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For: Massi F, Straub JE. Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide. J Comput Chem 2003;24:143-53. [PMID: 12497595 DOI: 10.1002/jcc.10101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Khatua P, Gupta M, Bandyopadhyay S. Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations. J Chem Inf Model 2022;62:3453-3462. [PMID: 35816665 DOI: 10.1021/acs.jcim.2c00593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
2
Aggarwal L, Biswas P. Effect of Alzheimer’s Disease Causative and Protective Mutations on the Hydration Environment of Amyloid-β. J Phys Chem B 2020;124:2311-2322. [DOI: 10.1021/acs.jpcb.9b10425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
3
Persson F, Söderhjelm P, Halle B. How proteins modify water dynamics. J Chem Phys 2018;148:215103. [PMID: 29884055 DOI: 10.1063/1.5026861] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
4
Hanczyc P, Mikhailovsky A, Boyer DR, Sawaya MR, Heeger A, Eisenberg D. Ultrafast Time-Resolved Studies on Fluorescein for Recognition Strands Architecture in Amyloid Fibrils. J Phys Chem B 2018;122:8-18. [DOI: 10.1021/acs.jpcb.7b07923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Rubinstein AI, Sabirianov RF, Namavar F. Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach. NANOTECHNOLOGY 2016;27:415703. [PMID: 27585807 DOI: 10.1088/0957-4484/27/41/415703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
6
Brotzakis ZF, Groot CCM, Brandeburgo WH, Bakker HJ, Bolhuis PG. Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin. J Phys Chem B 2016;120:4756-66. [DOI: 10.1021/acs.jpcb.6b02592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
7
Atsmon-Raz Y, Miller Y. Non-Amyloid-β Component of Human α-Synuclein Oligomers Induces Formation of New Aβ Oligomers: Insight into the Mechanisms That Link Parkinson's and Alzheimer's Diseases. ACS Chem Neurosci 2016;7:46-55. [PMID: 26479553 DOI: 10.1021/acschemneuro.5b00204] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
8
Shinobu A, Agmon N. The Hole in the Barrel: Water Exchange at the GFP Chromophore. J Phys Chem B 2015;119:3464-78. [DOI: 10.1021/jp5127255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
9
Kaur H, Sasidhar YU. Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α→β transition in full protein context. Phys Chem Chem Phys 2013;15:7819-30. [PMID: 23598905 DOI: 10.1039/c3cp44327b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
10
Halle B, Persson F. Analysis of Protein Dynamics Simulations by a Stochastic Point Process Approach. J Chem Theory Comput 2013;9:2838-48. [DOI: 10.1021/ct400161u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J 2012;102:315-24. [PMID: 22339868 DOI: 10.1016/j.bpj.2011.12.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/12/2011] [Accepted: 12/01/2011] [Indexed: 12/21/2022]  Open
12
Chong SH, Park M, Ham S. Structural and Thermodynamic Characteristics That Seed Aggregation of Amyloid-β Protein in Water. J Chem Theory Comput 2012;8:724-34. [DOI: 10.1021/ct200757a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
13
Lee C, Ham S. Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water. J Comput Chem 2010;32:349-55. [DOI: 10.1002/jcc.21628] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 05/12/2010] [Accepted: 06/14/2010] [Indexed: 12/21/2022]
14
Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010;110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
15
Rubinstein A, Sabirianov RF, Mei WN, Namavar F, Khoynezhad A. Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010;82:021915. [PMID: 20866845 DOI: 10.1103/physreve.82.021915] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Indexed: 05/29/2023]
16
Tsai HHG, Lee JB, Tseng SS, Pan XA, Shih YC. Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: Implications for aggregation and neurotoxicity. Proteins 2010;78:1909-25. [DOI: 10.1002/prot.22705] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
17
Kent A, Jha AK, Fitzgerald JE, Freed KF. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment. J Phys Chem B 2008;112:6175-86. [PMID: 18348560 PMCID: PMC2719849 DOI: 10.1021/jp077099h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol 2008;379:815-29. [PMID: 18479708 DOI: 10.1016/j.jmb.2008.04.028] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 11/23/2022]
19
Yu H, Ren J, Qu X. Different Hydration Changes Accompanying Copper and Zinc Binding to Amyloid β-Peptide: Water Contribution to Metal Binding. Chembiochem 2008;9:879-82. [DOI: 10.1002/cbic.200700633] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
20
Jang S, Shin S. Computational study on the structural diversity of amyloid Beta Peptide (abeta(10-35)) oligomers. J Phys Chem B 2008;112:3479-84. [PMID: 18303879 DOI: 10.1021/jp076450w] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
21
Rubinstein A, Sherman S. Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach. Biopolymers 2007;87:149-64. [PMID: 17626298 DOI: 10.1002/bip.20808] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
