoquinone–Dopamine hybrid. The FEBS Journal 288:14, pages 4267-4290.
Crossref
Crossref
Pablo G. Argudo & Juan J. Giner-Casares. (2021) Folding and self-assembly of short intrinsically disordered peptides and protein regions. Nanoscale Advances 3:7, pages 1789-1812.
Crossref
Crossref
Arghadwip Paul, Suman Samantray, Marco Anteghini, Mohammed Khaled & Birgit Strodel. (2021) Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment. Chemical Science.
Crossref
Crossref
Suman Samantray, Feng Yin, Batuhan Kav & Birgit Strodel. (2020) Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 60:12, pages 6462-6475.
Crossref
Crossref
Anupamjeet Kaur, Deepti Goyal & Bhupesh Goyal. (2020)
An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ
42
monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations
. Physical Chemistry Chemical Physics 22:48, pages 28055-28073.
Crossref
Crossref
Suresh Alagar & Ranjit Prasad Bahadur. (2020) DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination. International Journal of Biological Macromolecules 165, pages 918-929.
Crossref
Crossref
Xiaofeng Xing, Chengqiang Liu, Huijuan Yang, Muhammad Fahad Nouman & Hongqi Ai. (2020) Folding dynamics of Aβ42 monomer at pH 4.0–7.5 with and without physiological salt conditions – does the β1 or β2 region fold first?. New Journal of Chemistry 44:41, pages 18000-18013.
Crossref
Crossref
Rong-zu Nie, Yin-qiang Huo, Bo Yu, Chuan-ju Liu, Rui Zhou, Hong-hui Bao & Shang-wen Tang. (2020) Molecular insights into the inhibitory mechanisms of gallate moiety on the Aβ1–40 amyloid aggregation: A molecular dynamics simulation study. International Journal of Biological Macromolecules 156, pages 40-50.
Crossref
Crossref
Guru Krishnakumar Viswanathan, Dana Shwartz, Yelena Losev, Elad Arad, Chen Shemesh, Edward Pichinuk, Hamutal Engel, Avi Raveh, Raz Jelinek, Itzik Cooper, Fabien Gosselet, Ehud Gazit & Daniel Segal. (2019) Purpurin modulates Tau-derived VQIVYK fibrillization and ameliorates Alzheimer’s disease-like symptoms in animal model. Cellular and Molecular Life Sciences 77:14, pages 2795-2813.
Crossref
Crossref
Anupamjeet Kaur, Suniba Shuaib, Deepti Goyal & Bhupesh Goyal. (2020)
Interactions of a multifunctional di-triazole derivative with Alzheimer's Aβ
42
monomer and Aβ
42
protofibril: a systematic molecular dynamics study
. Physical Chemistry Chemical Physics 22:3, pages 1543-1556.
Crossref
Crossref
Justin A. Lemkul. 2020. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly
1
71
.
Pavan Krishna Kanchi & Ashok Kumar Dasmahapatra. (2019) Polyproline chains destabilize the Alzheimer’s amyloid-β protofibrils: A molecular dynamics simulation study. Journal of Molecular Graphics and Modelling 93, pages 107456.
Crossref
Crossref
Nikolaos Ntarakas, Inna Ermilova & Alexander P. Lyubartsev. (2019) Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations. European Biophysics Journal 48:8, pages 813-824.
Crossref
Crossref
Sanjay Kumar, V. Guru Krishnakumar, Vinod Morya, Sharad Gupta & Bhaskar Datta. (2019) Nanobiocatalyst facilitated aglycosidic quercetin as a potent inhibitor of tau protein aggregation. International Journal of Biological Macromolecules 138, pages 168-180.
Crossref
Crossref
Hoang Linh Nguyen, Pawel Krupa, Nguyen Minh Hai, Huynh Quang Linh & Mai Suan Li. (2019) Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations. The Journal of Physical Chemistry B 123:34, pages 7253-7269.
