Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study DOI Creative Commons

Rubén D. Parra

Molecules, Journal Year: 2023, Volume and Issue: 28(17), P. 6217 - 6217

Published: Aug. 24, 2023

DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting two N-α amido glycylglycine head groups linked by either one CH2 group or seven groups, is used as a building block for nanotube self-assembly. In addition hydrogen bonds between adjacent carboxy amide formation also driven weak C-H· · ·O methylene the OH group, an O=C group. The intratubular O-H· ·O=C account approximately third energies. Binding calculated with wB97XD/DGDZVP method show that hydrocarbon chains play stabilizing role in shortest has length single monomer diameter than increases number monomers. Lengthening tubular structure occurs through intertubular bonds. average bond energy estimated change size nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according method.

Language: Английский

Aromatic short peptide architectonics: Assembly and engineering DOI
Kai Tao, Haoran Wu, Lihi Adler‐Abramovich

et al.

Progress in Materials Science, Journal Year: 2024, Volume and Issue: 142, P. 101240 - 101240

Published: Jan. 7, 2024

Language: Английский

Citations

13
Deep Learning Empowers the Discovery of Self‐Assembling Peptides with Over 10 Trillion Sequences DOI Creative Commons
Jiaqi Wang, Zihan Liu, Shuang Zhao

et al.

Advanced Science, Journal Year: 2023, Volume and Issue: 10(31)

Published: Sept. 25, 2023

Self-assembling of peptides is essential for a variety biological and medical applications. However, it challenging to investigate the self-assembling properties within complete sequence space due enormous quantities. Here, demonstrated that transformer-based deep learning model effective in predicting aggregation propensity (AP) peptide systems, even decapeptide mixed-pentapeptide systems with over 10 trillion Based on predicted AP values, not only laws designing are derived, but transferability relation among APs pentapeptides, decapeptides, mixed pentapeptides also revealed, leading discoveries by concatenating or mixing, as consolidated experiments. This approach enables speedy, accurate, thorough search design oligopeptides, advancing science inspiring new

Language: Английский

Citations

18
Oxidation‐Responsive Supramolecular Hydrogel Based on a Simple Fmoc‐Cysteine Derivative Capable of Showing Autonomous Gel–Sol–Gel Transitions DOI Creative Commons

Yuki Shintani,

Hiroshi Katagiri, Masato Ikeda

et al.

Advanced Functional Materials, Journal Year: 2024, Volume and Issue: 34(25)

Published: Feb. 12, 2024

Abstract Aqueous soft matter, including supramolecular hydrogels capable of exhibiting stimuli–responsive macroscopic phase transitions, has attracted increasing attention for the exploration functional materials. However, investigation that undergo autonomous and multiple transitions (e.g., gel–sol–gel, sol–gel–sol) in response to surrounding environment without repeated additions stimuli remained largely unexplored. In this study, oxidation‐responsive gel–sol–gel fabricated via self‐assembly a simple fluorenylmethyloxycarbonyl (Fmoc)‐protected, benzylated cysteine ( Fmoc‐C Bzl ) is presented. During evaluation oxidation process , it revealed oxidized products, two diastereomeric sulfoxides ‐( R )‐O S ), exhibit significantly different propensities under aqueous conditions. It may be noteworthy chirality sulfoxide overlooked not effectively used modulate supramolecular, self‐assembled nanostructures. The difference kinetics self‐assembly/disassembly as well co‐assembly will contribute transitions.

Language: Английский

Citations

7
Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors DOI Creative Commons
Christopher M. Green, Deborah Sementa, Divita Mathur

et al.

Communications Chemistry, Journal Year: 2024, Volume and Issue: 7(1)

Published: Feb. 29, 2024

Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing drug delivery. In this study, we demonstrate that coacervates provide simple and biocompatible medium improve nucleic acid biosensors through the sequestration of both biosensor target strands within coacervate, thereby increasing local concentration. Using well-established polyarginine (R

Language: Английский

Citations

7
Therapeutic supramolecular polymers: Designs and applications DOI Creative Commons
Han Wang, Jason C. Mills, Boran Sun

et al.

Progress in Polymer Science, Journal Year: 2023, Volume and Issue: 148, P. 101769 - 101769

Published: Dec. 2, 2023

Language: Английский

Citations

15
Salt-induced Fmoc-tripeptide supramolecular hydrogels: a combined experimental and computational study of the self-assembly DOI Creative Commons
Miryam Criado‐Gonzalez, Mario Iván Peñas, Florent Barbault

et al.

