1
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Luo X, Yu T, Li NK, Zuckermann RN, Jiang X, Balsara NP, Prendergast D. Thermodynamic Driving Forces for the Self-Assembly of Diblock Polypeptoids. ACS NANO 2024; 18:14917-14924. [PMID: 38811008 PMCID: PMC11171762 DOI: 10.1021/acsnano.3c12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Peptoid polymers with sequence-defined side chains are observed to self-assemble into a variety of structures spanning nanometer and micron scales. We explored a diblock copolypeptoid, poly(N-decylglycine)10-block-poly(N-2-(2-(2-methoxyethoxy)ethoxy)-ethylglycine)10 (abbreviated as Ndc10-Nte10), which forms crystalline nanofibers and nanosheets as evidenced by recent cryo-transmission electron microscopy, atomic force microscopy, X-ray diffraction, and calorimetry. Using all-atom molecular dynamics simulations, we examined the thermodynamic forces driving such self-assembly and how nanoscale morphology is tailored through modification of the N-terminus or via the addition of small molecules (urea). We have found that the hydrophobic Ndc domain alignment is key to the formation of molecular stacks whose growth is limited by electrostatic repulsion between protonated N-termini. These stacks are the building blocks that assemble via cooperative van der Waals attraction between the tips of extended decyl side chains to form nanofibers or nanosheets with a well-converged intermolecular interaction energy. Assemblies are significantly more stable in urea solution due to its strong attraction to the peptoid-solvent interface. Isolated peptoids exhibit curved all-cis backbones, which straighten within molecular stacks to maximize contact and registry between neighboring molecules. We hypothesize that competition between this attractive interaction and a strain cost for straightening the backbone is what leads to finite stack widths that define crystalline nanofibers of protonated Ndc10-Nte10. Growth is proposed to proceed through backbone unfurling via trans defects, which is more prevalent in aqueous solution than in THF, indicating a possible pathway to self-assembly under experimentally defined synthesis conditions (viz., THF evaporation).
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Affiliation(s)
- Xubo Luo
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Nan K. Li
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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2
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Grant MJ, Fingler BJ, Buchanan N, Padmanabhan P. Coil-Helix Block Copolymers Can Exhibit Divergent Thermodynamics in the Disordered Phase. J Chem Theory Comput 2024; 20:1547-1558. [PMID: 37773005 DOI: 10.1021/acs.jctc.3c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Chiral building blocks have the ability to self-assemble and transfer chirality to larger hierarchical length scales, which can be leveraged for the development of novel nanomaterials. Chiral block copolymers, where one block is made completely chiral, are prime candidates for studying this phenomenon, but fundamental questions regarding the self-assembly are still unanswered. For one, experimental studies using different chemistries have shown unexplained diverging shifts in the order-disorder transition temperature. In this study, particle-based molecular simulations of chiral block copolymers in the disordered melt were performed to uncover the thermodynamic behavior of these systems. A wide range of helical models were selected, and several free energy calculations were performed. Specifically, we aimed to understand (1) the thermodynamic impact of changing the conformation of one block in chemically identical block copolymers and (2) the effect of the conformation on the Flory-Huggins interaction parameter, χ, when chemical disparity was introduced. We found that the effective block repulsion exhibits diverging behavior, depending on the specific conformational details of the helical block. Commonly used conformational metrics for flexible or stiff block copolymers do not capture the effective block repulsion because helical blocks are semiflexible and aspherical. Instead, pitch can quantitatively capture the effective block repulsion. Quite remarkably, the shift in χ for chemically dissimilar block copolymers can switch sign with small changes in the pitch of the helix.
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Affiliation(s)
- Michael J Grant
- Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Brennan J Fingler
- Department of Chemical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Natalie Buchanan
- Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Poornima Padmanabhan
- Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Chemical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
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3
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Swanson HWA, van Teijlingen A, Lau KHA, Tuttle T. Martinoid: the peptoid martini force field. Phys Chem Chem Phys 2024; 26:4939-4953. [PMID: 38275003 DOI: 10.1039/d3cp05907c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of in silico screening methods, which often benefit from the use of coarse-grained molecular dynamics (CG-MD) simulations. At the current level of development, CG models for peptoids are insufficient and we have been motivated to develop a Martini forcefield compatible peptoid model. A dual bottom-up and top-down parameterisation approach has been adopted, in keeping with the Martini parameterisation methodology, targeting the reproduction of atomistic MD dynamics and trends in experimentally obtained log D7.4 partition coefficients, respectively. This work has yielded valuable insights into the practicalities of parameterising peptoid monomers. Additionally, we demonstrate that our model can reproduce the experimental observations of two very different peptoid assembly systems, namely peptoid nanosheets and minimal tripeptoid assembly. Further we can simulate the peptoid helix secondary structure relevant for antimicrobial sequences. To be of maximum usefulness to the peptoid research community, we have developed freely available code to generate all requisite simulation files for the application of this model with Gromacs MD software.
