1
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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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2
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Alamdari S, Torkelson K, Wang X, Chen CL, Ferguson AL, Pfaendtner J. Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains. J Phys Chem B 2023. [PMID: 37379071 DOI: 10.1021/acs.jpcb.3c01913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)─to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. These results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.
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Affiliation(s)
- Sarah Alamdari
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Kaylyn Torkelson
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Xiaoqian Wang
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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3
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - 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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Wang M, Zhu Y. Defect Induced Charge Redistribution and Enhanced Adsorption of Lysozyme on Hydroxyapatite for Efficient Antibacterial Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10786-10796. [PMID: 34463099 DOI: 10.1021/acs.langmuir.1c01666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Defects in hydroxyapatite (HA) have attracted increasing research interest due to their significant functions to increase the bioactivity and antibacterial ability of hard-tissue implants. However, little is known about the natural property and functional mechanism of the defects in HA. Herein, we reported on the defect property concerned with the coordination state and charge distribution in Al doped HA, as well as the consequent interface and protein capture ability for improved antibacterial activity. Systemic investigations suggested that Al replacing Ca in HA induced coordination defect with decreased coordination number and bond distance, caused charge transfer and redistribution of surrounding O atom and resulted in an increase in negative charge of coordinated O atoms. These O atoms coordinated with Al further served as docking sites for lysozyme molecules via electrostatic and H-bonding interaction. The capacity of lysozyme adsorption for Al-HA increased approximately 10-fold more than that of HA, which significantly increased the antibacterial activity through lysozyme-catalyzed splitting of cell wall of bacteria. Moreover, in vitro studies indicated that Al-HA materials showed good cytocompatibility. These findings not only provided new insights into the important effect of defects on the performances of HA biomaterials by modulation of the coordination state, charge distribution, and chemical activity, but also proposed a promising method for efficient antibacterial activity of HA biomaterials.
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Affiliation(s)
- Ming Wang
- Key Lab of Inorganic Coating Materials CAS, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yingchun Zhu
- Key Lab of Inorganic Coating Materials CAS, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Science, Beijing 100049, China
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5
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Koumarianos S, Kaiyum R, Barrett CJ, Madras N, Mermut O. Theory and experiment of chain length effects on the adsorption of polyelectrolytes onto spherical particles: the long and the short of it. Phys Chem Chem Phys 2021; 23:300-310. [PMID: 33346762 DOI: 10.1039/d0cp04359a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study here the role of polyelectrolyte chain length, that is number of repeat units (mers), in the competitive adsorption of a simple model polyanion, poly(acrylic acid), onto 85 nm spherical silica particles capped with a model polycation, poly(allylamine hydrochloride). Performing fluorescence spectroscopy experiments, we measured chain-length dependence of dilute aqueous polyelectrolyte adsorption, at full surface coverage, onto an oppositely charged polyelectrolyte overtop spherical silica nanoparticles (10-3 g L-1). Preferential adsorption was determined by comparing the characteristic fluorescence intensities of the two fluorophore-labeled and narrowly disperse polyacrylic acid samples (NMA-PAA450k and Dan-PAA2k) of 450k- and 2k-molecular weight (6250- and 28-mers), respectively. To compare and validate experimental results, a lattice model was developed for computing the probabilities of the different arrangements of two polymer chain lengths of polyacrylic acid on the surface of the silica nanosphere. We then determined which numbers of long and short adsorbed chains corresponded to the most configurations in our model. Both spectroscopic experiment results and the combinatorial model demonstrated that there is an entropic preference for complete adsorption of the longer 450k polyacrylic acid chain vs. 2k. This study provides insights on entropy driven chain-length dependence of polyelectrolyte adsorption onto spherical nanoparticle surfaces for directing and optimizing their layer-by-layer self-assembly in organic films.
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Affiliation(s)
- Sperydon Koumarianos
- Department of Physics and Astronomy, York University, Toronto, ON M3J 1P3, Canada.
