☆ 4.8 Review

Integrating Computation, Experiment, and Machine Learning in the Design of Peptide-Based Supramolecular Materials and Systems

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2023)

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Article Biochemistry & Molecular Biology

Self-Assembly of Unprotected Dipeptides into Hydrogels: Water-Channels Make the Difference

Ottavia Bellotto et al.

Summary: This study investigated the self-assembling behavior of distinct stereoisomers of Ile-Phe and Phe-Ile in PBS to form hydrogels, confirming peptide purity and identity through NMR, mass spectrometry, and crystalline XRD data. One stereoisomer was found to exhibit fast kinetics and the highest elastic modulus, making it the only gelator in the study to self-organize into stable hydrogels with distinctive features.

CHEMBIOCHEM (2022)

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Article Biochemistry & Molecular Biology

Controlling Doxorubicin Release from a Peptide Hydrogel through Fine of Fiber Interactions

Mohamed A. Elsawy et al.

Summary: Hydrogels are versatile materials that have emerged in the biomedical field and show great potential for tissue engineering, regenerative medicine, and controlled drug delivery. Self-assembling peptide-based hydrogels have recently gained attention as potential vehicles for drug delivery. This study investigates how drug-peptide interactions influence the release of doxorubicin (Dox) from hydrogels. The amount of drug retained in the hydrogels is found to be proportional to the charge carried by the peptide fibers, and the position and number of end-lysine play a key role in the retention of Dox. The concentration and surface area of the hydrogels also affect the amount of drug retained and released.

BIOMACROMOLECULES (2022)

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Article Chemistry, Physical

Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization

Alexander van Teijlingen et al.

Summary: This study develops a simulation method for biochemical systems that considers pH dependence and demonstrates its effectiveness through experimental validation.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2022)

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Article Chemistry, Multidisciplinary

Disinfector-Assisted Low Temperature Reduced Graphene Oxide-Protein Surgical Dressing for the Postoperative Photothermal Treatment of Melanoma

Yuanhao Wu et al.

Summary: A disinfectant-assisted low temperature method to reduce GO-protein materials and fabricate surgical dressings with tuneable photothermal efficiency and bioactive properties for the postoperative treatment of melanoma is reported. In vitro and in vivo validation revealed the capacity of the dressings to prevent tumor recurrence and promote healing after tumor resection.

ADVANCED FUNCTIONAL MATERIALS (2022)

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Review Chemistry, Multidisciplinary

Protein Design: From the Aspect of Water Solubility and Stability

Rui Qing et al.

Summary: Water solubility and structural stability are important aspects of protein design, relying on accurate placement of amino acids and molecular interactions. Designer proteins have applications in computational design models and biomedical and nanotechnological applications. Advances in protein science, computing power, algorithms, and characterization techniques provide tools for solubility design. This review summarizes progress in protein design for solubility and stability.

CHEMICAL REVIEWS (2022)

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Article Chemistry, Multidisciplinary

Connected Peptide Modules Enable Controlled Co-Existence of Self-Assembled Fibers Inside Liquid Condensates

Ankit Jain et al.

Summary: A new approach using a three-component assembly method was proposed to create fibrous domains inside globally disordered liquid condensates. By mixing specific peptides, fibrous assembly can be achieved inside liquid coacervates, providing new opportunities for designing ordered structures within biomolecular condensates.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Article Chemistry, Multidisciplinary

Machine learning overcomes human bias in the discovery of self-assembling peptides

Rohit Batra et al.

Summary: Peptide materials have a wide range of functions, but increasing the sequence length leads to a larger number of candidate sequences. Traditional design methods guided by human expertise and intuition are not easily scalable or free from bias. This article introduces a machine learning-based computational search engine that efficiently discovers peptide sequences with high self-assembly potential, overcoming human bias and accelerating peptide discovery.

NATURE CHEMISTRY (2022)

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Article Chemistry, Physical

Mechanistic insights of evaporation-induced actuation in supramolecular crystals

Roxana Piotrowska et al.

Summary: Experiments and simulations demonstrate that the actuation of nanoporous tripeptide crystals upon dehydration is driven by pore contraction due to strengthened water hydrogen bonding. This mechanism facilitates the efficient energy transfer during evaporation-induced actuation, suggesting a general approach for designing high-energy molecular actuators.

NATURE MATERIALS (2021)

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Article Chemistry, Multidisciplinary

Peptide-Metal Frameworks with Metal Strings Guided by Dispersion Interactions

Tobias Schnitzer et al.

