1
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Jheng CP, Lee CI. Combination of structure-based virtual screening, molecular docking and molecular dynamics approaches for the discovery of anti-prion fibril flavonoids. Front Mol Biosci 2023; 9:1088733. [PMID: 36685276 PMCID: PMC9849400 DOI: 10.3389/fmolb.2022.1088733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Prion diseases are a group of rare neurodegenerative diseases caused by the structural conversion of cellular prion into Scrapie prion resulting aggregated fibrils. Therapy of prion diseases has been developed for several decades, especially drug designs based on the structure of prion monomers. Unfortunately, none of the designed anti-prion drugs function well clinically. To fight against prion fibrils, a drug design based on the precise structure of mammalian prion fibrils is highly required. Fortunately, based on the advantage of newly advanced cryo-electron microscopy (cryo-EM) in the deconvolution of large complexes, three prion fibril structures were resolved in the last 2 years. Based on the cryo-EM solved prion fibril structures, we are able to find some molecules fighting against prion fibrils. Quercetin, one flavonoid molecule in the polyphenol group, has been found to disaggregate the prion fibrils in vitro. In this study, we performed the molecular docking and molecular dynamics simulation on quercetin-like molecules possessing pharmacological properties to evaluate the anti-prion ability of tested molecules. As a result, four quercetin-like molecules interact with prion fibril and decrease the β-strand content by converting some β-strands into loop and helical structures to disintegrate the existing fibril structure. The results of this study are significant in the treatment of prion diseases, and the approaches used in this study are applicable to other amyloid diseases.
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Affiliation(s)
- Cheng-Ping Jheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Cheng-I Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan,Center for Nano Bio-Detections, National Chung Cheng University, Chia-Yi, Taiwan,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan,*Correspondence: Cheng-I Lee,
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2
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Li Y, Peng X. Comparison of the force fields on monomeric and fibrillar PHF6 of tau protein. Biophys Chem 2021; 277:106631. [PMID: 34116358 DOI: 10.1016/j.bpc.2021.106631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/18/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022]
Abstract
The hexapeptide 306VQIVYK311 (PHF6) plays an important role in the aggregation of Tau protein, which is a hallmark of the Alzheimer's disease (AD). In this article, we systematically compare the effects of eight popular all-atom force fields on the monomeric and fibrillar PHF6 in the molecular dynamics (MD) simulations, which could be helpful in the computer-aided drug design against PHF6. We show that the fibrillar PHF6 prefers β-strand-like structures in all the force fields while the monomer has different structural preferences depending on the force fields. The interactions for stabilizing the fibril are further investigated. In the end, according to the interactions revealed by NMR and the stability of the fibril in the literature, we benchmark the force fields.
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Affiliation(s)
- Yanchun Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China; Beijing Academy of Quantum Information Sciences, Beijing 100193, China.
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3
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Naveh Tassa S, Ben Zichri S, Lacham-Hartman S, Oren O, Slobodnik Z, Eremenko E, Toiber D, Jelinek R, Papo N. A Mechanism for the Inhibition of Tau Neurotoxicity: Studies with Artificial Membranes, Isolated Mitochondria, and Intact Cells. ACS Chem Neurosci 2021; 12:1563-1577. [PMID: 33904703 DOI: 10.1021/acschemneuro.1c00045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
It is currently believed that molecular agents that specifically bind to and neutralize the toxic proteins/peptides, amyloid β (Aβ42), tau, and the tau-derived peptide PHF6, hold the key to attenuating the progression of Alzheimer's disease (AD). We thus tested our previously developed nonaggregating Aβ42 double mutant (Aβ42DM) as a multispecific binder for three AD-associated molecules, wild-type Aβ42, the tauK174Q mutant, and a synthetic PHF6 peptide. Aβ42DM acted as a functional inhibitor of these molecules in in vitro assays and in neuronal cell-based models of AD. The double mutant bound both cytotoxic tauK174Q and synthetic PHF6 and protected neuronal cells from the accumulation of tau in cell lysates and mitochondria. Aβ42DM also reduced toxic intracellular levels of calcium and the overall cell toxicity induced by overexpressed tau, synthetic PHF6, Aβ42, or a combination of PHF6and Aβ42. Aβ42DM inhibited PHF6-induced overall mitochondrial dysfunction: In particular, Aβ42DM inhibited PHF6-induced damage to submitochondrial particles (SMPs) and suppressed PHF6-induced elevation of the ζ-potential of inverted SMPs (proxy for the inner mitochondrial membrane, IMM). PHF6 reduced the lipid fluidity of cardiolipin/DOPC vesicles (that mimic the IMM) but not DOPC (which mimics the outer mitochondrial membrane), and this effect was inhibited by Aβ42DM. This inhibition may be explained by the conformational changes in PHF6 induced by Aβ42DM in solution and in membrane mimetics. On this basis, the paper presents a mechanistic explanation for the inhibitory activity of Aβ42DM against Aβ42- and tau-induced membrane permeability and cell toxicity and provides confirmatory evidence for its protective function in neuronal cells.