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6
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Marichal L, Degrouard J, Gatin A, Raffray N, Aude JC, Boulard Y, Combet S, Cousin F, Hourdez S, Mary J, Renault JP, Pin S. From Protein Corona to Colloidal Self-Assembly: The Importance of Protein Size in Protein-Nanoparticle Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8218-8230. [PMID: 32585107 DOI: 10.1021/acs.langmuir.0c01334] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein adsorption on nanoparticles is an important field of study, particularly with regard to nanomedicine and nanotoxicology. Many factors can influence the composition and structure of the layer(s) of adsorbed proteins, the so-called protein corona. However, the role of protein size has not been specifically investigated, although some evidence has indicated its potential important role in corona composition and structure. To assess the role of protein size, we studied the interactions of hemoproteins (spanning a large size range) with monodisperse silica nanoparticles. We combined various techniques-adsorption isotherms, isothermal titration calorimetry, circular dichroism, and transmission electron cryomicroscopy-to address this issue. Overall, the results show that small proteins behaved as typical model proteins, forming homogeneous monolayers on the nanoparticle surface (protein corona). Their adsorption is purely enthalpy-driven, with subtle structural changes. In contrast, large proteins interact with nanoparticles via entropy-driven mechanisms. Their structure is completely preserved during adsorption, and any given protein can directly bind to several nanoparticles, forming bridges in these newly formed protein-nanoparticle assemblies. Protein size is clearly an overlooked factor that should be integrated into proteomics and toxicological studies.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Anouchka Gatin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | - Nolwenn Raffray
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | | | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Sophie Combet
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Fabrice Cousin
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Jean Mary
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
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7
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Alamdari S, Pfaendtner J. Impact of Glutamate Carboxylation in the Adsorption of the α-1 Domain of Osteocalcin to Hydroxyapatite and Titania. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:620-631. [PMID: 33791109 PMCID: PMC8009198 DOI: 10.1039/c9me00158a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One proposed mechanism of implant fouling is attributed to the nonspecific adsorption of non-collagenous bone matrix proteins (NCPs) onto a newly implanted interface. With the goal of capturing the fundamental mechanistic and thermodynamic forces that govern changes in these NCP recognition domains as a function of γ-carboxyglutamic acid (Gla) post-translational modification and surface chemistry, we probe the adsorption process of the most commonly occurring NCP, osteocalcin, onto a mineral and metal oxide surface. Here, we apply two enhanced sampling methods to independently probe the effects of post-translational modification and peptide structure on adsorption. First, well-tempered metadynamics was used to capture the binding of acetyl and N-methylamide capped glutamic acid and Gla single amino acids onto crystalline hydroxyapatite and titania model surfaces at physiological pH. Following this, parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) was used to study adsorption of the α-1 domain of osteocalcin onto hydroxyapatite and titania. Simulations were performed for the α-1 domain of osteocalcin in both its fully decarboxylated (dOC) and fully carboxylated (OC) form. Our simulations find that increased charge density due to carboxylation results in increased interactions at the interface, and stronger adsorption of the single amino acids to both surfaces. Interestingly, the role of Gla in promoting compact and helical structure in the α-1 domain resulted in disparate binding modes at the two surfaces, which is attributed to differences in interfacial water behavior. Overall, this work provides a benchmark for understanding the mechanisms that drive adsorption of Gla-containing mineralizing proteins onto different surface chemistries.
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Affiliation(s)
- Sarah Alamdari
- Dept. of Chemical Engineering, University of Washington, Seattle 98195-1750
| | - Jim Pfaendtner
- Dept. of Chemical Engineering, University of Washington, Seattle 98195-1750
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8
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Akbarian M, Tayebi L, Mohammadi-Samani S, Farjadian F. Mechanistic Assessment of Functionalized Mesoporous Silica-Mediated Insulin Fibrillation. J Phys Chem B 2020; 124:1637-1652. [DOI: 10.1021/acs.jpcb.9b10980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mohsen Akbarian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 7193371, Iran
| | - Lobat Tayebi
- School of Dentistry, Marquette University, Milwaukee, Wisconsin 53233-2186, United States
| | - Soliman Mohammadi-Samani
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 7193371, Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz 7193371, Iran
| | - Fatemeh Farjadian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 7193371, Iran
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9
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Zheng C, Lin S, Hu C, Li Y, Li B, Yang Y. Chirality-driven molecular packing structure difference and potential application for 3D printing of a series of bola-type Ala–Phe dipeptides. NEW J CHEM 2020. [DOI: 10.1039/d0nj04745g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For bola-type dipeptides based on Ala–Phe building block, the chirality of Phe residue at C-terminal determined the handedness of self-assemblies and stacking chirality of carbonyl groups.
