1
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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]
Abstract
Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1-13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1-13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1-13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable β-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.
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Affiliation(s)
- Marvin Bilog
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States
| | - Jayson Vedad
- PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; Chemistry and Biochemistry Department, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York, 11210, United States
| | - Charisse Capadona
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States
| | - Adam A Profit
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States
| | - Ruel Z B Desamero
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States.
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2
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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
Abstract
AA amyloidosis, characterized by the misfolding of serum amyloid A (SAA) protein, is the most common amyloid protein disorder across multiple species. SAA is a positive-acute phase protein synthesized by the liver in response to inflammation or stress, and it normally associates with high-density lipoprotein at its N-terminus. In this study, we focused on the 1-25 amino acid (aa) region of the complete 104 aa SAA sequence to examine the aggregation propensity of AA amyloid. A library comprising eight peptides from different species was assembled for analysis. To access the aggregation propensity of each peptide region, a bioinformatic study was conducted using the algorithm TANGO. Congo red (CR) binding assays, Thioflavin T (ThT) assays, and transmission electron microscopy (TEM) were utilized to evaluate whether the synthesized peptides formed amyloid-like fibrils. All synthetic SAA 1-25 congeners resulted in amyloid-like fibrils formation (per CR and/or ThT staining and TEM detection) at the exception of the ferret SAA1-25 fragment, which generated plaque-like materials by TEM. Ten residues were preserved among SAA 1-25 congeners resulting in amyloid-like fibrils, i.e. F6, E9, A10, G13, D16, M17, A20, Y21, D23, and M24. Amino acid residues highlighted by this study may have a role in increasing the propensity for amyloid-like fibril formation. This study put an emphasis on region 1-25 in the mechanism of SAA1 misfolding.
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Affiliation(s)
- Natalie G. Horgan
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Kendall B. E. Moore
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Jessica S. Fortin
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
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3
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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]
Abstract
Overexpression of serum amyloid A (SAA) can lead to a form of amyloidosis where the fibrils are made of SAA fragments, most often SAA1-76. Using Replica Exchange with Tunneling, we study the conversion of a SAA1-76 chain between the folded conformation and a fibril conformation. We find that the basins in the free energy landscape corresponding to the two motifs are separated by barriers of only about 2-3 k B T. Crucial for the assembly into the fibril structure is the salt bridge 26E-34K that provides a scaffold for forming the fibril conformation.
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Affiliation(s)
| | - Miranda S. Sheridan
- Department of Chemistry &
Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H. E. Hansmann
- Department of Chemistry &
Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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4
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Abstract
In systemic amyloidosis, serum amyloid A (SAA) fibril deposits cause widespread damages to tissues and organs that eventually may lead to death. A therapeutically intervention therefore has either to dissolve these fibrils or inhibit their formation. However, only recently has the human SAA fibril structure been resolved at a resolution that is sufficient for development of drug candidates. Here, we use molecular dynamic simulations to probe the factors that modulate the stability of this fibril model. Our simulations suggest that fibril formation starts with the stacking of two misfolded monomers into metastable dimers, with the stacking depending on the N-terminal amyloidogenic regions of different chains forming anchors. The resulting dimers pack in a second step into a 2-fold two-layer tetramer that is stable enough to nucleate fibril formation. The stability of the initial dimers is enhanced under acidic conditions by a strong salt bridge and side-chain hydrogen bond network in the C-terminal cavity (residues 23-51) but is not affected by the presence of the disordered C-terminal tail.
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Affiliation(s)
- Wenhua Wang
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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5
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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]
Abstract
Lymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using replica-exchange-with-tunneling, we study the conversion between the 2-folds. Unlike previously proposed, we find that the fold switching does not require unfolding of lymphotactin but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect the β2 and β3 strands and ease the transition between the hydrogen bond pattern by which the central three-stranded β-sheet in the two forms differs.
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Affiliation(s)
- Prabir Khatua
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Alan J Ray
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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6
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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
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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7
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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]
Abstract
Proteins, in general, fold to a well-organized three-dimensional structure in order to function. The stability of this functional shape can be perturbed by external environmental conditions, such as temperature. Understanding the molecular factors underlying the resistance of proteins to the thermal stress has important consequences. First of all, it can aid the design of thermostable enzymes able to perform efficient catalysis in the high-temperature regime. Second, it is an essential brick of knowledge required to decipher the evolutionary pathways of life adaptation on Earth. Thanks to the development of atomistic simulations and ad hoc enhanced sampling techniques, it is now possible to investigate this problem in silico, and therefore provide support to experiments. After having described the methodological aspects, the chapter proposes an extended discussion on two problems. First, we focus on thermophilic proteins, a perfect model to address the issue of thermal stability and molecular evolution. Second, we discuss the issue of how protein thermal stability is affected by crowded in vivo-like conditions.
