scholarly journals Breakdown of chiral recognition of amino acids in reduced dimensions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yongchan Jeong ◽  
Hyo Won Kim ◽  
JiYeon Ku ◽  
Jungpil Seo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Density Functional ◽  
Chiral Recognition ◽  
Density Functional Theory Calculations ◽  
The Self ◽  
Reduced Dimensions ◽  
Tunnelling Microscopy ◽  
Living Organisms

Abstract The homochirality of amino acids in living organisms is one of the great mysteries in the phenomena of life. To understand the chiral recognition of amino acids, we have used scanning tunnelling microscopy to investigate the self-assembly of molecules of the amino acid tryptophan (Trp) on Au(111). Earlier experiments showed only homochiral configurations in the self-assembly of amino acids, despite using a mixture of the two opposite enantiomers. In our study, we demonstrate that heterochiral configurations can be favored energetically when l- and d-Trp molecules are mixed to form self-assembly on the Au surface. Using density functional theory calculations, we show that the indole side chain strongly interacts with the Au surface, which reduces the system effectively to two-dimension, with chiral recognition disabled. Our study provides important insight into the recognition of the chirality of amino acid molecules in life.

scholarly journals Unusual Aggregation Properties of Single Amino Acid L-Lysine Hydrochloride

2021 ◽  
Author(s):  
Bharti Koshti ◽  
Ramesh Singh ◽  
Vivekshinh Kshtriya ◽  
Shanka Walia ◽  
Dhiraj Bhatia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Short Term Memory ◽  
Deionized Water ◽  
The Body ◽  
The Self ◽  
Single Amino Acid ◽  
Maple Syrup ◽  
Self Assembling

<p>.<br></p><p>The self-assembly of single amino acids is very important topic of research since there are plethora of diseases like phenylketonuria, tyrosinemia, hypertryptophanemia, hyperglycinemia, cystinuria and maple syrup urine disease to name a few which are caused by the accumulation or excess of amino acids. These are in-born errors of metabolisms (IEM’s) which are caused due to the deficiency of enzymes involved in catabolic pathways of these enzymes. Hence, it is very pertinent to understand the fate of these excess amino acids in the body and their self-assembling behaviour at molecular level. From the previous literature reports it may be surmised that the single amino acids like Phenylalanine, Tyrosine, Tryptophan, Cysteine and Methionine assemble to amyloid like structures, and hence have important implications in the pathophysiology of IEM’s like phenylketonuria, tyrosinemia, hypertryptophanemia, cystinuria and hypermethioninemia respectively. In this manuscript we report the self-assembly of lysine hydrocholride to fiber like structures in deionized water. It could be observed that lysine assemble to globular structures in fresh condition and then gradually changes to fiber like morphologies by self-association over time after 24 hours. These fibers gradually change to tubular morphologies after 3 day followed by fractal irregular morphologies in 10 and 15 days respectively. Notably, lysine exists as positively charged amino acid at physiological pH and the amine groups in lysine remain protonated. Hence, the self-assembling properties of lysine hydrochloride in deionized water is also pertinent and give insights into the fate of this amino acid in body in case it remains unmetabolized. Further, MTT assays were done to analyse the toxicities of these aggregates and the assay suggest their cytotoxic nature on SHSY5Y neural cell lines. Hence, the aggregation of lysine may be attributed to the pathological symptoms caused in diseases like hyperlysinemia which is associated with the neurological problems like seizures and short-term memory as observed in case of amyloid diseases like Parkinson’s and Alzheimer’s to name a few.</p>

scholarly journals Initiating Ullmann-like coupling of Br2Py by a semimetal surface

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinping Hu ◽  
Jinbang Hu ◽  
Hongbing Wang ◽  
Kongchao Shen ◽  
Huan Zhang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Reaction Mechanisms ◽  
Density Functional ◽  
Coupling Reaction ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Metallic Substrates ◽  
Organic Nanostructures ◽  
Tunnelling Microscopy ◽  
Ag Substrate