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Affiliation(s)
- Cheng Zheng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China, School of Optoelectronics Science and Engineering
- Suzhou
- China
| | - Chuanjiang Hu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
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10
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Grasso G, Mercuri S, Danani A, Deriu MA. Biofunctionalization of Silica Nanoparticles with Cell-Penetrating Peptides: Adsorption Mechanism and Binding Energy Estimation. J Phys Chem B 2019; 123:10622-10630. [DOI: 10.1021/acs.jpcb.9b08106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Stefano Mercuri
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Marco A. Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
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11
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Smith J, McMullen P, Yuan Z, Pfaendtner J, Jiang S. Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules 2019; 21:435-443. [DOI: 10.1021/acs.biomac.9b01191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Josh Smith
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Patrick McMullen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Zhefan Yuan
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
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12
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Sampath J, Pfaendtner J. Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1657192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Janani Sampath
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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13
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Dallin BC, Van Lehn RC. Spatially Heterogeneous Water Properties at Disordered Surfaces Decrease the Hydrophobicity of Nonpolar Self-Assembled Monolayers. J Phys Chem Lett 2019; 10:3991-3997. [PMID: 31265306 DOI: 10.1021/acs.jpclett.9b01707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the relationship between hydrophobicity and the properties of functionalized surfaces is vital to the design of materials that interact in aqueous environments. In this Letter, we use atomistic molecular dynamics simulations to investigate the effects of surface order on the hydrophobicity of self-assembled monolayers (SAMs) containing nonpolar ligands. We find that the interfacial hydrophobicity is highly correlated with SAM order and, strikingly, poorly correlated with the solvent-accessible surface area, which typically has been related to interfacial hydrophobicity. Analysis of spatial variations in both SAM and water properties reveals that the SAM-water interface is pinned near regions of disordered SAM surfaces with increased free volume, decreasing the overall interfacial hydrophobicity. Spatial variations in ligand end group positions at disordered SAM surfaces thus translate to spatial variations in hydrophobicity, yielding heterogeneous surface properties. These findings provide new insights into how surface order can alter the hydrophobicity of chemically uniform surfaces.
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Affiliation(s)
- Bradley C Dallin
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 , United States
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14
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Xue R, Wei S, Dong X, Zhu T, Yuan J, Feng L, Wang Q, Yang Y, Wang H. Enhanced room temperature phosphorescence of palladium‐porphyrin by dual‐ordered structure of micelle‐hybridized supramolecular gels. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ruru Xue
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Saisai Wei
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Xuelin Dong
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
- Key Laboratory of Rare Mineral Exploration and Utilization, Ministry of Land and Resources, Geological Experimental Testing Center of Hubei Province Wuhan 430034 China
| | - Tingyu Zhu
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Jianhui Yuan
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Lu Feng
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Qin Wang
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Yajiang Yang
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Hong Wang
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage of the Ministry of Education, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
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15
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First JT, Webb LJ. Agreement between Experimental and Simulated Circular Dichroic Spectra of a Positively Charged Peptide in Aqueous Solution and on Self-Assembled Monolayers. J Phys Chem B 2019; 123:4512-4526. [DOI: 10.1021/acs.jpcb.9b02102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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16
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Guo K, Zhang L, Lin S, Li Y, Li B, Yang Y. A “center-determination” phenomenon of C 13H 27CO-Gly-Ala-Ala lipotripetides: relationship between the molecular chirality and handedness of organic self-assemblies. NEW J CHEM 2019. [DOI: 10.1039/c9nj01693g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The chirality of the central alanine residue dominates the handedness of molecular packing and that of organic self-assemblies.
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Affiliation(s)
- Kexiao Guo
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Lianglin Zhang
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Shuwei Lin
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Yi Li
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Baozong Li
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Yonggang Yang
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
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17
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Lutz H, Jaeger V, Weidner T, de Groot BL. Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles. J Chem Theory Comput 2018; 15:698-707. [DOI: 10.1021/acs.jctc.8b00840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Helmut Lutz
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Vance Jaeger
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Tobias Weidner
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Bert L. de Groot
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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18
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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19
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Arsiccio A, McCarty J, Pisano R, Shea JE. Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism. J Phys Chem B 2018; 122:11390-11399. [DOI: 10.1021/acs.jpcb.8b07368] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Andrea Arsiccio
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - James McCarty
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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20
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Xu Z, Yang X, Wei Q, Zhao W, Cui B, Yang X, Sahai N. Quantitatively Identifying the Roles of Interfacial Water and Solid Surface in Governing Peptide Adsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7932-7941. [PMID: 29888924 DOI: 10.1021/acs.langmuir.8b01189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the molecular mechanism of protein adsorption on solids is critical to their applications in materials synthesis and tissue engineering. Although the water phase at the surface/water interface has been recognized as three types: bulk water, intermediate water phase and surface-bound water layers, the roles of the water and surface in determining the protein adsorption are not clearly identified, particularly at the quantitative level. Herein, we provide a methodology involving the combination of microsecond strengthen sampling simulation and force integration to quantitatively characterize the water-induced contribution and the peptide-surface interactions into the adsorption free energy. Using hydroxyapatite and graphene surfaces as examples, we demonstrate how the distinct interfacial features dominate the delicate force balance between these two thermodynamics parameters, leading to surface preference/resistance to peptide adsorption. Specifically, the water layer provides sustained repelling force against peptide adsorption, as indicated by a monotonic increase in the water-induced free energy profile, whereas the contribution from the surface-peptide interactions is thermodynamically favorable to peptide adsorptions. More importantly, the revealed adsorption mechanism is critically dictated by the distribution of water phase, which plays a crucial role in establishing the force balance between the interactions of the peptide with the water layer and the surface. For the HAP surface, the charged peptide exhibits strong binding affinity to the surface, due to the controlling contribution of peptide-surface interaction in the intermediate water phase. The surface-bound water layers are observed as the origin of bioresistance of solid surfaces toward the adsorption of charge-neutral peptides. The preferred peptide adsorption on the graphene, however, is dominated by the surface-induced component at the water layers adjacent to the surface. Our results further elucidate that the intermediate water phase significantly shortens the effective range of the surface dispersion force, in contrast to the observation on the hydrophilic surface.