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Affiliation(s)
- Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | | | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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8
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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]
Abstract
Various diseases cause overexpression of the serum amyloid A (SAA) protein, which in some cases, but not in all cases, leads to amyloidosis as a secondary disease. Response to the overexpression involves dissociation of the SAA hexamer and subsequent cleavage of the released monomers, most commonly yielding fragments SAA1-76 of the full-sized SAA1-104. We report results from molecular dynamic simulations that probe the role of this cleavage for downregulating the activity and concentration of SAA. We propose a mechanism that relies on two elements. First, the probability to assemble into hexamers is lower for the fragments than it is for the full-sized protein. Second, unlike other fragments, SAA1-76 can switch between two distinct configurations. The first kind is easy to proteolyse (allowing a fast reduction of the SAA concentration) but prone to aggregation, whereas the situation is opposite for the second kind. If the time scale for amyloid formation is longer than the one for proteolysis, the aggregation-prone species dominates. However, if environmental conditions such as low pH increases the risk of amyloid formation, the ensemble shifts toward the more protected form. We speculate that SAA amyloidosis is a failure of this switching mechanism leading to accumulation of the aggregation-prone species and subsequent amyloid formation.
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Affiliation(s)
- Wenhua Wang
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Prabir Khatua
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
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9
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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]
Abstract
Depending on the amino acid sequence, as well as the local environment, some peptides have the capability to fold into multiple secondary structures. Conformational switching between such structures is a key element of protein folding and aggregation. Specifically, understanding the molecular mechanism underlying the transition from an α-helix to a β-hairpin is critical because it is thought to be a harbinger of amyloid assembly. In this study, we explore the energy landscape for an 18-residue peptide (DP5), designed by Araki and Tamura to exhibit equal propensities for the α-helical and β-hairpin forms. We find that the degeneracy is encoded in the multifunnel nature of the underlying free energy landscape. In agreement with experiment, we also observe that mutation of tyrosine at position 12 to serine shifts the equilibrium in favor of the α-helix conformation, by altering the landscape topography. The transition from the α-helix to the β-hairpin is a complex stepwise process, and occurs via collapsed coil-like intermediates. Our findings suggest that even a single mutation can tune the emergent features of the landscape, providing an efficient route to protein design. Interestingly, the transition pathways for the conformational switch seem to be minimally perturbed upon mutation, suggesting that there could be universal microscopic features that are conserved among different switch-competent protein sequences.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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10
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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
Abstract
In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B, 1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent model under the AMBER14SB force field with the accelerated molecular dynamics (AMD) and traditional molecular dynamics (MD), respectively. We analyzed and compared the simulation results obtained by these two methods based on several aspects, such as root mean square deviation (RMSD), native contacts, cluster analysis, folding snapshots, free energy landscape, and the evolution of the radius of gyration, which showed that these eight proteins were successfully and consistently folded into the corresponding native structures by AMD simulations carried out at room temperature. In addition, the folding occurred in the range of 40~180 ns after starting from the linear structures of the eight proteins at 300 K. By contrast, these stable folding structures were not found when the traditional molecular dynamics (MD) simulation was used. At the same time, the influence of high temperatures (350, 400, and 450 K) is also further investigated. Study found that the simulation efficiency of AMD is higher than that of MD simulations, regardless of the temperature. Of these temperatures, 300 K is the most suitable temperature for protein folding for all systems. To further investigate the efficiency of AMD, another trajectory was simulated for eight proteins with the same linear structure but different random seeds at 300 K. Both AMD trajectories reached the correct folded structures. Our result clearly shows that AMD simulation are a highly efficient and reliable method for the study of protein folding.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xiaona Guo
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Guoqiang Feng
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Department of Chemistry, New York University, New York, NY, United States
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11
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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
Abstract
In this article, we present an enhanced sampling method based on a hybrid Hamiltonian which combines experimental distance restraints with a bias dependent from multiple path-dependent variables. This simulation method determines the bias-coordinates on the fly and does not require a priori knowledge about reaction coordinates. The hybrid Hamiltonian accelerates the sampling of proteins, and, combined with experimental distance information, the technique considers the restraints adaptively and in dependency of the system's intrinsic dynamics. We validate the methodology on the dipole relaxation of two water models and the conformational landscape of dialanine. Using experimental NMR-restraint data, we explore the folding landscape of the TrpCage mini-protein and in a second example apply distance restraints from chemical crosslinking/mass spectrometry experiments for the sampling of the conformation space of the Killer Cell Lectin-like Receptor Subfamily B Member 1A (NKR-P1A). The new methodology has the potential to adaptively introduce experimental restraints without affecting the conformational space of the system along an ergodic trajectory. Since only a limited number of input- and no-order parameters are required for the setup of the simulation, the method is broadly applicable and has the potential to be combined with coarse-graining methods.
