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Xue J, Ji M, Lu Y, Pan D, Yang X, Yang X, Xu Z. The impact of chemical properties of the solid-liquid-adsorbate interfaces on the entropy-enthalpy compensation involved in adsorption. Phys Chem Chem Phys 2024; 26:8704-8715. [PMID: 38415756 DOI: 10.1039/d3cp05669d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Despite extensive studies on the thermodynamic mechanism governing molecular adsorption at the solid-water interface, a comprehensive understanding of the crucial role of interface properties in mediating the entropy-enthalpy compensation during adsorption is lacking, particularly at a quantitative level. Herein, we employed two types of surface models (hydroxyapatite and graphene) along with a series of amino acids to successfully elucidate how distinct interfacial features dictate the delicate balance between entropy and enthalpy variations. The adsorption of all amino acids on the hydroxyapatite surface is an enthalpy-dominated process, where the water-induced enthalpic component of the free energy and the surface-adsorbate electrostatic interaction term alternatively act as the driving force for adsorption in different regions of the surface. Although favorable interactions are observed between amino acids and the graphene surface, the entropy-enthalpy compensation exhibits dependence on the molecular size of the adsorbates. For small amino acids, favorable enthalpy changes predominantly determine their adsorption behavior; however, larger amino acids tend to bind more tightly with the graphene surface, which is thermodynamically dominated by the entropy variations despite the structural characteristics of amino acids. This study reveals specific entropy-enthalpy mechanisms underlying amino acid adsorption at the solid-liquid interface, providing guidance for surface design and synthesis of new biomolecules.
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Affiliation(s)
- Jinling Xue
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Mingyu Ji
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Yuanyuan Lu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Dan Pan
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
- Zhangjiagang Institute of Nanjing Tech University, Zhangjiagang 215699, China
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Ouyang J, Sheng Y, Wang W. Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations. Cells 2022; 11:cells11244016. [PMID: 36552778 PMCID: PMC9776715 DOI: 10.3390/cells11244016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.
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Affiliation(s)
- Jun Ouyang
- School of Public Courses, Bengbu Medical College, Bengbu 233030, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- High Performance Computing Center, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
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3
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Li Z, Cai B, Yang W, Chen CL. Hierarchical Nanomaterials Assembled from Peptoids and Other Sequence-Defined Synthetic Polymers. Chem Rev 2021; 121:14031-14087. [PMID: 34342989 DOI: 10.1021/acs.chemrev.1c00024] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In nature, the self-assembly of sequence-specific biopolymers into hierarchical structures plays an essential role in the construction of functional biomaterials. To develop synthetic materials that can mimic and surpass the function of these natural counterparts, various sequence-defined bio- and biomimetic polymers have been developed and exploited as building blocks for hierarchical self-assembly. This review summarizes the recent advances in the molecular self-assembly of hierarchical nanomaterials based on peptoids (or poly-N-substituted glycines) and other sequence-defined synthetic polymers. Modern techniques to monitor the assembly mechanisms and characterize the physicochemical properties of these self-assembly systems are highlighted. In addition, discussions about their potential applications in biomedical sciences and renewable energy are also included. This review aims to highlight essential features of sequence-defined synthetic polymers (e.g., high stability and protein-like high-information content) and how these unique features enable the construction of robust biomimetic functional materials with high programmability and predictability, with an emphasis on peptoids and their self-assembled nanomaterials.