Crossref
Crossref
Chengqiang Liu, Wei Zhao, Xiaofeng Xing, Hu Shi, Baotao Kang, Haiying Liu, Ping Li & Hongqi Ai. (2019)
An Original Monomer Sampling from a Ready‐Made Aβ
42
NMR Fibril Suggests a Turn‐β‐Strand Synergetic Seeding Mechanism
. ChemPhysChem 20:12, pages 1649-1660.
Crossref
Crossref
Banafsheh Mehrazma & Arvi Rauk. (2019) Exploring Amyloid-β Dimer Structure Using Molecular Dynamics Simulations. The Journal of Physical Chemistry A 123:22, pages 4658-4670.
Crossref
Crossref
Maud Chan-Yao-Chong, Dominique Durand & Tâp Ha-Duong. (2019) Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. Journal of Chemical Information and Modeling 59:5, pages 1743-1758.
Crossref
Crossref
Viet Hoang Man, Xibing He, Philippe Derreumaux, Beihong Ji, Xiang-Qun Xie, Phuong H. Nguyen & Junmei Wang. (2019)
Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ
16–22
Dimer
. Journal of Chemical Theory and Computation 15:2, pages 1440-1452.
Crossref
Crossref
Deniz Meneksedag-Erol & Sarah Rauscher. 2019. Protein Self-Assembly. Protein Self-Assembly
243
262
.
Esraa Haj, Yelena Losev, V. Guru KrishnaKumar, Edward Pichinuk, Hamutal Engel, Avi Raveh, Ehud Gazit & Daniel Segal. (2018) Integrating in vitro and in silico approaches to evaluate the “dual functionality” of palmatine chloride in inhibiting and disassembling Tau-derived VQIVYK peptide fibrils. Biochimica et Biophysica Acta (BBA) - General Subjects 1862:7, pages 1565-1575.
Crossref
Crossref
Shayon Bhattacharya, Liang Xu & Damien Thompson. (2018) Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WIREs Computational Molecular Science 8:4.
Crossref
Crossref
Jie Zhong, Marcelo A. Carignano, Sabre Kais, Xiao Cheng Zeng, Joseph S. Francisco & Ivan Gladich. (2018) Tuning the Stereoselectivity and Solvation Selectivity at Interfacial and Bulk Environments by Changing Solvent Polarity: Isomerization of Glyoxal in Different Solvent Environments. Journal of the American Chemical Society 140:16, pages 5535-5543.
Crossref
Crossref
Orkid Coskuner-Weber & Vladimir Uversky. (2018) Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. International Journal of Molecular Sciences 19:2, pages 336.
Crossref
Crossref
Yanhua Ouyang, Likun Zhao & Zhuqing Zhang. (2018) Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Physical Chemistry Chemical Physics 20:13, pages 8676-8684.
Crossref
Crossref
Dingkun Hu, Wei Zhao, Yong Zhu, Hongqi Ai & Baotao Kang. (2017)
Bead‐Level Characterization of Early‐Stage Amyloid β
42
Aggregates: Nuclei and Ionic Concentration Effects
. Chemistry – A European Journal 23:64, pages 16257-16273.
Crossref
Crossref
Anupam Roy, Kousik Chandra, Sandip Dolui & Nakul C. Maiti. (2017) Envisaging the Structural Elevation in the Early Event of Oligomerization of Disordered Amyloid β Peptide. ACS Omega 2:8, pages 4316-4327.
Crossref
Crossref
Faezeh Kargar, Saeed Emadi & Hossein Fazli. (2017) The molecular behavior of a single β-amyloid inside a dipalmitoylphosphatidylcholine bilayer at three different temperatures: An atomistic simulation study: Aβ interaction with DPPC: Atomistic simulation. Proteins: Structure, Function, and Bioinformatics 85:7, pages 1298-1310.
Crossref
Crossref
Qinghua Liao, Michael C. Owen, Olujide O. Olubiyi, Bogdan Barz & Birgit Strodel. (2017) Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes. Israel Journal of Chemistry 57:7-8, pages 771-784.
Crossref
Crossref
Viet Hoang Man, Phuong H. Nguyen & Philippe Derreumaux. (2017) High-Resolution Structures of the Amyloid-β 1–42 Dimers from the Comparison of Four Atomistic Force Fields. The Journal of Physical Chemistry B 121:24, pages 5977-5987.