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Affiliation(s)
- Segev Naveh Tassa
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Shani Ben Zichri
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Shiran Lacham-Hartman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ofek Oren
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Zeev Slobodnik
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ekaterina Eremenko
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
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4
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Chatterjee S, Salimi A, Lee JY. Molecular mechanism of amyloidogenicity and neurotoxicity of a pro-aggregated tau mutant in the presence of histidine tautomerism via replica-exchange simulation. Phys Chem Chem Phys 2021; 23:10475-10486. [DOI: 10.1039/d1cp00105a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Considering ΔK280 tau mutation, δε isomer with highest sheet content may accelerate aggregation; generating small compounds to inhibit this would help tp prevent tauopathies.
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Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry
- Sungkyunkwan University
- Suwon 440-746
- Korea
| | - Jin Yong Lee
- Department of Chemistry
- Sungkyunkwan University
- Suwon 440-746
- Korea
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5
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Zhang P, Moretti M, Allione M, Tian Y, Ordonez-Loza J, Altamura D, Giannini C, Torre B, Das G, Li E, Thoroddsen ST, Sarathy SM, Autiero I, Giugni A, Gentile F, Malara N, Marini M, Di Fabrizio E. A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth. Commun Biol 2020; 3:457. [PMID: 32820203 PMCID: PMC7441408 DOI: 10.1038/s42003-020-01187-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/31/2020] [Indexed: 11/10/2022] Open
Abstract
Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by the temperature gradient of the sample is the main driving force in the growth of well-ordered protein fibrils. Particular attention was devoted to PHF6 peptide and full-length Tau441 protein to form amyloid fibrils. By a combined experimental with the molecular dynamics simulations, the conformational polymorphism of these amyloid fibrils were characterized. The study provided a feasible procedure to optimize the amyloid fibrils formation and characterizations of other types of proteins in future studies. Zhang et al present an integrated real-time imaging and flow field control platform based on water droplet evaporation on super-hydrophobic substrate (SHS) to enable amyloid fibril aggregation. They apply this methodology to observe structural polymorphism in PHF6 peptide and full length Tau441.
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Affiliation(s)
- Peng Zhang
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manola Moretti
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Marco Allione
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yuansi Tian
- High-Speed Fluids Imaging Lab, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Javier Ordonez-Loza
- Clean Combustion Research Center, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Davide Altamura
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Cinzia Giannini
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Bruno Torre
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Gobind Das
- Department of Physics, Khalifa University, P.O. Box: 127788, Abu Dhabi, UAE
| | - Erqiang Li
- Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Sigurdur T Thoroddsen
- High-Speed Fluids Imaging Lab, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - S Mani Sarathy
- Clean Combustion Research Center, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ida Autiero
- Molecular Horizon, Bettona, Italy.,National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy
| | - Andrea Giugni
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Francesco Gentile
- Department of electrical Engineering and Information Technology, University Federico II, Naples, Italy
| | - Natalia Malara
- BIONEM lab, University Magna Graecia, Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Monica Marini
- Materials and Microsystems Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 10129, Torino, Italy
| | - Enzo Di Fabrizio
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia. .,Materials and Microsystems Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 10129, Torino, Italy.