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Affiliation(s)
- Zhiliang Li
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Bin Cai
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemistry and Chemical Engineering, Shandong University, Shandong 250100, China
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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4
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Jiao F, Wu X, Jian T, Zhang S, Jin H, He P, Chen C, De Yoreo JJ. Hierarchical Assembly of Peptoid‐Based Cylindrical Micelles Exhibiting Efficient Resonance Energy Transfer in Aqueous Solution. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fang Jiao
- School of Chemistry and Molecular EngineeringEast China Normal University 500 DongChuan Road Shanghai 200241 China
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
| | - Xuepeng Wu
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
- School of Petroleum EngineeringState Key Laboratory of Heavy Oil ProcessingChina University of Petroleum (East China) Qingdao Shandong 266580 China
| | - Tengyue Jian
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
| | - Shuai Zhang
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
- Department of Materials Science and EngineeringUniversity of Washington Seattle WA 98195 USA
| | - Haibao Jin
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
| | - Pingang He
- School of Chemistry and Molecular EngineeringEast China Normal University 500 DongChuan Road Shanghai 200241 China
| | - Chun‐Long Chen
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
- Department of Chemical EngineeringUniversity of Washington Seattle WA 98195 USA
| | - James J. De Yoreo
- Physical Sciences DivisionPacific Northwest National Laboratory Richland WA 99352 USA
- Department of Materials Science and EngineeringUniversity of Washington Seattle WA 98195 USA
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5
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Jiao F, Wu X, Jian T, Zhang S, Jin H, He P, Chen CL, De Yoreo JJ. Hierarchical Assembly of Peptoid-Based Cylindrical Micelles Exhibiting Efficient Resonance Energy Transfer in Aqueous Solution. Angew Chem Int Ed Engl 2019; 58:12223-12230. [PMID: 31211884 DOI: 10.1002/anie.201904598] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 11/09/2022]
Abstract
Herein we show that by appending bulky β-cyclodextrin (CD) groups onto sheet-forming peptoids, we obtain cylindrical micelles that further assembly into membranes and intertwined ribbons on substrates in aqueous solution, depending on the choice of solution and substrate conditions. In situ atomic force microscopy (AFM) shows that micelle assembly occurs in two steps, starting with "precursor" particles that transform into worm-like micelles, which extend and coalesce to form the higher order structures with a rate and a degree of cooperativity dependent on pH and Ca2+ concentration. After co-assembly with hydrophobic 4-(2-hydroxyethylamino)-7-nitro-2,1,3-benzoxadiazole (NBD) donors that occupy the hydrophobic core, followed by exposure to hydrophilic Rhodamine B as acceptors that insert into cyclodextrin, the micelles exhibit highly efficient Förster resonance energy transfer efficiency in aqueous solution, thereby mimicking natural light harvesting systems.
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Affiliation(s)
- Fang Jiao
- School of Chemistry and Molecular Engineering, East China Normal University, 500 DongChuan Road, Shanghai, 200241, China.,Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xuepeng Wu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,School of Petroleum Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, Shandong, 266580, China
| | - Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Haibao Jin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 DongChuan Road, Shanghai, 200241, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
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6
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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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7
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Feng M, Kang H, Yang Z, Luan B, Zhou R. Potential disruption of protein-protein interactions by graphene oxide. J Chem Phys 2016; 144:225102. [PMID: 27306022 DOI: 10.1063/1.4953562] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.
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Affiliation(s)
- Mei Feng
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China
| | - Hongsuk Kang
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Ruhong Zhou
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China
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8
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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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9
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Chaudhuri B, Bhadra D, Moroni L, Pramanik K. Myoblast differentiation of human mesenchymal stem cells on graphene oxide and electrospun graphene oxide–polymer composite fibrous meshes: importance of graphene oxide conductivity and dielectric constant on their biocompatibility. Biofabrication 2015; 7:015009. [DOI: 10.1088/1758-5090/7/1/015009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Miriani M, Iametti S, Kurtz DM, Bonomi F. Rubredoxin refolding on nanostructured hydrophobic surfaces: evidence for a new type of biomimetic chaperones. Proteins 2014; 82:3154-62. [PMID: 25143010 DOI: 10.1002/prot.24675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/04/2014] [Accepted: 08/11/2014] [Indexed: 11/08/2022]
Abstract
Rubredoxins (Rds) are small proteins containing a tetrahedral Fe(SCys)4 site. Folded forms of metal free Rds (apoRds) show greatly impaired ability to incorporate iron compared with chaotropically unfolded apoRds. In this study, formation of the Rd holoprotein (holoRd) on addition of iron to a structured, but iron-uptake incompetent apoRd was investigated in the presence of polystyrene nanoparticles (NP). In our rationale, hydrophobic contacts between apoRd and the NP surface would expose protein regions (including ligand cysteines) buried in the structured apoRd, allowing iron incorporation and folding to the native holoRd. Burial of the hydrophobic regions in the folded holoRd would allow its detachment from the NP surface. We found that both rate and yield of holoRd formation increased significantly in the presence of NP and were influenced by the NP concentration and size. Rates and yields had an optimum at "catalytic" NP concentrations (0.2 g/L NP) when using relatively small NP (46 nm diameter). At these optimal conditions, only a fraction of the apoRd was bound to the NP, consistent with the occurrence of turnover events on the NP surface. Lower rates and yields at higher NP concentrations or when using larger NP (200 nm) suggest that steric effects and molecular crowding on the NP surface favor specific "iron-uptake-competent" conformations of apoRd on the NP surface. This bio-mimetic chaperone system may be applicable to other proteins requiring an unfolding step before cofactor-triggered refolding, particularly when over-expressed under limited cofactor accessibility.