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Affiliation(s)
- Emanuel K Peter
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
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12
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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]
Affiliation(s)
- Jerelle A. Joseph
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Debayan Chakraborty
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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13
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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]
Abstract
Colonic amyloidosis is the result of overexpression of the serum amyloid A (SAA) protein in inflammatory bowel disease or colon cancer. Crucial for amyloid formation are the first ten N-terminal residues, which in the crystal structure are a part of a 27-residue long helix. Here, we study this 27-residue N-terminal region of SAA by a multiexchange variant of replica exchange molecular dynamics. An ensemble of configurations is observed, dominated by three motifs: the single helix of the crystal structure, a helix-turn-helix configurations, and such where the residues 14-27 are the part of a helix but the first 13 residues form an extended and disordered segment that is prone to aggregation. The single point mutation E9A shifts the equilibrium to the latter motif, indicating the importance of interactions involving this residue for the stability of the SAA protein.
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14
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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
Abstract
To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager⁻Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.
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Grants
- JPMJPR1679 Japan Science and Technology Agency
- 16K00059 Ministry of Education, Culture, Sports, Science and Technology
- 17KT0101 Ministry of Education, Culture, Sports, Science and Technology
- 25840060 Ministry of Education, Culture, Sports, Science and Technology
- 15K18520 Ministry of Education, Culture, Sports, Science and Technology
- JP18am0101109 Japan Agency for Medical Research and Development
- 17gm0810012h0001 Japan Agency for Medical Research and Development
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan.
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Yasuhiro Matsunaga
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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15
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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]
Affiliation(s)
- Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Pengfei Tian
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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16
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Xi W, Hansmann UHE. Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant Aβ 40 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
Abstract
Using a variant of Hamilton-replica-exchange, we study for wild type and Iowa mutant Aβ40 the conversion between fibrils with antiparallel β-sheets and such with parallel β-sheets. We show that wild type and mutant form distinct salt bridges that in turn stabilize different fibril organizations. The conversion between the two fibril forms leads to the release of small aggregates that in the Iowa mutant may shift the equilibrium from fibrils to more toxic oligomers.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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17
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Xi W, Vanderford EK, Hansmann UHE. Out-of-Register Aβ 42 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]
Abstract
We propose a variant of the recently found S-shaped Aβ1-42-motif that is characterized by out-of-register C-terminal β-strands. We show that chains with this structure can form not only fibrils that are compatible with the NMR signals but also barrel-shaped oligomers that resemble the ones formed by the much smaller cylindrin peptides. By running long all-atom molecular dynamics simulations at physiological temperatures with an explicit solvent, we study the stability of these constructs and show that they are plausible models for neurotoxic oligomers. After analyzing the transitions between different assemblies, we suggest a mechanism for amyloid formation in Alzheimer's disease.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Elliott K Vanderford
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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18
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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]
Abstract
Proteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated C-terminal domain, dubbed by us as RfaH-C-terminal domain (RfaH-CTD), and is studied here with a variant of the replica-exchange-with-tunneling approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free-energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.
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Affiliation(s)
- Nathan A Bernhardt
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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19
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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
Affiliation(s)
- A. Aina
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| | - S. Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
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20
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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]
Abstract
We introduce Replica-Exchange-with-Tunneling (RET) simulations as a tool for studies of the conversion between polymorphic amyloids. For the 11-residue amyloid-forming cylindrin peptide we show that this technique allows for a more efficient sampling of the formation and interconversion between fibril-like and barrel-like assemblies. We describe a protocol for optimized analysis of RET simulations that allows us to propose a mechanism for formation and interconversion between various cylindrin assemblies. Especially, we show that an interchain salt bridge between residues K3 and D7 is crucial for formation of the barrel structure.
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Affiliation(s)
- Huiling Zhang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, China
| | - Wenhui Xi
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, China.,Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Yanjie Wei
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, China
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21
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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]
Abstract
Snapshots of the intermediate conformation of Trp-cage at various simulation times using AMBER03, EPB03, AMBER12SB, and EPB12SB. Here, the N terminal is always on the top.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
- School of Chemistry and Molecular Engineering
| | - Tong Zhu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Changge Ji
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
| | - Qinggang Zhang
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - John Z. H. Zhang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
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