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6
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Patel S, Krishnan B, Hosur RV, Chary KVR. Mechanistic Insights from Replica Exchange Molecular Dynamics Simulations into Mutation Induced Disordered-to-Ordered Transition in Hahellin, a βγ-Crystallin. J Phys Chem B 2019; 123:5086-5098. [DOI: 10.1021/acs.jpcb.9b03845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Bal Krishnan
- Indian Institute of Science Education and Research, Berhampur, 760010, India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V. R. Chary
- Tata Institute of Fundamental Research, Hyderabad 500107, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
- Indian Institute of Science Education and Research, Berhampur, 760010, India
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7
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Shen L, Xie L, Yang M. Thermodynamic properties of solvated peptides from selective integrated tempering sampling with a new weighting factor estimation algorithm. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1292009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lin Shen
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Liangxu Xie
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Mingjun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
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8
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Hughes ZE, Walsh TR. What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces. J Mater Chem B 2015; 3:3211-3221. [DOI: 10.1039/c5tb00004a] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular dynamics simulations of the aqueous biomolecule–graphene interface have predicted the free energy of adsorption of amino acids and the structure of peptides.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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9
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Abstract
Amyloid-β is an intrinsically disordered protein that forms fibrils in the brains of patients with Alzheimer's disease. To explore factors that affect the process of fibril growth, we computed the free energy associated with disordered amyloid-β monomers being added to growing amyloid fibrils using extensive molecular dynamics simulations coupled with umbrella sampling. We find that the mechanisms of Aβ40 and Aβ42 fibril elongation have many features in common, including the formation of an obligate on-pathway β-hairpin intermediate that hydrogen bonds to the fibril core. In addition, our data lead to new hypotheses for how fibrils may serve as secondary nucleation sites that can catalyze the formation of soluble oligomers, a finding in agreement with recent experimental observations. These data provide a detailed mechanistic description of amyloid-β fibril elongation and a structural link between the disordered free monomer and the growth of amyloid fibrils and soluble oligomers.
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Affiliation(s)
- Thomas Gurry
- Computational and Systems Biology Initiative and Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139-4307, United States
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10
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Bottaro S, Lindorff-Larsen K, Best RB. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data. J Chem Theory Comput 2013; 9:5641-5652. [PMID: 24748852 DOI: 10.1021/ct400730n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects.
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Affiliation(s)
- Sandro Bottaro
- Department of Biology, University of Copenhagen, Copenhagen, Denmark ; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, U.S.A. ; SISSA-Scuola Internazionale Superiore di Studi Avanzati,Trieste, Italy
| | - Kresten Lindorff-Larsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark ; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, U.S.A
| | - Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom ; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, U.S.A
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11
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How to design a drug for the disordered proteins? Drug Discov Today 2013; 18:910-5. [DOI: 10.1016/j.drudis.2013.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/25/2013] [Accepted: 04/22/2013] [Indexed: 11/20/2022]
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12
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Nurbaiti S, Martoprawiro MA, Akhmaloka, Hertadi R. The role of electrostatic interactions on klentaq1 insight for domain separation. Bioinform Biol Insights 2012; 6:225-34. [PMID: 23136465 PMCID: PMC3491847 DOI: 10.4137/bbi.s9390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We investigated the relationship between the thermostability of Klentaq1 and factors stabilizing interdomain interactions. When thermal adaptation of Klentaq1 was analyzed at the atomic level, the protein was stable at 300 and 350 K. It gradually unfolded at 373 K and almost spontaneously unfolded at 400 K. Domain separation was induced by disrupting electrostatic interactions in two salt bridges formed by Lys354-Glu445 and Asp371-Arg435 on the interface domain. The role of these interactions in protein stability was evaluated by comparing free energy solvation (ΔΔGsolv) between wild type and mutants. Substitution of Asp371 by Glu or Asn, and also Glu445 by Asn resulted in a positive value of ΔΔGsolv, suggesting that mutations destabilized the protein structure. Nevertheless, substitution of Glu445 by Asp gave a negative value to ΔΔGsolv reflecting increasing protein stability. Our results demonstrate that interactions at the interface domains of Klentaq1 are essential factors correlated with the Klentaq1 thermostability.
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Affiliation(s)
- Santi Nurbaiti
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia
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13
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Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1252-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Pu M, Garrahan JP, Hirst JD. Comparison of implicit solvent models and force fields in molecular dynamics simulations of the PB1 domain. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Finding order within disorder: elucidating the structure of proteins associated with neurodegenerative disease. Future Med Chem 2011; 1:467-82. [PMID: 21426127 DOI: 10.4155/fmc.09.40] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A number of neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease, involve the formation of protein aggregates. The primary constituent of these aggregates belongs to a unique class of heteropolymers known as intrinsically disordered proteins (IDPs). While many proteins fold to a unique conformation that is determined by their amino acid sequence, IDPs do not adopt a single well-defined conformation in solution. Instead, they populate a heterogeneous set of conformers under physiological conditions. Despite this intrinsic propensity for disorder, a number of these proteins can form ordered aggregates both in vitro and in vivo. As the formation of these aggregates may play an important role in disease pathogenesis, a detailed structural characterization of these proteins and their mechanism of aggregation is of critical importance. However, new methods are needed to understand the diversity of structures that make up the unfolded ensemble of these systems. In this review, we discuss recent advances in the structural analysis and modeling of IDPs involved in neurodegenerative diseases. While there are challenges in both the experimental characterization and the modeling of such proteins, a comprehensive understanding of the structure of IDPs will likely facilitate the development of effective therapies for a number of neurodegenerative diseases.
