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Saffari B, Amininasab M. Crocin Inhibits the Fibrillation of Human α-synuclein and Disassembles Mature Fibrils: Experimental Findings and Mechanistic Insights from Molecular Dynamics Simulation. ACS Chem Neurosci 2021; 12:4037-4057. [PMID: 34636232 DOI: 10.1021/acschemneuro.1c00379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The aggregation of human alpha-synuclein (hαS) is pivotally implicated in the development of most types of synucleinopathies. Molecules that can inhibit or reverse the aggregation process of amyloidogenic proteins have potential therapeutic value. The anti-aggregating activity of multiple carotenoid compounds has been reported over the past decades against a growing list of amyloidogenic polypeptides. Here, we aimed to determine whether crocin, the main carotenoid glycoside component of saffron, would inhibit hαS aggregation or could disassemble its preformed fibrils. By employing a series of biochemical and biophysical techniques, crocin was exhibited to inhibit hαS fibrillation in a dose-dependent fashion by stabilizing very early aggregation intermediates in off-pathway non-toxic conformations with little β-sheet content. We also observed that crocin at high concentrations could efficiently destabilize mature fibrils and disassemble them into seeding-incompetent intermediates by altering their β-sheet conformation and reshaping their structure. Our atomistic molecular dynamics (MD) simulations demonstrated that crocin molecules bind to both the non amyloid-β component (NAC) region and C-terminal domain of hαS. These interactions could thereby stabilize the autoinhibitory conformation of the protein and prevent it from adopting aggregation-prone structures. MD simulations further suggested that ligand molecules prefer to reside longitudinally along the fibril axis onto the edges of the inter-protofilament interface where they establish hydrogen and hydrophobic bonds with steric zipper stabilizing residues. These interactions turned out to destabilize hαS fibrils by altering the interstrand twist angles, increasing the rigidity of the fibril core, and elevating its radius of gyration. Our findings suggest the potential pharmaceutical implication of crocin in synucleinopathies.
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Affiliation(s)
- Babak Saffari
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
| | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
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2
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Alıcı H. In silico analysis: structural insights about inter-protofilaments interactions for α-synuclein (50–57) fibrils and its familial mutation. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1786084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hakan Alıcı
- Department of Physics, Zonguldak Bülent Ecevit University, Zonguldak, Turkey
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3
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John T, Bandak J, Sarveson N, Hackl C, Risselada HJ, Prager A, Elsner C, Abel B. Growth, Polymorphism, and Spatially Controlled Surface Immobilization of Biotinylated Variants of IAPP 21-27 Fibrils. Biomacromolecules 2020; 21:783-792. [PMID: 31887030 DOI: 10.1021/acs.biomac.9b01466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The islet amyloid polypeptide (IAPP) is a regulatory peptide that can aggregate into fibrillar structures associated with type 2 diabetes. In this study, the IAPP21-27 segment was modified with a biotin linker at the N-terminus (Btn-GNNFGAIL) to immobilize peptide fibrils on streptavidin-coated surfaces. Key residues for fibril formation of the N-terminal biotinylated IAPP21-27 segment were identified by using an alanine scanning approach combined with molecular dynamics simulations, thioflavin T fluorescence measurements, and scanning electron microscopy. Significant contributions of phenylalanine (F23), leucine (L27), and isoleucine (I26) for the fibrillation of the short peptide segment were identified. The fibril morphologies of the peptide variants differed depending on their primary sequence, ranging from flexible and semiflexible to stiff and crystal-like structures. These insights could advance the design of new functional hybrid bionanomaterials and fibril-engineered surface coatings using short peptide segments. To validate this concept, the biotinylated fibrils were immobilized on streptavidin-coated surfaces under spatial control.
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Affiliation(s)
- Torsten John
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany.,Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry , Leipzig University , Linnéstraße 3 , 04103 Leipzig , Germany
| | - Juhaina Bandak
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Nilushiya Sarveson
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Claudia Hackl
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Herre Jelger Risselada
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany.,Institute for Theoretical Physics , Georg-August-Universität Göttingen , Friedrich-Hund-Platz 1 , 37077 Göttingen , Germany
| | - Andrea Prager
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Christian Elsner
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Bernd Abel
- Leibniz-Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany.,Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry , Leipzig University , Linnéstraße 3 , 04103 Leipzig , Germany
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4
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Zhan M, Guo M, Jiang Y, Wang X. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy. Int J Mol Sci 2015; 16:14786-807. [PMID: 26140374 PMCID: PMC4519872 DOI: 10.3390/ijms160714786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/08/2015] [Accepted: 06/17/2015] [Indexed: 01/29/2023] Open
Abstract
The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.