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Affiliation(s)
- Matteo Miriani
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
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11
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Emamyari S, Fazli H. pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation. SOFT MATTER 2014; 10:4248-4257. [PMID: 24740580 DOI: 10.1039/c4sm00307a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-assembly behavior of the three types of ionic peptide, EAK16, is studied in the presence of a hydrophobic surface using coarse-grained molecular dynamics simulations at three pH ranges of the solution. It is found that the peptide chains of all the three types assemble on the hydrophobic surface. EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH. EAK16-IV peptide chains, however, assemble into ribbon-like structures at low and high pH ranges and form disc-shaped assemblies on the hydrophobic surface at the isoelectric point, pH = 7. Strong intra-chain electrostatic interactions in the case of EAK16-IV peptide play the main role in dependence of its self-assembly behavior on pH and the different morphology of its assembly relative to those of the two other types. Kinetics of growth of the assemblies on the hydrophobic surface is also studied.
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Affiliation(s)
- Soheila Emamyari
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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12
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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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14
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Pan H, Qin M, Meng W, Cao Y, Wang W. How do proteins unfold upon adsorption on nanoparticle surfaces? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12779-87. [PMID: 22913793 DOI: 10.1021/la302258k] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Owing to their many outstanding features, such as small size, large surface area, and cell penetration ability, nanoparticles have been increasingly used in medicine and biomaterials as drug carriers and diagnostic or therapeutic agents. However, our understanding of the interactions of biological entities, especially proteins, with nanoparticles is far behind the explosive development of nanotechnology. In typical protein-nanoparticle interactions, two processes (i.e., surface binding and conformational changes in proteins) are intermingled with each other and have not yet been quantitatively described. Here, by using a stopped-flow fast mixing technique, we were able to shed light on the kinetics of the adsorption-induced protein unfolding on nanoparticle surfaces in detail. We observed a biphasic denaturation behavior of protein GB1 on latex nanoparticle surfaces. Such kinetics can be adequately described by a fast equilibrium adsorption followed by a slow reversible unfolding of GB1. On the basis of this model, we quantitatively measured all rate constants that are involved in this process, from which the free-energy profile is constructed. This allows us to evaluate the effects of environmental factors, such as pH and ionic strength, on both the adsorption and the conformational change in GB1 on the latex nanoparticle surface. These studies provide a general physical picture of the adsorption-induced unfolding of proteins on nanoparticle surfaces and a quantitative description of the energetics of each transition. We anticipate that it will greatly advance our current understanding of protein-nanoparticle interactions and will be helpful for the rational control of such interactions in biomedical applications.
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Affiliation(s)
- Hai Pan
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu 210093, PR China
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15
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Keller K, Amirian A, Akcora P. Elastic properties of a protein-polymer-grafted surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:3807-3813. [PMID: 22272555 DOI: 10.1021/la204773u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Surfaces grafted with poly(methyl methacrylate) (PMMA) and streptavidin were synthesized through click chemistry to investigate the role of surface stiffness on protein adsorption as the hydrophilic and hydrophobic surface coverage of the substituents vary. Surface topographies coupled with the nanoindentation results indicated that, with the appropriate selections of polymer coverage and chain length, the extent of non-specific protein adhesion could be controlled by the hydrophobic interactions between PMMA, biotin, and streptavidin. It was shown that, when the molecular weight and stiffness of PMMA was close to that of streptavidin, patchy PMMA morphologies were obtained, which help inhibit the non-specific adsorption of streptavidin.