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Affiliation(s)
| | | | | | - Weilong Zhao
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
| | | | | | - Nita Sahai
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
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21
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Marichal L, Renault JP, Chédin S, Lagniel G, Klein G, Aude JC, Tellier-Lebegue C, Armengaud J, Pin S, Labarre J, Boulard Y. Importance of Post-translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5312-5322. [PMID: 29648834 DOI: 10.1021/acs.langmuir.8b00752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest for both basic research and practical applications involving nanotechnology. From the list of cellular proteins with the highest affinity for silica nanoparticles, we highlighted the group of proteins containing arginine-glycine-glycine (RGG) motifs. Biochemical experiments confirmed that RGG motifs interact strongly with the silica surfaces. The affinity of these motifs is further increased when the R residue is asymmetrically, but not symmetrically, dimethylated. Molecular dynamics simulations show that the asymmetrical dimethylation generates an electrostatic asymmetry in the guanidinium group of the R residue, orientating and stabilizing it on the silica surface. The RGG motifs (methylated or not) systematically target the siloxide groups on the silica surface through an ionic interaction, immediately strengthened by hydrogen bonds with proximal silanol and siloxane groups. Given that, in vivo, RGG motifs are often asymmetrically dimethylated by specific cellular methylases, our data add support to the idea that this type of methylation is a key mechanism for cells to regulate the interaction of the RGG proteins with their cellular partners.
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Affiliation(s)
- Laurent Marichal
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
- LIONS, IRAMIS, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Jean-Philippe Renault
- LIONS, IRAMIS, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Stéphane Chédin
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Gilles Lagniel
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Géraldine Klein
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
- LIONS, IRAMIS, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Jean-Christophe Aude
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
- I2BC, CEA, CNRS, Université Paris-Saclay , Orsay , 91400 , France
| | | | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA , F-30207 Bagnols sur Cèze , France
| | - Serge Pin
- LIONS, IRAMIS, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Jean Labarre
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
| | - Yves Boulard
- I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay , Gif-sur-Yvette , 91191 , France
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22
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Mafi A, Abbina S, Kalathottukaren MT, Morrissey JH, Haynes C, Kizhakkedathu JN, Pfaendtner J, Chou KC. Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups. Biomacromolecules 2018. [PMID: 29539260 DOI: 10.1021/acs.biomac.8b00327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inorganic polyphosphate (polyP) released by human platelets has recently been shown to activate blood clotting and identified as a potential target for the development of novel antithrombotics. Recent studies have shown that polymers with cationic binding groups (CBGs) inhibit polyP and attenuate thrombosis. However, a good molecular-level understanding of the binding mechanism is lacking for further drug development. While molecular dynamics (MD) simulation can provide molecule-level information, the time scale required to simulate these large biomacromolecules makes classical MD simulation impractical. To overcome this challenge, we employed metadynamics simulations with both all-atom and coarse-grained force fields. The force field parameters for polyethylene glycol (PEG) conjugated CBGs and polyP were developed to carry out coarse-grained MD simulations, which enabled simulations of these large biomacromolecules in a reasonable time scale. We found that the length of the PEG tail does not impact the interaction between the (PEG) n-CBG and polyP. As expected, increasing the number of the charged tertiary amine groups in the head group strengthens its binding to polyP. Our simulation shows that (PEG) n-CBG initially form aggregates, mostly with the PEG in the core and the hydrophilic CBG groups pointing toward water; then the aggregates approach the polyP and sandwich the polyP to form a complex. We found that the binding of (PEG) n-CBG remains intact against various lengths of polyP. Binding thermodynamics for two of the (PEG) n-CBG/polyP systems simulated were measured by isothermal titration calorimetry to confirm the key finding of the simulations that the length PEG tail does not influence ligand binding to polyP.