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Affiliation(s)
- Minzhong Zhan
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Ming Guo
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Yanke Jiang
- Research Center of Medical Chemistry & Chemical Biology, Chongqing Technology and Business University, Chongqing 400067, China.
| | - Xiaomeng Wang
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
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5
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Kaur H, Sasidhar YU. Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study. J Mol Model 2015; 21:88. [PMID: 25773700 DOI: 10.1007/s00894-015-2621-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
Abstract
Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the neighboring residues. The solution NMR of the parent helical sequence, sans its protein context, showed no inherent tendency to adopt a particular secondary structure in pure water but showed α-helical propensity in TFE/water and SDS micelles. In this study we investigate the conformational preference of the 'parent' and 'duplicate' sequences, sans the protein context, in pure water and an apolar TFE/water solution. Apolar TFE/water solution is a model for non-polar protein context. We performed MD simulations of the two peptides, in explicit water and 80% (v/v) TFE/water, using GROMOS 53a6 force field, at 300 K and 1 bar (under NPT conditions). We show that in TFE/water mixture, salt bridges are stabilized by apolar TFE molecules and main chain-main chain hydrogen bonds promote the α-helical conformation, particularly in the duplicate peptide. Solvent exposure, in pure water, resulted in an α→β transition to form a triple stranded β-sheet structure in the 'duplicate' sequence, with a rare psi-loop topology, while a mixture of turn/bend conformations were adopted by the 'parent' sequence. Thus the differences in conformational preference of the parent and duplicate sequence sans protein context, in pure water and TFE/water, implicate the importance of the environment polarity in dictating the peptide conformation. Mechanism of folding of the observed psi-loop in the duplicate sequence gives insights into folding of this rare β-sheet topology.
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Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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6
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Pouplana R, Campanera JM. Energetic contributions of residues to the formation of early amyloid-β oligomers. Phys Chem Chem Phys 2014; 17:2823-37. [PMID: 25503571 DOI: 10.1039/c4cp04544k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-weight amyloid-β (Aβ) oligomers formed at early stages of oligomerization rather than fibril assemblies seem to be the toxic components that drive neurodegeneration in Alzheimer's disease. Unfortunately, detailed knowledge of the structure of these early oligomers at the residue level is not yet available. In this study, we performed all-atom explicit solvent molecular dynamics simulations to examine the oligomerization process of Aβ10-35 monomers when forming dimers, trimers, tetramers and octamers, with four independent simulations of a total simulated time of 3 μs for each oligomer system. The decomposition of the stability free energy by MM-GBSA methodology allowed us to unravel the network of energetic interactions that stabilize such oligomers. The contribution of the intermonomeric van der Waals term is the most significant energy feature of the oligomerization process, consistent with the so-called hydrophobic effect. Furthermore, the decomposition of the stability free energy into residues and residue-pairwise terms revealed that it is mainly apolar interactions between the three specific hydrophobic fragments 31-35 (C-terminal region), 17-20 (central hydrophobic core) and 12-14 (N-terminal region) that are responsible for such a favourable effect. The conformation in which the hydrophobic cthr-chc interaction is oriented perpendicularly is particularly important. We propose three other model substructures that favour the oligomerization process and can thus be considered as molecular targets for future inhibitors. Understanding Aβ oligomerization at the residue level could lead to more efficient design of inhibitors of this process.
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Affiliation(s)
- R Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII, s/n, Diagonal Sud, 08028, Barcelona, Catalonia, Spain.
