Self-assembly of cyclic homo- and hetero-β-peptides with cis- furanoid sugar amino acid and β-hGly as building blocks

Supramolecular hydrogels formed by the self-assembly of amino-acid based gelators are receiving increasing attention from the fields of biomedicine and material science. Self-assembled systems exhibit well-ordered functional architectures and unique physicochemical properties. However, the control over the kinetics and mechanical properties of the end-products remains puzzling. A minimal alteration of the chemical environment could cause a significant impact. In this context, we report the effects of modifying the position of a single atom on the properties and kinetics of the self-assembly process. A combination of experimental and computational methods, used to investigate double-fluorinated Fmoc-Phe derivatives, Fmoc-3,4F-Phe and Fmoc-3,5F-Phe, reveals the unique effects of modifying the position of a single fluorine on the self-assembly process, and the physical properties of the product. The presence of significant physical and morphological differences between the two derivatives was verified by molecular-dynamics simulations. Analysis of the spontaneous phase-transition of both building blocks, as well as crystal X-ray diffraction to determine the molecular structure of Fmoc-3,4F-Phe, are in good agreement with known changes in the Phe fluorination pattern and highlight the effect of a single atom position on the self-assembly process. These findings prove that fluorination is an effective strategy to influence supramolecular organization on the nanoscale. Moreover, we believe that a deep understanding of the self-assembly process may provide fundamental insights that will facilitate the development of optimal amino-acid-based low-molecular-weight hydrogelators for a wide range of applications.

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Synthesis and characterization of poly(amino acid methacrylate)-stabilized diblock copolymer nano-objects

Polymer Chemistry ◽

10.1039/c4py01556h ◽

2015 ◽

Vol 6 (10) ◽

pp. 1805-1816 ◽

Cited By ~ 40

Author(s):

Vincent Ladmiral ◽

Alexandre Charlot ◽

Mona Semsarilar ◽

Steven. P. Armes

Keyword(s):

Amino Acid ◽

Diblock Copolymer ◽

Michael Addition ◽

Self Assembly ◽

Building Blocks ◽

Synthesis And Characterization

Two amino acid methacrylates prepared via Michael addition are used as building blocks to prepare novel diblock copolymer nano-objects via polymerisation-induced self-assembly.

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Amino Acid Functional Polymers: Biomimetic Polymer Design Enabling Catalysis, Chiral Materials, and Drug Delivery

Australian Journal of Chemistry ◽

10.1071/ch16028 ◽

2016 ◽

Vol 69 (7) ◽

pp. 705 ◽

Cited By ~ 15

Author(s):

Emma R. L. Brisson ◽

Zeyun Xiao ◽

Luke A. Connal

Keyword(s):

Drug Delivery ◽

Amino Acids ◽

Amino Acid ◽

Self Assembly ◽

Building Blocks ◽

Functional Polymers ◽

Responsive Materials ◽

Biomimetic Polymer ◽

Tunable Optical Properties ◽

Natural Building

Amino acids are the natural building blocks for the world around us. Highly functional, these small molecules have unique catalytic properties, chirality, and biocompatibility. Imparting these properties to surfaces and other macromolecules is highly sought after and represents a fast-growing field. Polymers functionalized with amino acids in the side chains have tunable optical properties, pH responsiveness, biocompatibility, structure and self-assembly properties. Herein, we review the synthesis of amino acid functional polymers, discuss manipulation of available strategies to achieve the desired responsive materials, and summarize some exciting applications in catalysis, chiral particles, and drug delivery.

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Self-assembly of amino acids toward functional biomaterials

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.12.85 ◽

2021 ◽

Vol 12 ◽

pp. 1140-1150

Author(s):

Huan Ren ◽

Lifang Wu ◽

Lina Tan ◽

Yanni Bao ◽

Yuchen Ma ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Self Assembly ◽

Functional Materials ◽

Building Blocks ◽

The Self ◽

Self Assembled ◽

Functional Biomaterials ◽

Proteins And Peptides

Biomolecules, such as proteins and peptides, can be self-assembled. They are widely distributed, easy to obtain, and biocompatible. However, the self-assembly of proteins and peptides has disadvantages, such as difficulty in obtaining high quantities of materials, high cost, polydispersity, and purification limitations. The difficulties in using proteins and peptides as functional materials make it more complicate to arrange assembled nanostructures at both microscopic and macroscopic scales. Amino acids, as the smallest constituent of proteins and the smallest constituent in the bottom-up approach, are the smallest building blocks that can be self-assembled. The self-assembly of single amino acids has the advantages of low synthesis cost, simple modeling, excellent biocompatibility and biodegradability in vivo. In addition, amino acids can be assembled with other components to meet multiple scientific needs. However, using these simple building blocks to design attractive materials remains a challenge due to the simplicity of the amino acids. Most of the review articles about self-assembly focus on large molecules, such as peptides and proteins. The preparation of complicated materials by self-assembly of amino acids has not yet been evaluated. Therefore, it is of great significance to systematically summarize the literature of amino acid self-assembly. This article reviews the recent advances in amino acid self-assembly regarding amino acid self-assembly, functional amino acid self-assembly, amino acid coordination self-assembly, and amino acid regulatory functional molecule self-assembly.

