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Wang Y, Wang K, Zhao X, Xu X, Sun T. Influence of pH on the self-assembly of diphenylalanine peptides: molecular insights from coarse-grained simulations. SOFT MATTER 2023; 19:5749-5757. [PMID: 37462931 DOI: 10.1039/d3sm00739a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nanostructures fabricated from peptide self-assemblies are attracting increasing attention owing to their possible applications in biology and nanotechnology. A known example is an aromatic dipeptide (diphenylalanine, FF) which is extracted from Alzheimer's β-amyloid polypeptide as the core recognition motif for molecular self-assembly. Many studies have been carried out to organize FF peptides into various functional ordered nanostructures. For potential applications of self-assembled FF-based nanomaterials, it becomes important to consider some influencing factors (e.g., solvents, peptide concentrations, pH, temperature, etc.) on the self-assembly process. Among these factors, the effect of pH on the self-assembly process of FF peptides into assembled nanostructures through simulation studies is the main focus of the present work. In the current study, we have investigated the assembly pathway of 1000 FF peptides and qualitatively evaluated the morphological changes of FF-based nanostructures at different pH values by performing extensive coarse-grained molecular dynamics (CG-MD) simulations. Structural analyses suggest that FF peptides can spontaneously assemble into nanotubes with different shapes under acidic, neutral and basic conditions. Based on the analysis of FF nanostructure formation pathways in different pH solutions, the self-assembly of the nanotube involves the aggregation of molecules to form a bilayer, the curling of a bilayer to form a vesicle and the transformation of a vesicle into a tubular structure. It is noted that a flat hollow columnar structure is observed as a special intermediate state during the transformation process of a vesicle-like to a tube-like structure. Energetic analysis suggests that the aggregation of FF peptides is driven by the vdW interactions but the aggregation shape is mainly affected by the electrostatic interactions. Overall, this study provides further understanding of the self-assembly behavior of aromatic short peptide derivatives in different pH solutions.
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Affiliation(s)
- Yan Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang 310008, China.
| | - Kang Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang 310008, China.
| | - Xinyi Zhao
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang 310008, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu 213001, China
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang 310008, China.
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Emamyari S, Mirzaei M, Mohammadinejad S, Fazli D, Fazli H. Impact of flexibility on the aggregation of polymeric macromolecules. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:66. [PMID: 37522950 DOI: 10.1140/epje/s10189-023-00324-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
Dependence of the dimerization probability and the aggregation behavior of polymeric macromolecules on their flexibility is studied using Langevin dynamics simulations. It is found that the dimerization probability is a non-monotonic function of the polymers persistence length. For a given value of inter-polymer attraction strength, semiflexible polymers have lower dimerization probability relative to flexible and rigid polymers of the same length. The threshold temperature of the formation of aggregates in a many-polymer system and its dependence on the polymers persistence length is also investigated. The simulation results of two- and many-polymer systems are in good agreement and show how the amount of flexibility affects the dimerization and the aggregation behaviors of polymeric macromolecules.
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Affiliation(s)
- Soheila Emamyari
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Masoud Mirzaei
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Sarah Mohammadinejad
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Davood Fazli
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran
| | - Hossein Fazli
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran.
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Prof. Yousef Sobouti Blvd., Zanjan, 45137-66731, Iran.