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7
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Berhanu WM, Masunov AE. Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer. J Biomol Struct Dyn 2014; 33:1399-411. [PMID: 25093402 DOI: 10.1080/07391102.2014.951689] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with many diseases affecting millions of people worldwide. Polyphenols such as Curcumin, Exifone, and Myricetin exhibit modest inhibition toward fibril formation of tau peptide which is associated with Alzheimer's disease. However, the molecular mechanisms of this inhibition remain elusive. We investigated the binding of three polyphenol molecules to the protofibrils of an amyloidogenic fragment VQIVYK of tau peptide by molecular dynamics simulations in explicit solvent. We find that polyphenols induce conformational changes in the oligomer aggregate. These changes disrupt the amyloid H bonding, perturbing the aggregate. While the structural evolution of the control oligomer with no ligand is limited to the twisting of the β-sheets without their disassembly, the presence of polyphenol molecule pushes the β-sheets apart, and leads to a loosely packed structure where two of four β-sheets dissociate in each of the three cases considered here. The H-bonding capacity of polyphenols is responsible for the observed behavior. The calculated binding free energies and its individual components enabled better understanding of the binding. Results indicated that the contribution from Van der Waals interactions is more significant than electrostatic contribution to the binding. The findings from this study are expected to assist in the development of aggregation inhibitors. Significant binding between polyphenols and aggregate oligomer identified in our simulations confirms the previous experimental observations in which polyphenols refold the tau peptide without forming covalent bonds.
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Affiliation(s)
- Workalemahu M Berhanu
- a NanoScience Technology Center and Department of Chemistry , University of Central Florida , Orlando , FL 32826 , USA
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8
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Berhanu WM, Hansmann UHE. Stability of amyloid oligomers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:113-41. [PMID: 25443956 DOI: 10.1016/bs.apcsb.2014.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Molecular simulations are now commonly used to complement experimental techniques in investigating amyloids and their role in human diseases. In this chapter, we will summarize techniques and approaches often used in amyloid simulations and will present recent success stories. Our examples will be focused on lessons learned from molecular dynamics simulations in aqueous environments that start from preformed aggregates. These studies explore the limitations that arise from the choice of force field, the role of mutations in the growth of amyloid aggregates, segmental polymorphism, and the importance of cross-seeding. Furthermore, they give evidence for potential toxicity mechanisms. We finally discuss the role of molecular simulations in the search for aggregation inhibitors.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA.
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9
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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10
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Berhanu WM, Yaşar F, Hansmann UHE. In silico cross seeding of Aβ and amylin fibril-like oligomers. ACS Chem Neurosci 2013; 4:1488-500. [PMID: 24007594 DOI: 10.1021/cn400141x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Recent epidemiological data have shown that patients suffering from Type 2 Diabetes Mellitus have an increased risk to develop Alzheimer's disease and vice versa. A possible explanation is the cross-sequence interaction between Aβ and amylin. Because the resulting amyloid oligomers are difficult to probe in experiments, we investigate stability and conformational changes of Aβ-amylin heteroassemblies through molecular dynamics simulations. We find that Aβ is a good template for the growth of amylin and vice versa. We see water molecules permeate the β-strand-turn-β-strand motif pore of the oligomers, supporting a commonly accepted mechanism for toxicity of β-rich amyloid oligomers. Aiming for a better understanding of the physical mechanisms of cross-seeding and cell toxicity of amylin and Aβ aggregates, our simulations also allow us to identify targets for the rational design of inhibitors against toxic fibril-like oligomers of Aβ and amylin oligomers.
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Affiliation(s)
- Workalemahu M. Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Fatih Yaşar
- 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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11
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Do TD, Economou NJ, LaPointe NE, Kincannon WM, Bleiholder C, Feinstein SC, Teplow DB, Buratto SK, Bowers MT. Factors that drive peptide assembly and fibril formation: experimental and theoretical analysis of Sup35 NNQQNY mutants. J Phys Chem B 2013; 117:8436-46. [PMID: 23802812 DOI: 10.1021/jp4046287] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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12
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Berhanu WM, Hansmann UHE. The stability of cylindrin β-barrel amyloid oligomer models-a molecular dynamics study. Proteins 2013; 81:1542-55. [PMID: 23606599 DOI: 10.1002/prot.24302] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/21/2013] [Accepted: 04/01/2013] [Indexed: 11/10/2022]
Abstract
Small-soluble amyloid oligomers are believed to play a significant role in the pathology of amyloid diseases. Recently, the atomic structure of a toxic oligomer formed by an 11 residue and its tandem repeat was found to have an out-off register antiparallel β-strands in the shape of a β-barrel. In the present article we investigate the effect of mutations in the hydrophobic cores on the structure and dynamic of the β-barrels using all atom multiple molecular dynamics simulations with an explicit solvent. Extending previous experiments with molecular dynamics simulations we systematically test how stability and formation of cylindrin depends on the interplay between hydrophobicity and steric effects of the core residues. We find that strong hydrophobic interactions between geometrically fitting residues keep the strands (both in register and out-off-register interface) in close proximity, which in turn stabilizes the side-chain and main-chain hydrogen bonds, and the salt bridges on the outer surface along the weak out-of-register interface. Our simulations also indicate presence of water molecules in the hydrophobic interior of the cylindrin β-barrel.Proteins 2013.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
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13
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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]
Abstract
An α→β transition underlies the first step of disease causing amyloidogenesis in many proteins. In view of this, many studies have been carried out using peptide models to characterize these secondary structural transitions. In this paper we show that an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme (M. Sagermann, W. A. Baase and B. W. Matthews, Proc. Natl. Acad. Sci. U.S.A., 1999, 96, 6078) displays an α→β transition. We performed molecular dynamics (MD) simulation of L20, using the GROMACS package of programs and united atom GROMOS 53a6 force field for a time period of 600 ns at 300 K, in explicit water. Our MD simulation demonstrated that the transition occurs in a duplicated α-helical region inserted tandemly at the N-terminus of the 'parent' helix. We show that a C-terminal β-sheet anchors the parent helix while the loosely held N-terminal loop in the duplicate region is vulnerable to solvent attack and thus undergoes an α→β transition. Main chain-solvent interactions were seen to stabilize the observed β-structure. Thus L20 serves as a good protein model for characterization of α→β transition in a full length protein.
