1
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Qi X, Pfaendtner J. High-Throughput Computational Screening of Solid-Binding Peptides. J Chem Theory Comput 2024; 20:2959-2968. [PMID: 38499981 DOI: 10.1021/acs.jctc.3c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Inspired by biomineralization, a naturally occurring, protein-facilitated process, solid-binding peptides (SBPs) have gained much attention for their potential to fabricate various shaped nanocrystals and hierarchical nanostructures. The advantage of SBPs over other traditionally used synthetic polymers or short ligands is their tunable interaction with the solid material surface via carefully programmed sequence and being solution-dependent simultaneously. However, designing a sequence with targeted binding affinity or selectivity often involves intensive processes such as phage display, and only a limited number of sequences can be identified. Other computational efforts have also been introduced, but the validation process remains prohibitively expensive once a suitable sequence has been identified. In this paper, we present a new model to rapidly estimate the binding free energy of any given sequence to a solid surface. We show how the overall binding of a polypeptide can be estimated from the free energy contribution of each residue based on the statistics of the thermodynamically stable structure ensemble. We validated our model using five silica-binding peptides of different binding affinities and lengths and showed that the model is accurate and robust across a wider range of chemistries and binding strengths. The computational cost of this method can be as low as 3% of the commonly used enhanced sampling scheme for similar studies and has a great potential to be used in high-throughput algorithms to obtain larger training data sets for machine learning SBP screening.
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Affiliation(s)
- Xin Qi
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03784, United States
| | - Jim Pfaendtner
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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2
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Le TTB, Finney AR, Zen A, Bui T, Tay WJ, Chellappah K, Salvalaglio M, Michaelides A, Striolo A. Mesoscale Simulations Reveal How Salt Influences Clay Particles Agglomeration in Aqueous Dispersions. J Chem Theory Comput 2024; 20:1612-1624. [PMID: 37916678 PMCID: PMC10902848 DOI: 10.1021/acs.jctc.3c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
The aggregation of clay particles is an everyday phenomenon of scientific and industrial relevance. However, it is a complex multiscale process that depends delicately on the nature of the particle-particle and particle-solvent interactions. Toward understanding how to control such phenomena, a multiscale computational approach is developed, building from molecular simulations conducted at atomic resolution to calculate the potential of mean force (PMF) profiles in both pure and saline water environments. We document how it is possible to use such a model to develop a fundamental understanding concerning the mechanism of particle aggregation. For example, using molecular dynamics simulations conducted at the mesoscale in implicit solvents, it is possible to quantify the size and shape of clay aggregates as a function of system conditions. The approach is used to emphasize the role of salt concentration, which directly affects the potentials of the mean forces between kaolinite particles. While particle agglomeration in pure water yields large aggregates, the presence of sodium chloride in the aqueous brine leads instead to a large number of small aggregates. These results are consistent with macroscopic experimental observations, suggesting that the simulation protocol developed could be relevant for preventing pore blocking in heterogeneous porous matrixes.
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Affiliation(s)
- Tran Thi Bao Le
- Department of Chemical Engineering, University College London, WC1E 7JE, London, United Kingdom
| | - Aaron R Finney
- Department of Chemical Engineering, University College London, WC1E 7JE, London, United Kingdom
| | - Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Tai Bui
- BP Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, United Kingdom
| | - Weparn J Tay
- BP Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, United Kingdom
| | - Kuhan Chellappah
- BP Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, United Kingdom
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, WC1E 7JE, London, United Kingdom
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Alberto Striolo
- Department of Chemical Engineering, University College London, WC1E 7JE, London, United Kingdom
- School of Sustainable Chemical, Biological and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
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3
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Cai Y, Qi X, Boese J, Zhao Y, Hellner B, Chun J, Mundy CJ, Baneyx F. Towards predictive control of reversible nanoparticle assembly with solid-binding proteins. SOFT MATTER 2024; 20:1935-1942. [PMID: 38323470 DOI: 10.1039/d4sm00094c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Although a broad range of ligand-functionalized nanoparticles and physico-chemical triggers have been exploited to create stimuli-responsive colloidal systems, little attention has been paid to the reversible assembly of unmodified nanoparticles with non-covalently bound proteins. Previously, we reported that a derivative of green fluorescent protein engineered with oppositely located silica-binding peptides mediates the repeated assembly and disassembly of 10-nm silica nanoparticles when pH is toggled between 7.5 and 8.5. We captured the subtle interplay between interparticle electrostatic repulsion and their protein-mediated short-range attraction with a multiscale model energetically benchmarked to collective system behavior captured by scattering experiments. Here, we show that both solution conditions (pH and ionic strength) and protein engineering (sequence and position of engineered silica-binding peptides) provide pathways for reversible control over growth and fragmentation, leading to clusters ranging in size from 25 nm protein-coated particles to micrometer-size aggregate. We further find that the higher electrolyte environment associated with successive cycles of base addition eventually eliminates reversibility. Our model accurately predicts these multiple length scales phenomena. The underpinning concepts provide design principles for the dynamic control of other protein- and particle-based nanocomposites.