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Affiliation(s)
- Hamish W A Swanson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - Alexander van Teijlingen
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - King Hang Aaron Lau
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
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4
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Swanson HA, Lau KHA, Tuttle T. Minimal Peptoid Dynamics Inform Self-Assembly Propensity. J Phys Chem B 2023; 127:10601-10614. [PMID: 38038956 PMCID: PMC10726364 DOI: 10.1021/acs.jpcb.3c03725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Peptoids are structural isomers of natural peptides, with side chain attachment at the amide nitrogen, conferring this class of compounds with the ability to access both cis and trans ω torsions as well as an increased diversity of ψ/φ states with respect to peptides. Sampling within these dimensions is controlled through side chain selection, and an expansive set of viable peptoid residues exists. It has been shown recently that "minimal" di- and tripeptoids with aromatic side chains can self-assemble into highly ordered structures, with size and morphological definition varying as a function of sequence pattern (e.g., XFF and FXF, where X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine, are regularly used in the design of minimal peptide assemblers. In recognition of this, and to draw parallels between these compounds classes, we have developed a series of descriptors for intramolecular dynamics of aromatic side chains to discern whether these dynamics, in a preassembly condition, can be related to experimentally observed nanoscale assemblies. To do this, we have built on the atomistic peptoid force field reported by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of partial charges and the collation of Charmm General Force Field (CGenFF) parameters relevant to these systems. Our study finds that the intramolecular dynamics of side chains, for a given sequence, is dependent on the specific combination of backbone ω torsions and that homogeneity of sampling across these states correlates well with the experimentally observed ability to assemble into nanomorphologies with long-range order. Sequence patterning is also shown to affect sampling, in a manner consistent for both tripeptoids and tripeptides. Additionally, sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf in the cc state, and the nanotube forming dipeptide FF, highlight a structural motif which may be relevant to the emergence of extended linear assemblies. To assess these properties, a variety of computational approaches have been employed.
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Affiliation(s)
- Hamish
W. A. Swanson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - King Hang Aaron Lau
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
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5
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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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6
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Ge Y, Wang X, Zhu Q, Yang Y, Dong H, Ma J. Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids. J Chem Theory Comput 2023; 19:6718-6732. [PMID: 37725682 DOI: 10.1021/acs.jctc.3c00809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]- solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P-P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL-water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.
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Affiliation(s)
- Yang Ge
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xueping Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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7
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Harris BS, Bejagam KK, Baer MD. Development of a Systematic and Extensible Force Field for Peptoids (STEPs). J Phys Chem B 2023; 127:6573-6584. [PMID: 37462325 DOI: 10.1021/acs.jpcb.3c01424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.
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Affiliation(s)
- Bradley S Harris
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Karteek K Bejagam
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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8
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Kang L, Wang Q, Zhang L, Zou H, Gao J, Niu K, Jiang N. Recent Experimental Advances in Characterizing the Self-Assembly and Phase Behavior of Polypeptoids. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16114175. [PMID: 37297308 DOI: 10.3390/ma16114175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Polypeptoids are a family of synthetic peptidomimetic polymers featuring N-substituted polyglycine backbones with large chemical and structural diversity. Their synthetic accessibility, tunable property/functionality, and biological relevance make polypeptoids a promising platform for molecular biomimicry and various biotechnological applications. To gain insight into the relationship between the chemical structure, self-assembly behavior, and physicochemical properties of polypeptoids, many efforts have been made using thermal analysis, microscopy, scattering, and spectroscopic techniques. In this review, we summarize recent experimental investigations that have focused on the hierarchical self-assembly and phase behavior of polypeptoids in bulk, thin film, and solution states, highlighting the use of advanced characterization tools such as in situ microscopy and scattering techniques. These methods enable researchers to unravel multiscale structural features and assembly processes of polypeptoids over a wide range of length and time scales, thereby providing new insights into the structure-property relationship of these protein-mimetic materials.