Summary: Despite the challenges in forming networks from peptidic ligands, a peptide-metal framework consisting of helical oligoproline ligands and Zn/K (or Zn/Rb) has been successfully created in this study. The crystal network contains pleated nanosheets with metal ions aligned in strings, with the unique architecture derived from under-appreciated London dispersion interactions between the ligands. The secondary structure of the peptidic ligand plays an important role in the creation of new MOF architectures.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Nanoscale Assembly of Functional Peptides with Divergent Programming Elements

Ana M. Garcia et al.

Summary: Self-assembling peptides with proline as a beta-breaker and diphenylalanine motif were studied for their ability to form diverse nanostructures. The stereo-configuration of amino acids played a crucial role in directing these peptides to assemble into nanoparticles, nanotapes, or fibrils. Additionally, the study found that heterochirality could strategically interfere with pathological processes, potentially offering future therapeutic applications with resistance to degradation and biocompatibility.

ACS NANO (2021)

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Article Chemistry, Multidisciplinary

Expanding the Conformational Landscape of Minimalistic Tripeptides by Their O-Glycosylation

Alexandra Brito et al.

Summary: This study demonstrates that the substitution of serine with threonine affects the morphology of aggregates, while O-glycosylation decreases aggregation propensity by rebalancing pi interactions. The glycopeptides form aggregates with reduced stiffness but increased thermal stability, showing promising potential for elucidating molecular mechanisms and inspiring the design of functional glycopeptide-based biomaterials.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Active Controlled and Tunable Coacervation Using Side-Chain Functional α-Helical Homopolypeptides

Wendell A. Scott et al.

Summary: Developed new side-chain amino acid-functionalized alpha-helical homopolypeptides can reversibly form coacervate phases in aqueous media. Their multifunctional side-chains can actively control coacervation through mild, biomimetic redox chemistry and respond to changes in pH, temperature, and counterions, mimicking properties observed in natural coacervate forming intrinsically disordered proteins. Despite alpha-helical conformations that traditionally disfavor coacervation, molecular dynamics simulations suggest that high side-chain conformational disorder and hydration around the ordered backbone may explain the ability of these polypeptides to form coacervates.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Engineering, Biomedical

An interfacial self-assembling bioink for the manufacturing of capillary-like structures with tuneable and anisotropic permeability

Yuanhao Wu et al.

Summary: The study introduces a self-assembling bioink based on ELR and GO, with reproducibility and optimized printing parameters for fabricating novel structures with physiological relevance, as well as the capability to modulate pore size and permeability.

BIOFABRICATION (2021)

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Article Chemistry, Multidisciplinary

Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity

Ana S. Pina et al.

Summary: This study demonstrates phage-display screening on self-assembled ligands to identify oligopeptides that selectively bind dynamic supramolecular targets. The selected peptides show cationic and proline residues enrichment without sequence consensus, with the lead peptide interacting with the ligand exclusively in its self-assembled state. Additionally, the study shows phage dynamics and conformation-dependent activity on supramolecular ligand binding.

CHEMICAL SCIENCE (2021)

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Article Chemistry, Physical

Beyond Tripeptides Two-Step Active Machine Learning for Very Large Data sets

Alexander van Teijlingen et al.

Summary: A machine learning method has been developed to search for ideal candidates for self-assembling peptide nanostructures, leveraging two different resolution datasets for iterative learning. Controlling selected candidates through curation of a lower-resolution dataset is explored as a method to achieve the best results with minimal computational demand.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Review Chemistry, Multidisciplinary

Peptide-Based Supramolecular Systems Chemistry

Fahmeed Sheehan et al.

Summary: Peptide-based supramolecular systems chemistry aims to mimic the ability of life forms to achieve a wide range of functions using conserved building blocks and chemical reactions. This field is increasingly focused on system-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated.

CHEMICAL REVIEWS (2021)

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Article Chemistry, Multidisciplinary

Prediction and characterization of liquid-liquid phase separation of minimalistic peptides

Yiming Tang et al.

Summary: This study comprehensively explores the abilities of all 400 dipeptide combinations to undergo LLPS and validates the predictions, demonstrating that dipeptides possess multivalent interactions sufficient for LLPS. This paves the way for predicting and characterizing peptide phase behavior at the molecular level.

CELL REPORTS PHYSICAL SCIENCE (2021)

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Review Chemistry, Multidisciplinary

Peptide-based coacervates as biomimetic protocells

Manzar Abbas et al.