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Affiliation(s)
- Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Julia Boese
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Yundi Zhao
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Brittney Hellner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
- Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York, New York 10031, USA
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
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4
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Li C, Liu L, Zhang Z, Zhang D, Yi S, Yang H, Fan Z. Anisotropy in Near-Spherical Colloidal Nanoparticles. ACS NANO 2023; 17:17873-17883. [PMID: 37682625 DOI: 10.1021/acsnano.3c03466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Two major aspects of functional colloidal nanoparticles are their colloidal stability (dispersion) and controlled assembly of nanoparticles into ordered structures. Simplifying colloidal nanoparticles as isotropically interacting spheres is unsuitable for small nanoparticles capped with hydrocarbon chain ligands in which the ligand-ligand interaction plays a prominent role in the assembly processes. However, experimentally characterizing the ligand shell structure in solution presents significant challenges, and computer simulations yield divergent results without effective validation. Moreover, the connection between detailed information regarding ligand shell structures and interparticle interactions, in relation to the diverse dynamical behaviors of colloidal nanoparticles, remains poorly understood. In this study, we reveal the relationship between the ligand shell structures, interparticle interactions, and dynamical behaviors of few-nm-sized near-spherical nanoparticles capped with hydrocarbon chain ligands immersed in nonpolar solvents. Our study shows a transformation of the interparticle interactions from anisotropic attractions to isotropic repulsions as a result of the change in the ligand shell structures from order to disorder caused by varying temperature and other factors. The interplay between anisotropic attractions from ligand bundles and isotropic repulsions from disordered ligands dictates the nanoparticle dynamical behaviors of dispersion, uncontrolled aggregation, and controlled assembly.
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Affiliation(s)
- Chuncheng Li
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Lei Liu
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Ziyan Zhang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Dan Zhang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- Department of Chemistry, Shanghai University, Shanghai 200444, P. R. China
| | - Shangzhao Yi
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Hongchao Yang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Zhaochuan Fan
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
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5
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Yang W, Zhou Y, Jin B, Qi X, Cai B, Yin Q, Pfaendtner J, De Yoreo JJ, Chen CL. Designing sequence-defined peptoids for fibrillar self-assembly and silicification. J Colloid Interface Sci 2023; 634:450-459. [PMID: 36542974 DOI: 10.1016/j.jcis.2022.11.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/10/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
In the biological environment, mineral crystals exquisitely controlled by biomacromolecules often show intricate hierarchical structures and superior mechanical properties. Among these biominerals, spicules, hybrid silica/protein superstructures serving as skeletal elements in demosponges, represent an excellent example for motivating the synthesis of silica materials. Herein, by designing sequence-defined peptoids containing side chains with a strong binding to silica, we demonstrated that self-assembly of these peptoids into fiber structures enables the mimicking of both biocatalytic and templating functions of silicatein filaments for the formation of silica fibers at near-neutral pH and ambient temperature. We further showed that the presence of amino groups is significant for the nucleation of silica on self-assembled peptoid nanofibers. Molecular dynamics simulation further confirmed that having silica-binding of amino side chains is critical for self-assembled peptoid fibers in triggering silica formation. We demonstrated that tuning inter-peptoid interactions by varying carboxyl and amino side chains significantly influences the assembly kinetics and final morphologies of peptoid assemblies as scaffolds for directing silica mineralization to form silica spheres, fibers, and sheets. The formation of silica shell on peptoid fibers increased the mechanical property of peptoid hydrogel materials by nearly 1000-fold, highlighting the great potential of using silicification to enhance the mechanical property of hydrogel materials for applications including tissue engineering. Since peptoids are highly robust and programmable, we expect that self-assembly of peptoids containing solid-binding side chains into hierarchical materials opens new opportunities in the design and synthesis of highly tunable scaffolds that direct the formation of composite nanomaterials.