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Taherkhani A, Fazli H, Taherkhani F. Application of Janus Magnetic Nanoparticle Fe
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@SiN functionalized with beta‐cyclodextrin in thymol drug delivery procedure: An in vitro study. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ali Taherkhani
- Department of Physics Institute for Advanced Studies in Basic Sciences (IASBS) Zanjan Iran
| | - Hossein Fazli
- Department of Physics Institute for Advanced Studies in Basic Sciences (IASBS) Zanjan Iran
| | - Farid Taherkhani
- Departments of Production Engineering University of Bremen Bremen Germany
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Calvanese L, Brun P, Messina GML, Russo T, Zamuner A, Falcigno L, D’Auria G, Gloria A, Vitagliano L, Marletta G, Dettin M. EAK Hydrogels Cross-Linked by Disulfide Bonds: Cys Number and Position Are Matched to Performances. ACS Biomater Sci Eng 2019; 6:1154-1164. [DOI: 10.1021/acsbiomaterials.9b01556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Luisa Calvanese
- CIRPeB, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Grazia M. L. Messina
- Department of Chemical Sciences, University of Catania, Via A. Doria 6, 95125 Catania, Italy
| | - Teresa Russo
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, Viale J.F. Kennedy 54−Mostra d’Oltremare PAD. 20, 80125 Naples, Italy
| | - Annj Zamuner
- Department of Industrial Engineering, University of Padua, Via Marzolo 9, 35131 Padua, Italy
| | - Lucia Falcigno
- Department of Pharmacy, University of Naples “Federico II”, Via Mezzocannone 16, 80134 Naples, Italy
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gabriella D’Auria
- Department of Pharmacy, University of Naples “Federico II”, Via Mezzocannone 16, 80134 Naples, Italy
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Antonio Gloria
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, Viale J.F. Kennedy 54−Mostra d’Oltremare PAD. 20, 80125 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Giovanni Marletta
- Department of Chemical Sciences, University of Catania, Via A. Doria 6, 95125 Catania, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padua, Via Marzolo 9, 35131 Padua, Italy
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Emamyari S, Fazli H. Single-Chain Conformational Characteristics of Comb-Like Polyelectrolytes: Molecular Dynamics Simulation Study. Macromol Res 2018. [DOI: 10.1007/s13233-019-7010-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Forte G, Messina G, Zamuner A, Dettin M, Grassi A, Marletta G. Surface-driven first-step events of nanoscale self-assembly for molecular peptide fibers: An experimental and theoretical study. Colloids Surf B Biointerfaces 2018; 168:148-155. [DOI: 10.1016/j.colsurfb.2018.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/13/2017] [Accepted: 01/13/2018] [Indexed: 01/20/2023]
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Betush RJ, Urban JM, Nilsson BL. Balancing hydrophobicity and sequence pattern to influence self-assembly of amphipathic peptides. Biopolymers 2018; 110. [PMID: 29292825 DOI: 10.1002/bip.23099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 01/25/2023]
Abstract
Amphipathic peptides with alternating polar and nonpolar amino acid sequences efficiently self-assemble into functional β-sheet fibrils as long as the nonpolar residues have sufficient hydrophobicity. For example, the Ac-(FKFE)2 -NH2 peptide rapidly self-assembles into β-sheet bilayer nanoribbons, while Ac-(AKAE)2 -NH2 fails to self-assemble under similar conditions due to the significantly reduced hydrophobicity and β-sheet propensity of Ala relative to Phe. Herein, we systematically explore the effect of substituting only two of the four Ala residues at various positions in the Ac-(AKAE)2 -NH2 peptide with amino acids of increasing hydrophobicity, β-sheet potential, and surface area (including Phe, 1-naphthylalanine (1-Nal), 2-naphthylalanine (2-Nal), cyclohexylalanine (Cha), and pentafluorophenylalanine (F5 -Phe)) on the self-assembly propensity of the resulting sequences. It was found that double Phe variants, regardless of the position of substitution, failed to self-assemble under the conditions used in this study. In contrast, all double 1-Nal and 2-Nal variants readily self-assembled, albeit at differing rates depending on the substitution patterns. To determine whether this was due to hydrophobicity or side chain surface area, we also prepared double Cha and F5 -Phe variant peptides (both side chain groups are more hydrophobic than Phe). Each of these variants also underwent effective self-assembly, with the aromatic F5 -Phe peptides doing so with greater efficiency. These findings provide insight into the role of amino acid hydrophobicity and sequence pattern on self-assembly proclivity of amphipathic peptides and on how targeted substitutions of nonpolar residues in these sequences can be exploited to tune the characteristics of the resulting self-assembled materials.
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Affiliation(s)
- Ria J Betush
- Department of Chemistry, Gannon University, Erie, Pennsylvania
| | - Jennifer M Urban
- Department of Chemistry, University of Rochester, Rochester, New York
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York
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Ekiz MS, Cinar G, Khalily MA, Guler MO. Self-assembled peptide nanostructures for functional materials. NANOTECHNOLOGY 2016; 27:402002. [PMID: 27578525 DOI: 10.1088/0957-4484/27/40/402002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
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Affiliation(s)
- Melis Sardan Ekiz
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800 Turkey
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Liu W, Saunders MJ, Bagia C, Freeman EC, Fan Y, Gawalt ES, Waggoner AS, Meng WS. Local retention of antibodies in vivo with an injectable film embedded with a fluorogen-activating protein. J Control Release 2016; 230:1-12. [PMID: 27038493 DOI: 10.1016/j.jconrel.2016.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/25/2016] [Accepted: 03/22/2016] [Indexed: 11/17/2022]
Abstract
Herein we report an injectable film by which antibodies can be localized in vivo. The system builds upon a bifunctional polypeptide consisting of a fluorogen-activating protein (FAP) and a β-fibrillizing peptide (βFP). The FAP domain generates fluorescence that reflects IgG binding sites conferred by Protein A/G (pAG) conjugated with the fluorogen malachite green (MG). A film is generated by mixing these proteins with molar excess of EAK16-II, a βFP that forms β-sheet fibrils at high salt concentrations. The IgG-binding, fluorogenic film can be injected in vivo through conventional needled syringes. Confocal microscopic images and dose-response titration experiments showed that loading of IgG into the film was mediated by pAG(MG) bound to the FAP. Release of IgG in vitro was significantly delayed by the bioaffinity mechanism; 26% of the IgG were released from films embedded with pAG(MG) after five days, compared to close to 90% in films without pAG(MG). Computational simulations indicated that the release rate of IgG is governed by positive cooperativity due to pAG(MG). When injected into the subcutaneous space of mouse footpads, film-embedded IgG were retained locally, with distribution through the lymphatics impeded. The ability to track IgG binding sites and distribution simultaneously will aid the optimization of local antibody delivery systems.