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Affiliation(s)
- Liying Kang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Qi Wang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Lei Zhang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hang Zou
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jun Gao
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Kangmin Niu
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Naisheng Jiang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
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9
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Banerjee A, Dutt M. A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly. J Chem Phys 2023; 158:114105. [PMID: 36948821 DOI: 10.1063/5.0138510] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Protein mimics such as peptoids form self-assembled nanostructures whose shape and function are governed by the side chain chemistry and secondary structure. Experiments have shown that a peptoid sequence with a helical secondary structure assembles into microspheres that are stable under various conditions. The conformation and organization of the peptoids within the assemblies remains unknown and is elucidated in this study via a hybrid, bottom-up coarse-graining approach. The resultant coarse-grained (CG) model preserves the chemical and structural details that are critical for capturing the secondary structure of the peptoid. The CG model accurately captures the overall conformation and solvation of the peptoids in an aqueous solution. Furthermore, the model resolves the assembly of multiple peptoids into a hemispherical aggregate that is in qualitative agreement with the corresponding results from experiments. The mildly hydrophilic peptoid residues are placed along the curved interface of the aggregate. The composition of the residues on the exterior of the aggregate is determined by two conformations adopted by the peptoid chains. Hence, the CG model simultaneously captures sequence-specific features and the assembly of a large number of peptoids. This multiscale, multiresolution coarse-graining approach could help in predicting the organization and packing of other tunable oligomeric sequences of relevance to biomedicine and electronics.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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10
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Hwang IC, Rick SW. The pH Response of a Peptoid Oligomer. J Phys Chem B 2023; 127:2872-2878. [PMID: 36926948 DOI: 10.1021/acs.jpcb.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Polypeptoids are N-substituted glycine polymers, which differ from peptides in the placement of the side chain on the amide nitrogen rather than the Cα carbon. A peptoid with a chiral side chain containing both an aromatic group and carboxylic acid has a structure that responds to pH changes. All-atom molecular dynamics simulations using a force field specifically tuned for peptoids were carried out with an advanced sampling method for the peptoid (S)-N-(1-carboxy-2-phenylethyl)glycine in the high and low pH limits. The simulations show that the structure changes from mostly cis amide bonds at low pH to mostly trans bonds at high pH. The structural changes are driven by side chain-backbone hydrogen bonds at low pH and side chain repulsions and increased water contact at high pH.
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Affiliation(s)
- In Chul Hwang
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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11
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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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12
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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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13
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Dai Y, Xie Z, Liang L. Pore Formation Mechanism of A-Beta Peptide on the Fluid Membrane: A Combined Coarse-Grained and All-Atomic Model. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123924. [PMID: 35745043 PMCID: PMC9231318 DOI: 10.3390/molecules27123924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/05/2022] [Accepted: 06/13/2022] [Indexed: 11/27/2022]
Abstract
In Alzheimer’s disease, ion permeability through the ionic channel formed by Aβ peptides on cellular membranes appears to underlie neuronal cell death. An understanding of the formation mechanism of the toxic ionic channel by Aβ peptides is very important, but remains unclear. Our simulation results demonstrated the dynamics and mechanism of channel formation by Aβ1-28 peptides on the DPPC and POPC membrane by the coarse-grained method. The ionic channel formation is driven by the gyration of the radius and solvent accessible molecular surface area of Aβ1-28 peptides. The ionic channel formation mechanism was explored by the free energy profile based on the distribution of the gyration of the radius and solvent accessible molecular surface area of Aβ1-28 peptides on the fluid membrane. The stability and water permeability of the ionic channel formed by Aβ peptides was investigated by all-atomic model simulation. Our simulation showed that the ionic channel formed by Aβ1-28 peptides is very stable and has a good water permeability. This could help us to understand the pore formation mechanism by Aβ1-28 peptides on the fluidic membrane. It also provides us with a guideline by which to understand the toxicity of Aβ1-28 peptides’ pores to the cell.