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16
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Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models. J Mol Model 2010; 17:37-48. [PMID: 20358386 DOI: 10.1007/s00894-010-0696-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
Abstract
Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.
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17
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Lerbret A, Affouard F, Bordat P, Hédoux A, Guinet Y, Descamps M. Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study. J Chem Phys 2009; 131:245103. [DOI: 10.1063/1.3273218] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Yoon MK, Venkatachalam V, Huang A, Choi BS, Stultz CM, Chou JJ. Residual structure within the disordered C-terminal segment of p21(Waf1/Cip1/Sdi1) and its implications for molecular recognition. Protein Sci 2009; 18:337-47. [PMID: 19165719 DOI: 10.1002/pro.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Probably the most unusual class of proteins in nature is the intrinsically unstructured proteins (IUPs), because they are not structured yet play essential roles in protein-protein signaling. Many IUPs can bind different proteins, and in many cases, adopt different bound conformations. The p21 protein is a small IUP (164 residues) that is ubiquitous in cellular signaling, for example, cell cycle control, apoptosis, transcription, differentiation, and so forth; it binds to approximately 25 targets. How does this small, unstructured protein recognize each of these targets with high affinity? Here, we characterize residual structural elements of the C-terminal segment of p21 encompassing residues 145-164 using a combination of NMR measurements and molecular dynamics simulations. The N-terminal half of the peptide has a significant helical propensity which is recognized by calmodulin while the C-terminal half of the peptide prefers extended conformations that facilitate binding to the proliferating cell nuclear antigen (PCNA). Our results suggest that the final bound conformations of p21 (145-164) pre-exist in the free peptide even without its binding partners. While the conformational flexibility of the p21 peptide is essential for adapting to diverse binding environments, the intrinsic structural preferences of the free peptide enable promiscuous yet high affinity binding to a diverse array of molecular targets.
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Affiliation(s)
- Mi-Kyung Yoon
- Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejon, Republic of Korea
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Brooks B, Brooks C, MacKerell A, Nilsson L, Petrella R, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner A, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R, Post C, Pu J, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York D, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009; 30:1545-614. [PMID: 19444816 PMCID: PMC2810661 DOI: 10.1002/jcc.21287] [Citation(s) in RCA: 5996] [Impact Index Per Article: 399.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
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Affiliation(s)
- B.R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and
Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - C.L. Brooks
- Departments of Chemistry & Biophysics, University of
Michigan, Ann Arbor, MI 48109
| | - A.D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD, 21201
| | - L. Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition,
SE-141 57, Huddinge, Sweden
| | - R.J. Petrella
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Department of Medicine, Harvard Medical School, Boston, MA
02115
| | - B. Roux
- Department of Biochemistry and Molecular Biology, University of
Chicago, Gordon Center for Integrative Science, Chicago, IL 60637
| | - Y. Won
- Department of Chemistry, Hanyang University, Seoul
133–792 Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - M. Karplus
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Laboratoire de Chimie Biophysique, ISIS, Université de
Strasbourg, 67000 Strasbourg France
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20
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Suárez M, Tortosa P, Jaramillo A. PROTDES: CHARMM toolbox for computational protein design. SYSTEMS AND SYNTHETIC BIOLOGY 2009; 2:105-13. [PMID: 19572216 PMCID: PMC2735645 DOI: 10.1007/s11693-009-9026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 05/17/2009] [Accepted: 05/30/2009] [Indexed: 12/13/2022]
Abstract
We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html.