Nanoscale, Journal Year: 2024, Volume and Issue: 16(20), P. 9887 - 9898

Published: Jan. 1, 2024

Delving into the mechanism behind molecular interactions at atomic level of short-sequence peptides plays a key role in development nanomaterials with specific structure–property–function relationships from bottom-up perspective.

Language: Английский

Citations

5
Reshaping the discovery of self-assembling peptides with generative AI guided by hybrid deep learning DOI
Marko Njirjak, Lucija Žužić, Marko Babić

et al.

Nature Machine Intelligence, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

Language: Английский

Citations

5
Investigation of Peptides for Molecular Recognition of C-Reactive Protein–Theoretical and Experimental Studies DOI Creative Commons
Katarzyna Szot-Karpińska,

Patryk Kudła,

Urszula Orzeł

et al.

Analytical Chemistry, Journal Year: 2023, Volume and Issue: 95(38), P. 14475 - 14483

Published: Sept. 11, 2023

We investigate the interactions between C-reactive protein (CRP) and new CRP-binding peptide materials using experimental (biological physicochemical) methods with support of theoretical simulations (computational modeling analysis). Three specific peptides (P2, P3, P9) derived from an M13 bacteriophage have been identified phage-display technology. The binding efficiency exposed on phages toward CRP was demonstrated via biological methods. Fibers selected phages/peptides interact differently due to different compositions amino acid sequences peptides, which confirmed by transmission electron microscopy. Numerical studies consistently showed that P3 is best binder. A combination demonstrates identifying binder can be performed simply, cheaply, fast. Such approach has not reported previously for screening a trend in science where calculations replace or laborious techniques. Finally, binder─the peptide─was used recognition silicate-modified indium tin oxide-coated glass electrodes. obtained electrodes exhibit wide range operation (1.0-100 μg mL-1) detection limit (LOD = 3σ/S) 0.34 mL-1. Moreover, dissociation constant Kd 4.2 ± 0.144 mL-1 (35 1.2 nM) evaluated change current. selectivity electrode presence three interfering proteins. These results prove presented potential candidate as receptor CRP, antibodies.

Language: Английский

Citations

12
Tuning Supramolecular Chirality in Iodinated Amphiphilic Peptides Through Tripeptide Linker Editing DOI
Douglas MacPherson, Dhwanit Dave, Salma Kassem

et al.

Biomacromolecules, Journal Year: 2024, Volume and Issue: 25(4), P. 2277 - 2285

Published: March 6, 2024

Protease-cleavable supramolecular oligopeptide nanofilaments are promising materials for targeted therapeutics and diagnostics. In these systems, single amino acid substitutions can have profound effects on the structure consequent proteolytic degradation, which critical parameters their intended applications. Herein, we describe changes to self-assembly cleavage of iodine containing sequences future translation into matrix metalloprotease (MMP-9)-activated radio-imaging probes. We use a systematic exchange in tripeptide linker region peptide amphiphiles provide insights role each residue assemblies. These modifications resulted dramatic nature assembled structures formed, including an unexpected chiral inversion. By using circular dichroism, atomic force microscopy, Fourier transform infrared spectroscopy, molecular dynamics simulations, found that GD loop, common motif β-turn elements, induced reversal orientation nanofibers. addition impact packing chirality, MMP-9-catalyzed hydrolysis was evaluated four peptides, with β-sheet content be stronger determinant enzymatic than chirality. observations fundamental sequence design protease cleavable amphiphilic peptides potential radio-labeling selective biomedical

Language: Английский

Citations

4
Predicting the Mechanical Properties of Supramolecular Gels DOI Creative Commons
Jack D. Simpson, Lisa Thomson, Christopher M. Woodley

et al.

Advanced Materials, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Abstract The prediction of gelation is an important target, yet current models do not predict any post‐gel properties. Gels can be formed through the self‐assembly many molecules, but close analogs often form gels. There has been success using a number computational approaches to understand and from molecular structures. However, these focus on whether or gel will form, properties resulting Critically, it gels that are for specific application, simply formed. Supramolecular kinetically trapped, meaning predicting inherently difficult challenge. Here, first successful priori such self‐assembled, supramolecular systems reported.

Language: Английский

Citations

0