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Affiliation(s)
- Yuxi Dai
- College of Automation, Hangzhou Dianzi University, Hangzhou 310018, China;
| | - Zhexing Xie
- College of Accounting, Hangzhou Dianzi University, Hangzhou 310018, China;
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou 310018, China;
- Correspondence:
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14
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Raubenolt BA, Rick SW. Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing. J Comput Chem 2022; 43:1229-1236. [PMID: 35543334 DOI: 10.1002/jcc.26887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/15/2022] [Accepted: 04/22/2022] [Indexed: 11/06/2022]
Abstract
Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. The results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.
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Affiliation(s)
- Bryan A Raubenolt
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
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15
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Gupta A, Verma S, Javed R, Sudhakar S, Srivastava S, Nair NN. Exploration of high dimensional free energy landscapes by a combination of temperature-accelerated sliced sampling and parallel biasing. J Comput Chem 2022; 43:1186-1200. [PMID: 35510789 DOI: 10.1002/jcc.26882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022]
Abstract
Temperature-accelerated sliced sampling (TASS) is an enhanced sampling method for achieving accelerated and controlled exploration of high-dimensional free energy landscapes in molecular dynamics simulations. With the aid of umbrella bias potentials, the TASS method realizes a controlled exploration and divide-and-conquer strategy for computing high-dimensional free energy surfaces. In TASS, diffusion of the system in the collective variable (CV) space is enhanced with the help of metadynamics bias and elevated-temperature of the auxiliary degrees of freedom (DOF) that are coupled to the CVs. Usually, a low-dimensional metadynamics bias is applied in TASS. In order to further improve the performance of TASS, we propose here to use a highdimensional metadynamics bias, in the same form as in a parallel bias metadynamics scheme. Here, a modified reweighting scheme, in combination with artificial neural network is used for computing unbiased probability distribution of CVs and projections of high-dimensional free energy surfaces. We first validate the accuracy and efficiency of our method in computing the four-dimensional free energy landscape for alanine tripeptide in vacuo. Subsequently, we employ the approach to calculate the eight-dimensional free energy landscape of alanine pentapeptide in vacuo. Finally, the method is applied to a more realistic problem wherein we compute the broad four-dimensional free energy surface corresponding to the deacylation of a drug molecule which is covalently complexed with a β-lactamase enzyme. We demonstrate that using parallel bias in TASS improves the efficiency of exploration of high-dimensional free energy landscapes.
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Affiliation(s)
- Abhinav Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shivani Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ramsha Javed
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Suraj Sudhakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Saurabh Srivastava
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India.,Department of Chemistry, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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16
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Zhao M, Lachowski KJ, Zhang S, Alamdari S, Sampath J, Mu P, Mundy CJ, Pfaendtner J, De Yoreo JJ, Chen CL, Pozzo LD, Ferguson AL. Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets. Biomacromolecules 2022; 23:992-1008. [PMID: 35020390 DOI: 10.1021/acs.biomac.1c01385] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Peptoids (N-substituted glycines) are a class of tailorable synthetic peptidomic polymers. Amphiphilic diblock peptoids have been engineered to assemble 2D crystalline lattices with applications in catalysis and molecular separations. Assembly is induced in an organic solvent/water mixture by evaporating the organic phase, but the assembly pathways remain uncharacterized. We conduct all-atom molecular dynamics simulations of Nbrpe6Nc6 as a prototypical amphiphilic diblock peptoid comprising an NH2-capped block of six hydrophobic N-((4-bromophenyl)ethyl)glycine residues conjugated to a polar NH3(CH2)5CO tail. We identify a thermodynamically controlled assembly mechanism by which monomers assemble into disordered aggregates that self-order into 1D chiral helical rods then 2D achiral crystalline sheets. We support our computational predictions with experimental observations of 1D rods using small-angle X-ray scattering, circular dichroism, and atomic force microscopy and 2D crystalline sheets using X-ray diffraction and atomic force microscopy. This work establishes a new understanding of hierarchical peptoid assembly and principles for the design of peptoid-based nanomaterials.