22
Chung YH, Xia J, Margulis CJ. Diffusion and residence time of hydrogen peroxide and water in crowded protein environments. J Phys Chem B 2007;111:13336-44. [PMID: 17973519 DOI: 10.1021/jp075251+] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
23
Kwon YE, Park JY, No KT, Shin JH, Lee SK, Eun JS, Yang JH, Shin TY, Kim DK, Chae BS, Leem JY, Kim KH. Synthesis, in vitro assay, and molecular modeling of new piperidine derivatives having dual inhibitory potency against acetylcholinesterase and Aβ1–42 aggregation for Alzheimer’s disease therapeutics. Bioorg Med Chem 2007;15:6596-607. [PMID: 17681794 DOI: 10.1016/j.bmc.2007.07.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 06/30/2007] [Accepted: 07/06/2007] [Indexed: 11/16/2022]
24
Mukherjee S, Chowdhury P, Gai F. Infrared Study of the Effect of Hydration on the Amide I Band and Aggregation Properties of Helical Peptides. J Phys Chem B 2007;111:4596-602. [PMID: 17419612 DOI: 10.1021/jp0689060] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
25
Tsintsarska S, Huber H. The equilibrium constant of carbon dioxide dimerization and the lifetime of the dimer. Mol Phys 2007. [DOI: 10.1080/00268970601126726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
26
Baumketner A, Shea JE. The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent. J Mol Biol 2007;366:275-85. [PMID: 17166516 DOI: 10.1016/j.jmb.2006.11.015] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 10/29/2006] [Accepted: 11/03/2006] [Indexed: 11/28/2022]
27
Park S, Saven JG. Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 2006;60:450-63. [PMID: 15937899 DOI: 10.1002/prot.20511] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Bratko D, Cellmer T, Prausnitz JM, Blanch HW. Effect of single-point sequence alterations on the aggregation propensity of a model protein. J Am Chem Soc 2006;128:1683-91. [PMID: 16448142 DOI: 10.1021/ja056837h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
29
Chen C, Beck BW, Krause K, Pettitt BM. Solvent participation in Serratia marcescens endonuclease complexes. Proteins 2006;62:982-95. [PMID: 16355414 DOI: 10.1002/prot.20694] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
30
Huang H, Melacini G. High-resolution protein hydration NMR experiments: Probing how protein surfaces interact with water and other non-covalent ligands. Anal Chim Acta 2006;564:1-9. [PMID: 17723356 DOI: 10.1016/j.aca.2005.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/13/2005] [Accepted: 10/20/2005] [Indexed: 10/25/2022]
31
Nguyen HD, Hall CK. Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations. J Am Chem Soc 2006;128:1890-901. [PMID: 16464090 PMCID: PMC3215763 DOI: 10.1021/ja0539140] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
Jang S, Shin S. Amyloid β-Peptide Oligomerization in Silico:  Dimer and Trimer. J Phys Chem B 2006;110:1955-8. [PMID: 16471767 DOI: 10.1021/jp055568e] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
33
Cruz L, Urbanc B, Borreguero JM, Lazo ND, Teplow DB, Stanley HE. Solvent and mutation effects on the nucleation of amyloid beta-protein folding. Proc Natl Acad Sci U S A 2005;102:18258-63. [PMID: 16339896 PMCID: PMC1317965 DOI: 10.1073/pnas.0509276102] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
34
Fujisaki H, Straub JE. Vibrational energy relaxation in proteins. Proc Natl Acad Sci U S A 2005;102:6726-31. [PMID: 15767588 PMCID: PMC1100765 DOI: 10.1073/pnas.0409083102] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Nguyen HD, Hall CK. Kinetics of fibril formation by polyalanine peptides. J Biol Chem 2004;280:9074-82. [PMID: 15591317 DOI: 10.1074/jbc.m407338200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
36
Morgan C, Colombres M, Nuñez MT, Inestrosa NC. Structure and function of amyloid in Alzheimer's disease. Prog Neurobiol 2004;74:323-49. [PMID: 15649580 DOI: 10.1016/j.pneurobio.2004.10.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Accepted: 10/26/2004] [Indexed: 12/21/2022]
37
Nguyen HD, Hall CK. Phase diagrams describing fibrillization by polyalanine peptides. Biophys J 2004;87:4122-34. [PMID: 15465859 PMCID: PMC1304921 DOI: 10.1529/biophysj.104.047159] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
38
Stoica I. Solvent Interactions and Protein Dynamics in Spin-labeled T4 Lysozyme. J Biomol Struct Dyn 2004;21:745-60. [PMID: 15106997 DOI: 10.1080/07391102.2004.10506965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
39
Sanjeev BS, Vishveshwara S. Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study. Proteins 2004;55:915-23. [PMID: 15146489 DOI: 10.1002/prot.20114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
40
Bitan G, Vollers SS, Teplow DB. Elucidation of primary structure elements controlling early amyloid beta-protein oligomerization. J Biol Chem 2003;278:34882-9. [PMID: 12840029 DOI: 10.1074/jbc.m300825200] [Citation(s) in RCA: 252] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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