Crossref
Crossref
Ya Gao, Chaomin Zhang, John Z. H. Zhang & Ye Mei. (2017) Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling 57:2, pages 267-274.
Crossref
Crossref
Suniba Shuaib, Rajneet Kaur Saini, Deepti Goyal & Bhupesh Goyal. (2017)
Insights into the Inhibitory Mechanism of Dicyanovinyl-Substituted J147 Derivative against Aβ
42
Aggregation and Protofibril Destabilization: A Molecular Dynamics Simulation Study
. ChemistrySelect 2:4, pages 1645-1657.
Crossref
Crossref
Martín Carballo-Pacheco & Birgit Strodel. (2017) Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins. Protein Science 26:2, pages 174-185.
Crossref
Crossref
Luca Bellucci, Giovanni Bussi, Rosa Di Felice & Stefano Corni. (2017) Fibrillation-prone conformations of the amyloid-?-42 peptide at the gold/water interface. Nanoscale 9:6, pages 2279-2290.
Crossref
Crossref
Bhupesh Goyal, Kinshuk Raj Srivastava & Susheel Durani. (2016) Examination of the Effect of N‐terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine–based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 1:19, pages 6321-6327.
Crossref
Crossref
Anne M. Brown & David R. Bevan. (2016) Molecular Dynamics Simulations of Amyloid β -Peptide (1-42): Tetramer Formation and Membrane Interactions. Biophysical Journal 111:5, pages 937-949.
Crossref
Crossref
Ashish Verma, Akhil Kumar & Mira Debnath. (2016) Molecular docking and simulation studies to give insight of surfactin amyloid interaction for destabilizing Alzheimer’s Aβ42 protofibrils. Medicinal Chemistry Research 25:8, pages 1616-1622.
Crossref
Crossref
Tairan Yuwen, Yi Xue & Nikolai R. Skrynnikov. (2016) Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos. Biochemistry 55:12, pages 1784-1800.
Crossref
Crossref
Bhupesh Goyal, Anil Kumar, Kinshuk Raj Srivastava & Susheel Durani. (2016) Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Advances 6:78, pages 74162-74176.
Crossref
Crossref
Luca Bellucci, Albert Ardèvol, Michele Parrinello, Helmut Lutz, Hao Lu, Tobias Weidner & Stefano Corni. (2016) The interaction with gold suppresses fiber-like conformations of the amyloid β (16–22) peptide. Nanoscale 8:16, pages 8737-8748.
Crossref
Crossref
Sarah Rauscher, Vytautas Gapsys, Michal J. Gajda, Markus Zweckstetter, Bert L. de Groot & Helmut Grubmüller. (2015) Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment. Journal of Chemical Theory and Computation 11:11, pages 5513-5524.
Crossref
Crossref
Maria Giovanna Di Carlo, Velia Minicozzi, Vito Foderà, Valeria Militello, Valeria Vetri, Silvia Morante & Maurizio Leone. (2015) Thioflavin T templates amyloid β(1–40) conformation and aggregation pathway. Biophysical Chemistry 206, pages 1-11.
Crossref
Crossref
Arun Kumar Somavarapu & Kasper P. Kepp. (2015) The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models. ChemPhysChem 16:15, pages 3278-3289.
Crossref
Crossref
Qianjun Liu, Guodong Hu, Zanxia Cao, Jihua Wang & Haifeng Chen. (2015) Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation. Journal of Molecular Modeling 21:5.
Crossref
Crossref
Ferruccio Palazzesi, Meher K. Prakash, Massimiliano Bonomi & Alessandro Barducci. (2014) Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States. Journal of Chemical Theory and Computation 11:1, pages 2-7.
Crossref
Crossref
Anne M. Brown, Justin A. Lemkul, Nicholas Schaum & David R. Bevan. (2014) Simulations of monomeric amyloid β-peptide (1–40) with varying solution conditions and oxidation state of Met35: Implications for aggregation. Archives of Biochemistry and Biophysics 545, pages 44-52.
Crossref
Crossref