Summary: Coacervates are condensed liquid-like droplets formed by liquid-liquid phase separation of molecules through weak associative interactions. Peptides, with diverse amino acid residues, can tailor their phase separation propensity and selectivity in guest molecule uptake, making them attractive as building blocks for biomimetic protocells. This review summarizes recent developments in peptide-based coacervates and outlines the potential for active droplets in moving away from thermodynamic equilibrium.

CHEMICAL SOCIETY REVIEWS (2021)

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Article Chemistry, Multidisciplinary

Tuning the mechanistic pathways of peptide self-assembly by aromatic interactions

Goutam Ghosh et al.

Summary: The study highlights the significant influence of aromatic interactions on the mechanistic pathways of peptide self-assembly. Despite the peptides having similar morphologies, the minor structural difference leads to different packing modes and self-assembly mechanisms.

CHEMICAL COMMUNICATIONS (2021)

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Review Chemistry, Physical

Recent advances in short peptide self-assembly: from rational design to novel applications

Xuzhi Hu et al.

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2020)

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Article Materials Science, Multidisciplinary

Can machine learning find extraordinary materials?

Steven K. Kauwe et al.

COMPUTATIONAL MATERIALS SCIENCE (2020)

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Article Chemistry, Multidisciplinary

Supramolecular Polymers - we've Come Full Circle

Takuzo Aida et al.

ISRAEL JOURNAL OF CHEMISTRY (2020)

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Article Multidisciplinary Sciences

Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices

Yuanhao Wu et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Physical

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Kirill Shmilovich et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Review Chemistry, Multidisciplinary

Biomimetic peptide self-assembly for functional materials

Aviad Levin et al.

NATURE REVIEWS CHEMISTRY (2020)

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Review Polymer Science

Design of materials with supramolecular polymers

Tristan D. Clemons et al.

PROGRESS IN POLYMER SCIENCE (2020)

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Article Chemistry, Physical

Supramolecular hydrogels from unprotected dipeptides: a comparative study on stereoisomers and structural isomers

Ottavia Bellotto et al.

SOFT MATTER (2020)

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Review Chemistry, Physical

Water-responsive materials for sustainable energy applications

Yaewon Park et al.

JOURNAL OF MATERIALS CHEMISTRY A (2020)

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Review Chemistry, Multidisciplinary

Assemblies of Peptides in a Complex Environment and their Applications

Huaimin Wang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

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Rigid helical-like assemblies from a self-aggregating tripeptide

Santu Bera et al.

NATURE MATERIALS (2019)

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Design of self-assembly dipeptide hydrogels and machine learning via their chemical features

Fei Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Review Biochemical Research Methods

The de novo design of α-helical peptides for supramolecular self-assembly

Joseph L. Beesley et al.

CURRENT OPINION IN BIOTECHNOLOGY (2019)

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Article Nanoscience & Nanotechnology

Design and Characterization of Nucleopeptides for Hydrogel Self-Assembly

Kiheon Baek et al.

ACS APPLIED BIO MATERIALS (2019)

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Unbiased Discovery of Dynamic Peptide-ATP Complexes

Daniela Kroiss et al.

CHEMSYSTEMSCHEM (2019)

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Article Polymer Science

Supramolecular Tripeptide Hydrogel Assembly with 5-Fluorouracil

Evelina Parisi et al.

GELS (2019)

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Review Chemistry, Multidisciplinary

Guiding principles for peptide nanotechnology through directed discovery

A. Lampel et al.

CHEMICAL SOCIETY REVIEWS (2018)

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Multicomponent peptide assemblies

Danielle M. Raymond et al.

CHEMICAL SOCIETY REVIEWS (2018)

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Mordred: a molecular descriptor calculator

Hirotomo Moriwaki et al.

JOURNAL OF CHEMINFORMATICS (2018)

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Chirality Effects on Peptide Self-Assembly Unraveled from Molecules to Materials

Ana M. Garcia et al.

CHEM (2018)

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Reversible self-assembly of superstructured networks

Ronit Freeman et al.

SCIENCE (2018)

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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

Brian K. Radak et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

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Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics

Steven Boeynaems et al.

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Polymeric peptide pigments with sequence-encoded properties

Ayala Lampel et al.

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Sequence and entropy-based control of complex coacervates

Li-Wei Chang et al.

NATURE COMMUNICATIONS (2017)

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Supramolecular Assembly of Peptide Amphiphiles

Mark P. Hendricks et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

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Tripeptide Emulsifiers

Gary G. Scott et al.

ADVANCED MATERIALS (2016)

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Supramolecular Fibers in Gels Can Be at Thermodynamic Equilibrium: A Simple Packing Model Reveals Preferential Fibril Formation versus Crystallization

Ivan Ramos Sasselli et al.