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Affiliation(s)
- Amirhossein Mafi
- Department of Chemistry , University of British Columbia , Vancouver , BC V6T 1Z1 , Canada
| | | | | | - James H Morrissey
- Department of Biological Chemistry , University of Michigan Medical School , Ann Arbor , Michigan 48109 , United States
| | | | | | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Keng C Chou
- Department of Chemistry , University of British Columbia , Vancouver , BC V6T 1Z1 , Canada
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23
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Prakash A, Sprenger K, Pfaendtner J. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation. Biochem Biophys Res Commun 2018; 498:274-281. [DOI: 10.1016/j.bbrc.2017.07.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/09/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022]
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24
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Prakash A, Baer MD, Mundy CJ, Pfaendtner J. Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation. Biomacromolecules 2018; 19:1006-1015. [PMID: 29443506 DOI: 10.1021/acs.biomac.7b01813] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Peptoids are peptide-mimetic biopolymers that are easy to synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semiempirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids toward these conformations.
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Affiliation(s)
- Arushi Prakash
- Department of Chemical Engineering , University of Washington , Seattle , Washington , United States
| | - Marcel D Baer
- Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Christopher J Mundy
- Department of Chemical Engineering , University of Washington , Seattle , Washington , United States.,Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , Seattle , Washington , United States.,Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
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25
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Sprenger KG, Prakash A, Drobny G, Pfaendtner J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1199-1207. [PMID: 28981294 DOI: 10.1021/acs.langmuir.7b02868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
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26
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Walsh TR, Knecht MR. Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials. Chem Rev 2017; 117:12641-12704. [DOI: 10.1021/acs.chemrev.7b00139] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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27
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Krause KD, Roy S, Hore DK. Interplay between adsorbed peptide structure, trapped water, and surface hydrophobicity. Biointerphases 2017; 12:02D407. [PMID: 28506069 PMCID: PMC5432376 DOI: 10.1116/1.4983408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/05/2023] Open
Abstract
Atomistic molecular dynamics simulations were used to study the influence of interfacial water on the orientation and conformation of a facewise amphipathic α-helical peptide adsorbed to hydrophilic and hydrophobic substrates. Water behavior beneath the peptide adsorbed to a hydrophilic surface was observed to vary with the height of the peptide above the surface. In general, the orientation of water close to the peptide (with the oxygen atom pointing up toward the peptide) was complementary to that observed near the hydrophilic surface in the absence of peptide. That is, no change in orientation of water trapped between the peptide and a hydrophilic surface is required as the peptide approaches the surface. The adsorption of the peptide to the hydrophilic surface was observed to be mediated by a layer of ordered water. Water was found to be largely excluded on adsorption to the hydrophobic surface. However, the small amount of water present was observed to be highly ordered. At the closest point of contact to the hydrophobic surface, the peptide was observed to make direct contact. These findings shed light on the fundamental driving forces of peptide adsorption to hydrophobic and hydrophilic surfaces in aqueous environments.
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Affiliation(s)
- Katherine D Krause
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Sandra Roy
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Dennis K Hore
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
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28
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Chan AJ, Sarkar P, Gaboriaud F, Fontaine-Aupart MP, Marlière C. Control of interface interactions between natural rubber and solid surfaces through charge effects: an AFM study in force spectroscopic mode. RSC Adv 2017. [DOI: 10.1039/c7ra08589c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adhesion of nanoparticles (natural rubber) is monitored by slight changes in the surface charge state of the contacting solid surfaces.
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Affiliation(s)
- Alan Jenkin Chan
- Institut des Sciences Moléculaires d'Orsay, ISMO
- Université Paris-Sud
- CNRS
- 91405 Orsay Cedex
- France
| | | | - Fabien Gaboriaud
- Manufacture Française des Pneumatiques Michelin
- F-63040 Clermont Ferrand 9
- France
| | | | - Christian Marlière
- Institut des Sciences Moléculaires d'Orsay, ISMO
- Université Paris-Sud
- CNRS
- 91405 Orsay Cedex
- France
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29
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Lin S, Li Y, Li B, Yang Y. Molecular packing and the handedness of the self-assemblies of C17H35CO-Ala-Phe sodium salts. NEW J CHEM 2017. [DOI: 10.1039/c7nj02553j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular packing structure dominates the handedness of the self-assemblies of a series of lipodipeptide sodium salts.
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Affiliation(s)
- Shuwei Lin
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Yi Li
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Baozong Li
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Yonggang Yang
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
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