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Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.5385 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Hueyling Tan

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Molecular Engineering ◽

Molecular Structures ◽

Polymer Science ◽

New Approach ◽

Factors Affecting ◽

Dna Structures ◽

Self Assembling ◽

Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

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A Bottom-Up Approach to Solution-Processed, Atomically Precise Graphitic Cylinders on Surfaces

10.26434/chemrxiv.7158959 ◽

2018 ◽

Author(s):

Erik Leonhardt ◽

Jeff M. Van Raden ◽

David Miller ◽

Lev N. Zakharov ◽

Benjamin Aleman ◽

...

Keyword(s):

Self Assembly ◽

Carbon Nanostructures ◽

Carbon Nanomaterials ◽

Circle Packing ◽

Pyrolytic Graphite ◽

Building Blocks ◽

Bottom Up ◽

Casting Technique ◽

New Class ◽

Solution Casting Technique

Extended carbon nanostructures, such as carbon nanotubes (CNTs), exhibit remarkable properties but are difficult to synthesize uniformly. Herein, we present a new class of carbon nanomaterials constructed via the bottom-up self-assembly of cylindrical, atomically-precise small molecules. Guided by supramolecular design principles and circle packing theory, we have designed and synthesized a fluorinated nanohoop that, in the solid-state, self-assembles into nanotube-like arrays with channel diameters of precisely 1.63 nm. A mild solution-casting technique is then used to construct vertical “forests” of these arrays on a highly-ordered pyrolytic graphite (HOPG) surface through epitaxial growth. Furthermore, we show that a basic property of nanohoops, fluorescence, is readily transferred to the bulk phase, implying that the properties of these materials can be directly altered via precise functionalization of their nanohoop building blocks. The strategy presented is expected to have broader applications in the development of new graphitic nanomaterials with π-rich cavities reminiscent of CNTs.

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Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

10.26434/chemrxiv.5972173.v1 ◽

2018 ◽

Author(s):

Nidhi Gour ◽

Bharti Koshti ◽

Chandra Kanth P. ◽

Dhruvi Shah ◽

Vivek Shinh Kshatriya ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Self Assembly ◽

Aromatic Amino Acids ◽

Neutral Condition ◽

Single Amino Acid ◽

Binding Assays ◽

Human Neuroblastoma ◽

Cytotoxicity Assays ◽

First Time

We report for the very first time self-assembly of Cysteine and Methionine to discrenible strucutres under neutral condition. To get insights into the structure formation, thioflavin T and Congo red binding assays were done which revealed that aggregates may not have amyloid like characteristics. The nature of interactions which lead to such self-assemblies was purported by coincubating assemblies in urea and mercaptoethanol. Further interaction of aggregates with short amyloidogenic dipeptide diphenylalanine (FF) was assessed. While cysteine aggregates completely disrupted FF fibres, methionine albeit triggered fibrillation. The cytotoxicity assays of cysteine and methionine structures were performed on Human Neuroblastoma IMR-32 cells which suggested that aggregates are not cytotoxic in nature and thus, may not have amyloid like etiology. The results presented in the manuscript are striking, since to the best of our knowledge,this is the first report which demonstrates that even non-aromatic amino acids (cysteine and methionine) can undergo spontaneous self-assembly to form ordered aggregates.

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Reversible microscale assembly of nanoparticles driven by the phase transition of a thermotropic liquid crystal

10.26434/chemrxiv.5691169 ◽

2017 ◽

Author(s):

Niamh Mac Fhionnlaoich ◽

Stephen Schrettl ◽

Nicholas B. Tito ◽

Ye Yang ◽

Malavika Nair ◽

...

Keyword(s):

Phase Transition ◽

Liquid Crystal ◽

Self Assembly ◽

Nematic Phase ◽

Hierarchical Control ◽

Building Blocks ◽

Model System ◽

Microscopic Level ◽

Reversible Process ◽

Thermotropic Liquid Crystal

The arrangement of nanoscale building blocks into patterns with microscale periodicity is challenging to achieve via self-assembly processes. Here, we report on the phase transition-driven collective assembly of gold nanoparticles in a thermotropic liquid crystal. A temperature-induced transition from the isotropic to the nematic phase leads to the assembly of individual nanometre-sized particles into arrays of micrometre-sized aggregates, whose size and characteristic spacing can be tuned by varying the cooling rate. This fully reversible process offers hierarchical control over structural order on the molecular, nanoscopic, and microscopic level and is an interesting model system for the programmable patterning of nanocomposites with access to micrometre-sized periodicities.

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PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

Current Bioinformatics ◽

10.2174/1574893615999200707141926 ◽

2020 ◽

Vol 15 ◽

Author(s):

Affan Alim ◽

Abdul Rafay ◽

Imran Naseem

Keyword(s):

Amino Acid ◽

Dimension Reduction ◽

Protein Identification ◽

Cold Water ◽

Genomic Sequence ◽

Sequence Data ◽

Antifreeze Proteins ◽

Building Blocks ◽

Gradient Boosting ◽

Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

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Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19980211 ◽

1998 ◽

Vol 63 (2) ◽

pp. 211-221 ◽

Cited By ~ 5

Author(s):

Miloš Tichý ◽

Luděk Ridvan ◽

Miloš Buděšínský ◽

Jiří Závada ◽

Jaroslav Podlaha ◽

...

Keyword(s):

Amino Acid ◽

Nmr Spectra ◽

Building Blocks ◽

X Ray Diffraction ◽

Amino Groups ◽

X Ray ◽

Configurational Assignment ◽

Symmetry Properties ◽

Axially Chiral ◽

Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

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