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Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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14
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Berhanu WM, Hansmann UHE. Side-chain hydrophobicity and the stability of Aβ₁₆₋₂₂ aggregates. Protein Sci 2012; 21:1837-48. [PMID: 23015407 PMCID: PMC3575914 DOI: 10.1002/pro.2164] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/06/2012] [Accepted: 09/14/2012] [Indexed: 11/05/2022]
Abstract
Recent mutagenesis studies using the hydrophobic segment of Aβ suggest that aromatic π-stacking interactions may not be critical for fibril formation. We have tested this conjecture by probing the effect of Leu, Ile, and Ala mutation of the aromatic Phe residues at positions 19 and 20, on the double-layer hexametric chains of Aβ fragment Aβ₁₆₋₂₂ using explicit solvent all-atom molecular dynamics. As these simulations rely on the accuracy of the utilized force fields, we first evaluated the dynamic and stability dependence on various force fields of small amyloid aggregates. These initial investigations led us to choose AMBER99SB-ILDN as force field in multiple long molecular dynamics simulations of 100 ns that probe the stability of the wild-type and mutants oligomers. Single-point and double-point mutants confirm that size and hydrophobicity are key for the aggregation and stability of the hydrophobic core region (Aβ₁₆₋₂₂). This suggests as a venue for designing Aβ aggregation inhibitors the substitution of residues (especially, Phe 19 and 20) in the hydrophobic region (Aβ₁₆₋₂₂) with natural and non-natural amino acids of similar size and hydrophobicity.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry and Biochemistry, University of OklahomaNorman, Oklahoma 73019
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of OklahomaNorman, Oklahoma 73019
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15
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Berhanu WM, Hansmann UHE. Structure and dynamics of amyloid-β segmental polymorphisms. PLoS One 2012; 7:e41479. [PMID: 22911797 PMCID: PMC3404032 DOI: 10.1371/journal.pone.0041479] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/21/2012] [Indexed: 11/23/2022] Open
Abstract
It is believed that amyloid-beta (Aβ) aggregates play a role in the pathogenesis of Alzheimer's disease. Aβ molecules form β-sheet structures with multiple interaction sites. This polymorphism gives rise to differences in morphology, physico-chemical property and level of cellular toxicity. We have investigated the conformational stability of various segmental polymorphisms using molecular dynamics simulations and find that the segmental polymorphic models of Aβ retain a U-shaped architecture. Our results demonstrate the importance of inter-sheet side chain-side chain contacts, hydrophobic contacts among the strands (β1 and β2) and of salt bridges in stabilizing the aggregates. Residues in β-sheet regions have smaller fluctuation while those at the edge and loop region are more mobile. The inter-peptide salt bridges between Asp23 and Lys28 are strong compared to intra-chain salt bridge and there is an exchange of the inter-chain salt-bridge with intra-chain salt bridge. As our results suggest that Aβ exists under physiological conditions as an ensemble of distinct segmental polymorphs, it may be necessary to account in the development of therapeutics for Alzheimer's disease the differences in structural stability and aggregation behavior of the various Aβ polymorphic forms.
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Affiliation(s)
- Workalemahu M. Berhanu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Ulrich H. E. Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
- * E-mail:
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