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Affiliation(s)
- Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States; School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Biao Jin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States
| | - Bin Cai
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States; School of Chemistry and Chemical Engineering, Shandong University, Shandong 250100, China
| | - Qiuxiang Yin
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China; The Co-Innovation Center of Chemistry and Chemical Engineering of Tianjin, Tianjin University, Tianjin 300072, China
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States; Materials Science and Engineering, University of Washington, Seattle, WA 98105, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States.
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6
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Ma J, Jin B, Guye KN, Chowdhury ME, Naser NY, Chen CL, De Yoreo JJ, Baneyx F. Controlling Mineralization with Protein-Functionalized Peptoid Nanotubes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207543. [PMID: 36281797 DOI: 10.1002/adma.202207543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Sequence-defined foldamers that self-assemble into well-defined architectures are promising scaffolds to template inorganic mineralization. However, it has been challenging to achieve robust control of nucleation and growth without sequence redesign or extensive experimentation. Here, peptoid nanotubes functionalized with a panel of solid-binding proteins are used to mineralize homogeneously distributed and monodisperse anatase nanocrystals from the water-soluble TiBALDH precursor. Crystallite size is systematically tuned between 1.4 and 4.4 nm by changing protein coverage and the identity and valency of the genetically engineered solid-binding segments. The approach is extended to the synthesis of gold nanoparticles and, using a protein encoding both material-binding specificities, to the fabrication of titania/gold nanocomposites capable of photocatalysis under visible-light illumination. Beyond uncovering critical roles for hierarchical organization and denticity on solid-binding protein mineralization outcomes, the strategy described herein should prove valuable for the fabrication of hierarchical hybrid materials incorporating a broad range of inorganic components.
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Affiliation(s)
- Jinrong Ma
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
| | - Biao Jin
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kathryn N Guye
- Department of Chemistry, University of Washington, Seattle, WA, 98115, USA
| | - Md Emtias Chowdhury
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - Chun-Long Chen
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - James J De Yoreo
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98115, USA
| | - François Baneyx
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
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7
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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: 17] [Impact Index Per Article: 8.5] [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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8
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Ruffino R, Tuccitto N, Sfuncia G, Nicotra G, Li-Destri G, Marletta G. Direct Measurement of Surfactant-Mediated Picoforces among Nanoparticles in a Quasi-Two-Dimensional Environment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12281-12291. [PMID: 36172718 PMCID: PMC9558483 DOI: 10.1021/acs.langmuir.2c01928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The lack of methodologies which enable us to measure forces acting between nanomaterials is one of the factors limiting the full comprehension of their behavior and their more effective exploitation in new devices. Here we exploit the irreversible adsorption of surfactant-decorated nanoparticles at the air/water interface to investigate interparticle forces and the effect of the surfactant structure on them. We measured the interparticle repulsive forces as a function of the modulation of the interparticle distance by simultaneously performing compression isotherms and the grazing incidence small-angle X-ray scattering (GISAXS) structural characterization of the monolayers at water-vapor interfaces. Our results demonstrate that the short-range interparticle forces are strongly affected by the presence of the organic ligands, which are shown to be able to influence the interparticle repulsions even when added in micromolar amounts. In particular, we demonstrate the predominant steric nature of short-range forces, which are accounted for in terms of the compression-induced stretched-to-coiled conformational transition of the ligand hydrophobic tail.
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Affiliation(s)
- Roberta Ruffino
- Laboratory
for Molecular Surfaces and Nanotechnology (LAMSUN) and CSGI, Department
of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Nunzio Tuccitto
- Laboratory
for Molecular Surfaces and Nanotechnology (LAMSUN) and CSGI, Department
of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Gianfranco Sfuncia
- Consiglio
Nazionale delle Ricerche, Istituto per la Microelettronica e Microsistemi, 95121 Catania I, Italy
| | - Giuseppe Nicotra
- Consiglio
Nazionale delle Ricerche, Istituto per la Microelettronica e Microsistemi, 95121 Catania I, Italy
| | - Giovanni Li-Destri
- Laboratory
for Molecular Surfaces and Nanotechnology (LAMSUN) and CSGI, Department
of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Giovanni Marletta
- Laboratory
for Molecular Surfaces and Nanotechnology (LAMSUN) and CSGI, Department
of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy
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