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Affiliation(s)
- María Suárez
- Biochemistry Laboratory, CNRS—UMR 7654, Ecole Polytechnique, 91128 Palaiseau, France
- SYNTH-BIO group Epigenomics Project, Genopole Tour Evry2, etage 10, 523, Terrasses de l’Agora, 91034 Evry Cedex, France
| | - Pablo Tortosa
- Biochemistry Laboratory, CNRS—UMR 7654, Ecole Polytechnique, 91128 Palaiseau, France
| | - Alfonso Jaramillo
- Biochemistry Laboratory, CNRS—UMR 7654, Ecole Polytechnique, 91128 Palaiseau, France
- SYNTH-BIO group Epigenomics Project, Genopole Tour Evry2, etage 10, 523, Terrasses de l’Agora, 91034 Evry Cedex, France
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21
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Moltó G, Suárez M, Tortosa P, Alonso JM, Hernández V, Jaramillo A. Protein Design Based on Parallel Dimensional Reduction. J Chem Inf Model 2009; 49:1261-71. [DOI: 10.1021/ci8004594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Germán Moltó
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
| | - María Suárez
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
| | - Pablo Tortosa
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
| | - José M. Alonso
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
| | - Vicente Hernández
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
| | - Alfonso Jaramillo
- Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain, Epigenomics Project, Genopole-Université d'Évry Val d'Essonne-CNRS UPS 3201, 91034 Évry, France, and Laboratoire de Biochimie, École Polytechnique-CNRS UMR 7654, 91128, Palaiseau, France
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22
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Yeh IC, Lee MS, Olson MA. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models. J Phys Chem B 2009; 112:15064-73. [PMID: 18959439 DOI: 10.1021/jp802469g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins and their disorder-order phase transition of folding. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures, their solvent environment, and configurational averaging. To better understand these factors on calculating a protein heat capacity, we provide a comparative analysis of simulation models that differ in their implicit solvent description and force-field resolution. Our model protein system is the src Homology 3 (SH3) domain of alpha-spectrin, and we report a series of 10 ns replica-exchange molecular dynamics simulations performed at temperatures ranging from 298 to 550 K, starting from the SH3 native structure. We apply the all-atom CHARMM22 force field with different modified analytical generalized Born solvent models (GBSW and GBMV2) and compare these simulation models with the distance-dependent dielectric screening of charge-charge interactions. A further comparison is provided with the united-atom CHARMM19 plus a pairwise GB model. Unfolding-folding transition temperatures of SH3 were estimated from the temperature-dependent profiles of the heat capacity, root-mean-square distance from the native structure, and the fraction of native contacts, each calculated from the density of states by using the weighted histogram analysis method. We observed that, for CHARMM22, the unfolding transition and energy probability density were quite sensitive to the implicit solvent description, in particular, the treatment of the protein-solvent dielectric boundary in GB models and their surface-area-based hydrophobic term. Among the solvent models tested, the calculated melting temperature varied in the range 353-438 K and was higher than the experimental value near 340 K. A reformulated GBMV2 model of employing a smoother molecular-volume dielectric interface was the most accurate in reproducing the native conformation and a two-state folding landscape, although the melting transition temperature did not show the smallest deviation from experiment. For the lower-resolution CHARMM19/GB model, the simulations failed to yield a bimodal energy distribution, yet the melting temperature was observed to be a good estimate of higher-resolution simulation models. We also demonstrate that a careful analysis of a relatively long simulation is necessary to avoid trapping in local minima and to find a true thermodynamic transition temperature.
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Affiliation(s)
- In-Chul Yeh
- Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, USA
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23
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Huang A, Stultz CM. The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau. PLoS Comput Biol 2008; 4:e1000155. [PMID: 18725924 PMCID: PMC2494868 DOI: 10.1371/journal.pcbi.1000155] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 07/10/2008] [Indexed: 12/14/2022] Open
Abstract
Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease. To decipher the mechanism underlying the formation of tau aggregates, we developed a novel approach for constructing models of natively unfolded proteins. The method, energy-minima mapping and weighting (EMW), samples local energy minima of subsequences within a natively unfolded protein and then constructs ensembles from these energetically favorable conformations that are consistent with a given set of experimental data. A unique feature of the method is that it does not strive to generate a single ensemble that represents the unfolded state. Instead we construct a number of candidate ensembles, each of which agrees with a given set of experimental constraints, and focus our analysis on local structural features that are present in all of the independently generated ensembles. Using EMW we generated ensembles that are consistent with chemical shift measurements obtained on tau constructs. Thirty models were constructed for the second microtubule binding repeat (MTBR2) in wild-type (WT) tau and a DeltaK280 mutant, which is found in some forms of frontotemporal dementia. By focusing on structural features that are preserved across all ensembles, we find that the aggregation-initiating sequence, PHF6*, prefers an extended conformation in both the WT and DeltaK280 sequences. In addition, we find that residue K280 can adopt a loop/turn conformation in WT MTBR2 and that deletion of this residue, which can adopt nonextended states, leads to an increase in locally extended conformations near the C-terminus of PHF6*. As an increased preference for extended states near the C-terminus of PHF6* may facilitate the propagation of beta-structure downstream from PHF6*, these results explain how a deletion at position 280 can promote the formation of tau aggregates.