ACS NANO (2016)

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Review Chemistry, Medicinal

The Unexpected Advantages of Using D-Amino Acids for Peptide Self-Assembly into Nanostructured Hydrogels for Medicine

Michele Melchionna et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2016)

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Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles

I. R. Sasselli et al.

SOFT MATTER (2016)

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Review Chemistry, Multidisciplinary

Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures

Tell Tuttle

ISRAEL JOURNAL OF CHEMISTRY (2015)

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PRISM-Based Theory of Complex Coacervation: Excluded Volume versus Chain Correlation

Sarah L. Perry et al.

MACROMOLECULES (2015)

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Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

Felipe Garcia Quiroz et al.

NATURE MATERIALS (2015)

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Exploring the sequence space for (tri-) peptide self-assembly to design and discover

Pim W. J. M. Frederix et al.

NATURE CHEMISTRY (2015)

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Design of nanostructures based on aromatic peptide amphiphiles

Scott Fleming et al.

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Assessing the Utility of Infrared Spectroscopy as a Structural Diagnostic Tool for β-Sheets in Self-Assembling Aromatic Peptide Amphiphiles

Scott Fleming et al.

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Thermodynamic Characterization of Polypeptide Complex Coacervation

Dimitrios Priftis et al.

LANGMUIR (2012)

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Unzipping the role of chirality in nanoscale self-assembly of tripeptide hydrogels

Silvia Marchesan et al.

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Functional Supramolecular Polymers

T. Aida et al.

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Phase behaviour and complex coacervation of aqueous polypeptide solutions

Dimitrios Priftis et al.

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Review Materials Science, Multidisciplinary

Peptide self-assembly for crafting functional biological materials

John B. Matson et al.

CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE (2011)

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PaDEL-Descriptor: An Open Source Software to Calculate Molecular Descriptors and Fingerprints

Chun Wei Yap

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

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Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

Pim W. J. M. Frederix et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)

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Tuning the Self-Assembly of the Bioactive Dipeptide L-Carnosine by Incorporation of a Bulky Aromatic Substituent

V. Castelletto et al.

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Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model

Shogo Koga et al.

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Biocatalytic self-assembly of 2D peptide-based nanostructures

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An investigation of the conductivity of peptide nanotube networks prepared by enzyme-triggered self-assembly

Haixia Xu et al.

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Relationship between molecular structure, gelation behaviour and gel properties of Fmoc-dipeptides

Dave J. Adams et al.

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Fmoc-Diphenylalanine Self-Assembly Mechanism Induces Apparent pKa Shifts

Claire Tang et al.

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Richard J. Williams et al.

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Fmoc-Diphenylalanine self assembles to a hydrogel via a novel architecture based on π-π interlocked β-sheets

Andrew M. Smith et al.

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Biomolecular engineering by combinatorial design and high-throughput screening: Small, soluble peptides that permeabilize membranes

Ramesh Rathinakumar et al.

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Self-assembly of large and small molecules into hierarchically ordered sacs and membranes

Ramille M. Capito et al.

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Siewert J. Marrink et al.

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OligoCalc: an online oligonucleotide properties calculator

Warren A. Kibbe

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Microporous organic materials from hydrophobic dipeptides

Carl Henrik Gorbitz

CHEMISTRY-A EUROPEAN JOURNAL (2007)

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Bioinspired design of nanocages by self-assembling triskelion peptide elements

Surajit Ghosh et al.

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Rigid, self-assembled hydrogel composed of a modified aromatic dipeptide

Assaf Mahler et al.

ADVANCED MATERIALS (2006)

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Nanostructured hydrogels for three-dimensional cell culture through self-assembly of fluorenylmethoxycarbonyl-dipeptides

V Jayawarna et al.

ADVANCED MATERIALS (2006)

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The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's beta-amyloid polypeptide

Carl Henrik Goerbitz

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Rapid combinatorial screening of peptide libraries for the selection of lanthanide-binding tags (LBTs)

LL Martin et al.

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Self-assembly of the ionic peptide EAK16: The effect of charge distributions on self-assembly

S Jun et al.

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Supramolecular hydrogels respond to ligand-receptor interaction

Y Zhang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

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Casting metal nanowires within discrete self-assembled peptide nanotubes

M Reches et al.

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A possible role for pi-stacking in the self-assembly of amyloid fibrils

E Gazit

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Self-assembly and mineralization of peptide-amphiphile nanofibers

JD Hartgerink et al.

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