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Affiliation(s)
- Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Kacper J Lachowski
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Shuai Zhang
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Janani Sampath
- Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States.,Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, New York 13902, United States
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - James J De Yoreo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Lilo D Pozzo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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17
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Banerjee A, Lu CY, Dutt M. A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. Phys Chem Chem Phys 2021; 24:1553-1568. [PMID: 34940778 DOI: 10.1039/d1cp04205j] [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]
Abstract
Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices. This study investigates the relative organization of one such peptide sequence V6K2 (V: valine and K: lysine) within assemblies. Given the expansive spatiotemporal scales associated with this study, a hybrid coarse-grained (CG) model which captures the structure, conformation and aggregation of the peptide is adopted. The CG model uses a combination of iterative Boltzmann inversion and force matching to provide insight into the relative organization of V6K2 in assemblies. The CG model reproduces the structure of a V6K2 peptide sequence along with its all atom (AA) solvation structure. The relative organization of multiple peptides in an assembly, as captured by CG simulations, is in agreement with corresponding results from AA simulations. Also, a backmapping procedure reintroduces the AA details of the peptides within the aggregates captured by the CG model to demonstrate the relative organization of the peptides. Furthermore, a large number of peptides self-assemble into an elongated micelle in the CG simulation, which is consistent with experimental findings. The coarse-graining procedure is tested for transferability to longer peptide sequences, and hence can be extended to other amphiphilic peptide sequences.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Chien Yu Lu
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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18
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Zhao X, He F, Yu G, Feng Y, Li J. High-viscosity Pickering emulsion stabilized by amphiphilic alginate/SiO 2 via multiscale methodology for crude oil-spill remediation. Carbohydr Polym 2021; 273:118492. [PMID: 34560936 DOI: 10.1016/j.carbpol.2021.118492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/04/2021] [Accepted: 07/25/2021] [Indexed: 01/21/2023]
Abstract
The separation of crude oil from oily water and collection of the emulsion constituents has attracted significant attention. We demonstrate that the relationships between inherent dynamic factors and the performance of a Pickering emulsion stabilized by SiO2 particles with adsorbed hydrophobically modified sodium alginate derivatives (HMSA), a natural pH-sensitive polysaccharide, can be clarified via a multi-scale methodology. Functionalization of the silica surface with HMSA controls particle dispersibility, as verified by turbidity and stability analyses, the zeta potential, and transmission electron microscopy measurements. The interaction mechanism between HMSA and SiO2 nanoparticles was elucidated by both experimental adsorption measurements and computer simulations, which showed qualitative consistency. The aggregation/disaggregation of HMSA/SiO2 particles achieved by tuning the pH of the solution facilitated reversible dispersibility/collectability behavior. Overall, a high-viscosity Pickering emulsion system based on particle-particle and droplet-droplet interactions, which can be filtered for the recovery of spilled crude oil, was demonstrated.
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Affiliation(s)
- Xinyu Zhao
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, School of Chemical Engineering and Technology, Hainan University, 58 Renmin Road, Haikou, Hainan 570228, China
| | - Furui He
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, School of Chemical Engineering and Technology, Hainan University, 58 Renmin Road, Haikou, Hainan 570228, China
| | - Gaobo Yu
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, School of Chemical Engineering and Technology, Hainan University, 58 Renmin Road, Haikou, Hainan 570228, China.
| | - Yuhong Feng
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, School of Chemical Engineering and Technology, Hainan University, 58 Renmin Road, Haikou, Hainan 570228, China.
| | - Jiacheng Li
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, School of Chemical Engineering and Technology, Hainan University, 58 Renmin Road, Haikou, Hainan 570228, China.
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19
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Herlan CN, Feser D, Schepers U, Bräse S. Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond. Chem Commun (Camb) 2021; 57:11131-11152. [PMID: 34611672 DOI: 10.1039/d1cc04237h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dominik Feser
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
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20
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DeStefano A, Segalman RA, Davidson EC. Where Biology and Traditional Polymers Meet: The Potential of Associating Sequence-Defined Polymers for Materials Science. JACS AU 2021; 1:1556-1571. [PMID: 34723259 PMCID: PMC8549048 DOI: 10.1021/jacsau.1c00297] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/08/2023]
Abstract
Polymers with precisely defined monomeric sequences present an exquisite tool for controlling material properties by harnessing both the robustness of synthetic polymers and the ability to tailor the inter- and intramolecular interactions so crucial to many biological materials. While polymer scientists traditionally synthesized and studied the physics of long molecules best described by their statistical nature, many biological polymers derive their highly tailored functions from precisely controlled sequences. Therefore, significant effort has been applied toward developing new methods of synthesizing, characterizing, and understanding the physics of non-natural sequence-defined polymers. This perspective considers the synergistic advantages that can be achieved via tailoring both precise sequence control and attributes of traditional polymers in a single system. Here, we focus on the potential of sequence-defined polymers in highly associating systems, with a focus on the unique properties, such as enhanced proton conductivity, that can be attained by incorporating sequence. In particular, we examine these materials as key model systems for studying previously unresolvable questions in polymer physics including the role of chain shape near interfaces and how to tailor compatibilization between dissimilar polymer blocks. Finally, we discuss the critical challenges-in particular, truly scalable synthetic approaches, characterization and modeling tools, and robust control and understanding of assembly pathways-that must be overcome for sequence-defined polymers to attain their potential and achieve ubiquity.