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Affiliation(s)
- Wen Liu
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States
| | - Matthew J Saunders
- Molecular Biosensor and Imaging Center and Carnegie Mellon University, Pittsburgh, PA 15213, United States; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Christina Bagia
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States
| | - Eric C Freeman
- College of Engineering, University of Georgia, Athens, GA 30602, United States
| | - Yong Fan
- Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Pittsburgh, PA 15212, United States; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Ellen S Gawalt
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, United States; McGowan Institute for Regenerative Medicine, Pittsburgh, PA 15213, United States
| | - Alan S Waggoner
- Molecular Biosensor and Imaging Center and Carnegie Mellon University, Pittsburgh, PA 15213, United States; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Wilson S Meng
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States.
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Wang Y, Li QY, Liu XB, Zhang CY, Wu ZM, Guo XD. Mesoscale Simulations and Experimental Studies of pH-Sensitive Micelles for Controlled Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2015; 7:25592-25600. [PMID: 26539742 DOI: 10.1021/acsami.5b08366] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The microstructures of doxorubicin-loaded micelles prepared from block polymers His(x)Lys10 (x = 0, 5, 10) conjugated with docosahexaenoic acid (DHA) are investigated under different pH conditions, using dissipative particle dynamics (DPD) simulations. The conformation of micelles and the DOX distributions in micelles were obviously influenced by pH values and the length of the histidine segment. At pH >6.0, the micelles self-assembled from the polymers were dense and compact. The drugs were entrapped well within the micellar core. The particle size increases as the histidine length increases. With the decrease of pH value to be lower than 6.0, there was no distinct difference for the micelles self-assembled from the polymer without histidine residues. However, the micelles prepared from the polymers with histidine residues shows a structural transformation from dense to swollen conformation, leading to an increased particle size from 10.3 to 14.5 DPD units for DHD-His10Lys10 micelles. This structural transformation of micelles can accelerate the DOX release from micelles under lower pH conditions. The in vitro drug release from micelles is accelerated by the decrease of pH value from 7.4 (physiological environment) to 5.0 (lysosomal environment). The integration of simulation and experiments might be a valuable method for the optimization and design of biomaterials for drug delivery with desired properties.
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Affiliation(s)
- Yan Wang
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology , Beijing, 100029, People's Republic of China
- School of Chemical Engineering, Xiangtan University , Xiangtan 411105, People's Republic of China
| | - Qiu Yu Li
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology , Beijing, 100029, People's Republic of China
| | - Xu Bo Liu
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology , Beijing, 100029, People's Republic of China
| | - Can Yang Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China , Beijing 100190, People's Republic of China
| | - Zhi Min Wu
- School of Chemical Engineering, Xiangtan University , Xiangtan 411105, People's Republic of China
| | - Xin Dong Guo
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology , Beijing, 100029, People's Republic of China
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Wang X, Weber JK, Liu L, Dong M, Zhou R, Li J. A novel form of β-strand assembly observed in Aβ(33-42) adsorbed onto graphene. NANOSCALE 2015; 7:15341-15348. [PMID: 26331805 DOI: 10.1039/c5nr00555h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.
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Affiliation(s)
- Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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Chun BJ, Choi JI, Jang SS. Molecular dynamics simulation study of sodium dodecyl sulfate micelle: Water penetration and sodium dodecyl sulfate dissociation. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Emamyari S, Kargar F, Sheikh-hasani V, Emadi S, Fazli H. Mechanisms of the self-assembly of EAK16-family peptides into fibrillar and globular structures: molecular dynamics simulations from nano- to micro-seconds. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:263-76. [DOI: 10.1007/s00249-015-1024-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/19/2015] [Accepted: 03/23/2015] [Indexed: 12/18/2022]
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Emamyari S, Fazli H. All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:143-55. [DOI: 10.1007/s00249-014-0949-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 10/25/2022]
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