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Affiliation(s)
- Austin Huang
- Harvard–MIT Division of Health Sciences and Technology, Department of Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Collin M. Stultz
- Harvard–MIT Division of Health Sciences and Technology, Department of Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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24
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Strodel B, Fitzpatrick AW, Vendruscolo M, Dobson CM, Wales DJ. Characterizing the First Steps of Amyloid Formation for the ccβ Peptide. J Phys Chem B 2008; 112:9998-10004. [DOI: 10.1021/jp801222x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Birgit Strodel
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom and Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
| | - Anthony W. Fitzpatrick
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom and Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
| | - Michele Vendruscolo
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom and Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
| | - Christopher M. Dobson
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom and Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
| | - David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom and Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
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25
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Strodel B, Wales DJ. Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide. J Chem Theory Comput 2008; 4:657-72. [DOI: 10.1021/ct700305w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Birgit Strodel
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
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26
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Li DW, Han L, Huo S. Structural and Pathway Complexity of β-Strand Reorganization within Aggregates of Human Transthyretin(105−115) Peptide. J Phys Chem B 2007; 111:5425-33. [PMID: 17432900 DOI: 10.1021/jp0703051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interstrand conformational rearrangements of human transthyretin peptide (TTR(105-115)) within dimeric aggregates were simulated by means of molecular dynamics (MD) with implicit solvation model for a total length of 48 micros. The conformations sampled in the MD simulations were clustered to identify free energy minima without any projections of free energy surface. A connected graph was constructed with nodes (=clusters) and edges corresponding to free energy minima and transitions between nodes, respectively. This connected graph which reflects the complexity of the free energy surface was used to extract the transition disconnectivity graph, which reflects the overall free energy barriers between pairs of free energy minima but does not contain information on transition paths. The routes of transitions between important free energy minima were obtained by further processing the original graph and the MD data. We have found that both parallel and antiparallel aggregates are populated. The parallel aggregates with different alignment patterns are separated by nonnegligible free energy barriers. Multiroutes exist in the interstrand conformational reorganization. Most visited routes do not dominant the kinetics, while less visited routes contribute a little each but they are numerous and their total contributions are actually dominant. There are various kinds of reptation motions, including those through a beta-bulge, side-chain aided reptation, and flipping or rotation of a hairpin formed by one strand.
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Affiliation(s)
- Da-Wei Li
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
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Bruston F, Lacombe C, Zimmermann K, Piesse C, Nicolas P, El Amri C. Structural malleability of plasticins: Preorganized conformations in solution and relevance for antimicrobial activity. Biopolymers 2007; 86:42-56. [PMID: 17309077 DOI: 10.1002/bip.20703] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasticins (23 long-residue glycine-leucine-rich dermaseptin-related peptides produced by the skin of South American hylids) have very similar amino acid sequences, hydrophobicities, and amphipathicities, but differ in their membrane-damaging properties and structurations (i.e. destabilized helix states, beta-hairpin, beta-sheet, and disordered states) at anionic and zwitterionic membrane interfaces. Structural malleability of plasticins in aqueous solutions together with parameters that may govern their ability to fold within beta-hairpin like structures were analyzed through circular dichroism and FTIR spectroscopic studies completed by molecular dynamics simulations in polar mimetic media. The goal of this study was to probe to which extent pre-existent peptide conformations, i.e. intrinsic "conformational landscape", may be responsible for variability in bioactive conformation and antimicrobial/hemolytic mechanisms of action of these peptides in relation with their various membrane disturbing properties. All plasticins present a turn region that does not always result in folding into a beta-hairpin shaped conformation. Residue at position 8 plays a major role in initiating the folding, while position 12 is not critical. Conformational stability has no major impact on antimicrobial efficacy. However, preformed beta-hairpin in solution may act as a conformational lock that prevents switch to alpha-helical structure. This lock lowers the antimicrobial efficiency and explains subtle differences in potencies of the most active antimicrobial plasticins.
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Affiliation(s)
- F Bruston
- FRE 2852 Protéines: Biochimie Structurale et Fonctionnelle, Université Paris 6-CNRS, Peptidome de la peau d'amphibiens, tour 43, 4, Place Jussieu 75252 Paris Cedex 05, France
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