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For: Bernhardt NA, Xi W, Wang W, Hansmann UHE. Simulating Protein Fold Switching by Replica Exchange with Tunneling. J Chem Theory Comput 2016;12:5656-5666. [PMID: 27767301 DOI: 10.1021/acs.jctc.6b00826] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Number Cited by Other Article(s)
1
Bilog M, Vedad J, Capadona C, Profit AA, Desamero RZB. Key charged residues influence the amyloidogenic propensity of the helix-1 region of serum amyloid A. Biochim Biophys Acta Gen Subj 2024;1868:130690. [PMID: 39117048 DOI: 10.1016/j.bbagen.2024.130690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
2
Horgan NG, Moore KBE, Fortin JS. Investigation of serum amyloid a within animal species focusing on the 1-25 amino acid region. Vet Q 2023;43:1-8. [PMID: 37800590 PMCID: PMC10614707 DOI: 10.1080/01652176.2023.2267605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]  Open
3
Yasar F, Sheridan MS, Hansmann UHE. Interconversion between Serum Amyloid A Native and Fibril Conformations. ACS OMEGA 2022;7:12186-12192. [PMID: 35449919 PMCID: PMC9016813 DOI: 10.1021/acsomega.2c00566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
4
Wang W, Hansmann UHE. Stability of Human Serum Amyloid A Fibrils. J Phys Chem B 2020;124:10708-10717. [PMID: 33197318 DOI: 10.1021/acs.jpcb.0c08280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
5
Khatua P, Ray AJ, Hansmann UHE. Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin. J Phys Chem B 2020;124:6555-6564. [PMID: 32609521 PMCID: PMC7429337 DOI: 10.1021/acs.jpcb.0c04565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
6
Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020;8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022]  Open
7
Timr S, Madern D, Sterpone F. Protein thermal stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020;170:239-272. [PMID: 32145947 DOI: 10.1016/bs.pmbts.2019.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
8
Wang W, Khatua P, Hansmann UHE. Cleavage, Downregulation, and Aggregation of Serum Amyloid A. J Phys Chem B 2020;124:1009-1019. [PMID: 31955564 DOI: 10.1021/acs.jpcb.9b10843] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
9
Chakraborty D, Chebaro Y, Wales DJ. A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide. Phys Chem Chem Phys 2020;22:1359-1370. [PMID: 31854397 DOI: 10.1039/c9cp04778f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
10
Duan L, Guo X, Cong Y, Feng G, Li Y, Zhang JZH. Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water. Front Chem 2019;7:540. [PMID: 31448259 PMCID: PMC6691143 DOI: 10.3389/fchem.2019.00540] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/15/2019] [Indexed: 12/26/2022]  Open
11
Peter EK, Černý J. A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints. Int J Mol Sci 2019;20:E370. [PMID: 30654563 PMCID: PMC6359555 DOI: 10.3390/ijms20020370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/25/2022]  Open
12
Joseph JA, Chakraborty D, Wales DJ. Energy Landscape for Fold-Switching in Regulatory Protein RfaH. J Chem Theory Comput 2018;15:731-742. [DOI: 10.1021/acs.jctc.8b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
13
Wang W, Xi W, Hansmann UHE. Stability of the N-Terminal Helix and Its Role in Amyloid Formation of Serum Amyloid A. ACS OMEGA 2018;3:16184-16190. [PMID: 30533585 PMCID: PMC6275945 DOI: 10.1021/acsomega.8b02377] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/16/2018] [Indexed: 05/03/2023]
14
Fujisaki H, Moritsugu K, Matsunaga Y. Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions. Int J Mol Sci 2018;19:E3177. [PMID: 30326661 PMCID: PMC6213965 DOI: 10.3390/ijms19103177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 01/07/2023]  Open
15
Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. J Phys Chem B 2018;122:11174-11185. [DOI: 10.1021/acs.jpcb.8b06335] [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]
16
Xi W, Hansmann UHE. Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant Aβ40 fibrils. J Chem Phys 2018;148:045103. [PMID: 29390821 DOI: 10.1063/1.5016166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
17
Xi W, Vanderford EK, Hansmann UHE. Out-of-Register Aβ42 Assemblies as Models for Neurotoxic Oligomers and Fibrils. J Chem Theory Comput 2018;14:1099-1110. [PMID: 29357242 DOI: 10.1021/acs.jctc.7b01106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
18
Bernhardt NA, Hansmann UHE. Multifunnel Landscape of the Fold-Switching Protein RfaH-CTD. J Phys Chem B 2018;122:1600-1607. [PMID: 29323497 DOI: 10.1021/acs.jpcb.7b11352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Aina A, Wallin S. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins. J Chem Phys 2017;147:095102. [DOI: 10.1063/1.4986933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
20
Zhang H, Xi W, Hansmann UHE, Wei Y. Fibril-Barrel Transitions in Cylindrin Amyloids. J Chem Theory Comput 2017;13:3936-3944. [PMID: 28671829 DOI: 10.1021/acs.jctc.7b00383] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
21
Duan L, Zhu T, Ji C, Zhang Q, Zhang JZH. Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys Chem Chem Phys 2017;19:15273-15284. [DOI: 10.1039/c7cp02101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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