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Affiliation(s)
- Audra
J. DeStefano
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
| | - Emily C. Davidson
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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21
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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22
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Zhao M. Hierarchical assemblies of polypeptoids for rational design of advanced functional nanomaterials. Biopolymers 2021; 112:e23469. [PMID: 34406644 DOI: 10.1002/bip.23469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Polypeptoids (poly-N-substituent glycines) are a class of highly tailorable peptidomimetic polymers. Polypeptoids have identical backbones as polypeptides (poly-C-substituent glycines), but sidechains of polypeptoids are appended to backbone nitrogen rather than α-carbon of polypeptides. As a result, peptoid backbone lacks of chirality and hydrogen bond donors. This unique structure gives polypeptoids a combined merit of both high stability as synthetic polymers and biocompatibility as biopolymers. In addition, peptoid sequences can be engineered precisely to assemble specific crystalline patterns such as spheres, fibers, ribbons, tubes, and sheets, which shows promising potentials of polypeptoids for different applications such as antimicrobials, catalysts, drug delivery, and templating inorganic materials. In this review, we summarize recent investigations into hierarchical self-assembly pathways and molecular structures of peptoid crystals that are of interest as templates for fabricating functional materials for potential biomedical, biochemical, and bioengineering applications. This review provides a summary of recent experimental and computational studies of polypeptoid assembly in solution and solid-liquid interfaces, current achievements in the field, and discusses future challenges and opportunities for the rational design of self-assembled polypeptoid nanomaterials.
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Affiliation(s)
- Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
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23
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Ma Z, Wang S, Kim M, Liu K, Chen CL, Pan W. Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics. SOFT MATTER 2021; 17:5864-5877. [PMID: 34096961 DOI: 10.1039/d1sm00364j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers.
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Affiliation(s)
- Zhan Ma
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Shu Wang
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Minhee Kim
- Department of Industrial and Systems Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kaibo Liu
- Department of Industrial and Systems Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wenxiao Pan
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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24
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Jiao S, DeStefano A, Monroe JI, Barry M, Sherck N, Casey T, Segalman RA, Han S, Shell MS. Quantifying Polypeptoid Conformational Landscapes through Integrated Experiment and Simulation. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Jacob I. Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Thomas Casey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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25
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Alessandri R, Grünewald F, Marrink SJ. The Martini Model in Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2008635. [PMID: 33956373 DOI: 10.1002/adma.202008635] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.
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Affiliation(s)
- Riccardo Alessandri
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
| | - Fabian Grünewald
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
| | - Siewert J Marrink
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
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26
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Abstract
Four decades of molecular theory and computation have helped form the modern understanding of the physical chemistry of organic semiconductors. Whereas these efforts have historically centered around characterizations of electronic structure at the single-molecule or dimer scale, emerging trends in noncrystalline molecular and polymeric semiconductors are motivating the need for modeling techniques capable of morphological and electronic structure predictions at the mesoscale. Provided the challenges associated with these prediction tasks, the community has begun to evolve a computational toolkit for organic semiconductors incorporating techniques from the fields of soft matter, coarse-graining, and machine learning. Here, we highlight recent advances in coarse-grained methodologies aimed at the multiscale characterization of noncrystalline organic semiconductors. As organic semiconductor performance is dependent on the interplay of mesoscale morphology and molecular electronic structure, specific emphasis is placed on coarse-grained modeling approaches capable of both structural and electronic predictions without recourse to all-atom representations.
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Affiliation(s)
- Nicholas E Jackson
- Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, United States
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