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Affiliation(s)
- Kristen Keller
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, USA
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Jiang Z, Yu Y, Du L, Ding X, Xu H, Sun Y, Zhang Q. Peptide derived from Pvfp-1 as bioadhesive on bio-inert surface. Colloids Surf B Biointerfaces 2012; 90:227-35. [DOI: 10.1016/j.colsurfb.2011.10.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 10/17/2011] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
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17
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Wu X, Damjanovic A, Brooks BR. Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics. ADVANCES IN CHEMICAL PHYSICS 2012; 150:255-326. [PMID: 23913991 PMCID: PMC3731171 DOI: 10.1002/9781118197714.ch6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. It has been demonstrated that with moderate parameters, SGLD can routinely cross energy barriers of 20 kT at a rate that molecular dynamics (MD) or Langevin dynamics (LD) crosses 10 kT barriers. The core of these methods is the use of local averages of forces and momenta in a direct manner that can preserve the canonical ensemble. The use of such local averages results in methods where low frequency motion "borrows" energy from high frequency degrees of freedom when a barrier is approached and then returns that excess energy after a barrier is crossed. This self-guiding effect also results in an accelerated diffusion to enhance conformational sampling efficiency. The resulting ensemble with SGLD deviates in a small way from the canonical ensemble, and that deviation can be corrected with either an on-the-fly or a post processing reweighting procedure that provides an excellent canonical ensemble for systems with a limited number of accelerated degrees of freedom. Since reweighting procedures are generally not size extensive, a newer method, SGLDfp, uses local averages of both momenta and forces to preserve the ensemble without reweighting. The SGLDfp approach is size extensive and can be used to accelerate low frequency motion in large systems, or in systems with explicit solvent where solvent diffusion is also to be enhanced. Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health(NIH), 5635 Fishers Lane, Room T900, Bethesda, MD 20892-9314
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health(NIH), 5635 Fishers Lane, Room T900, Bethesda, MD 20892-9314
- Johns Hopkins University, Department of Biophysics, 3400 N. Charles Street, Baltimore, MD 21218
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health(NIH), 5635 Fishers Lane, Room T900, Bethesda, MD 20892-9314
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Wu X, Brooks BR. Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble. J Chem Phys 2011; 135:204101. [PMID: 22128922 PMCID: PMC3248022 DOI: 10.1063/1.3662489] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 11/01/2011] [Indexed: 11/14/2022] Open
Abstract
The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
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Mücksch C, Urbassek HM. Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12938-12943. [PMID: 21877733 DOI: 10.1021/la201972f] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.
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Affiliation(s)
- Christian Mücksch
- Fachbereich Physik und Forschungszentrum OPTIMAS, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
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Ou L, Luo Y, Wei G. Atomic-Level Study of Adsorption, Conformational Change, and Dimerization of an α-Helical Peptide at Graphene Surface. J Phys Chem B 2011; 115:9813-22. [DOI: 10.1021/jp201474m] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Luchun Ou
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
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Mereghetti P, Wade RC. Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. BMC BIOPHYSICS 2011; 4:9. [PMID: 21595866 PMCID: PMC3114038 DOI: 10.1186/2046-1682-4-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 04/21/2011] [Indexed: 12/17/2022]
Abstract
Background Hydrophobins are small proteins produced by filamentous fungi that have a variety of biological functions including coating of spores and surface adhesion. To accomplish these functions, they rely on unique interface-binding properties. Using atomic-detail implicit solvent rigid-body Brownian dynamics simulations, we studied the diffusion of HFBI, a class II hydrophobin from Trichoderma reesei, in aqueous solution in the presence and absence of a graphite surface. Results In the simulations, HFBI exists in solution as a mixture of monomers in equilibrium with different types of oligomers. The oligomerization state depends on the conformation of HFBI. When a Highly Ordered Pyrolytic Graphite (HOPG) layer is present in the simulated system, HFBI tends to interact with the HOPG layer through a hydrophobic patch on the protein. Conclusions From the simulations of HFBI solutions, we identify a tetrameric encounter complex stabilized by non-polar interactions between the aliphatic residues in the hydrophobic patch on HFBI. After the formation of the encounter complex, a local structural rearrangement at the protein interfaces is required to obtain the tetrameric arrangement seen in HFBI crystals. Simulations performed with the graphite surface show that, due to a combination of a geometric hindrance and the interaction of the aliphatic sidechains with the graphite layer, HFBI proteins tend to accumulate close to the hydrophobic surface.
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Affiliation(s)
- Paolo Mereghetti
- Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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Zou D, Cao Y, Qin M, Dai W, Wang W. Formation of α-helix-based twisted ribbon-like fibrils from ionic-complementary peptides. Chem Commun (Camb) 2011; 47:7413-5. [DOI: 10.1039/c1cc12001h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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