AbstractIntensive efforts have been devoted to surface Ullmann-like coupling in recent years, due to its appealing success towards on-surface synthesis of tailor-made nanostructures. While attentions were mostly drawn on metallic substrates, however, Ullmann dehalogenation and coupling reaction on semimetal surfaces has been seldom addressed. Herein, we demonstrate the self-assembly of 2, 7-dibromopyrene (Br2Py) and the well controllable dehalogenation reaction of Br2Py on the Bi(111)–Ag substrate with a combination of scanning tunnelling microscopy (STM) and density functional theory calculations (DFT). By elaborately investigating the reaction path and formed organic nanostructures, it is revealed that the pristinely inert bismuth layer supported on the silver substrate can initiate Ullmann-like coupling in a desired manner by getting alloyed with Ag atoms underneath, while side products have not been discovered. By clarifying the pristine nature of Bi–Ag(111) and Ullmann-like reaction mechanisms, our report proposes an ideal template for thoroughly exploring dehalogenative coupling reaction mechanisms with atomic insights and on-surface synthesis of carbon-based architectures.

scholarly journals Unusual Aggregation Properties of Single Amino Acid L-Lysine Hydrochloride

2021 ◽  
Author(s):  
Bharti Koshti ◽  
Ramesh Singh ◽  
Vivekshinh Kshtriya ◽  
Shanka Walia ◽  
Dhiraj Bhatia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Short Term Memory ◽  
Deionized Water ◽  
The Body ◽  
The Self ◽  
Single Amino Acid ◽  
Maple Syrup ◽  
Self Assembling

<p>.<br></p><p>The self-assembly of single amino acids is very important topic of research since there are plethora of diseases like phenylketonuria, tyrosinemia, hypertryptophanemia, hyperglycinemia, cystinuria and maple syrup urine disease to name a few which are caused by the accumulation or excess of amino acids. These are in-born errors of metabolisms (IEM’s) which are caused due to the deficiency of enzymes involved in catabolic pathways of these enzymes. Hence, it is very pertinent to understand the fate of these excess amino acids in the body and their self-assembling behaviour at molecular level. From the previous literature reports it may be surmised that the single amino acids like Phenylalanine, Tyrosine, Tryptophan, Cysteine and Methionine assemble to amyloid like structures, and hence have important implications in the pathophysiology of IEM’s like phenylketonuria, tyrosinemia, hypertryptophanemia, cystinuria and hypermethioninemia respectively. In this manuscript we report the self-assembly of lysine hydrocholride to fiber like structures in deionized water. It could be observed that lysine assemble to globular structures in fresh condition and then gradually changes to fiber like morphologies by self-association over time after 24 hours. These fibers gradually change to tubular morphologies after 3 day followed by fractal irregular morphologies in 10 and 15 days respectively. Notably, lysine exists as positively charged amino acid at physiological pH and the amine groups in lysine remain protonated. Hence, the self-assembling properties of lysine hydrochloride in deionized water is also pertinent and give insights into the fate of this amino acid in body in case it remains unmetabolized. Further, MTT assays were done to analyse the toxicities of these aggregates and the assay suggest their cytotoxic nature on SHSY5Y neural cell lines. Hence, the aggregation of lysine may be attributed to the pathological symptoms caused in diseases like hyperlysinemia which is associated with the neurological problems like seizures and short-term memory as observed in case of amyloid diseases like Parkinson’s and Alzheimer’s to name a few.</p>

Impact of amino acids on the aqueous self-assembly of benzenetrispeptides into supramolecular polymer bottlebrushes

2020 ◽  
Vol 11 (42) ◽  
pp. 6763-6771 ◽  
Author(s):  
Tobias Klein ◽  
Hans F. Ulrich ◽  
Franka V. Gruschwitz ◽  
Maren T. Kuchenbrod ◽  
Rintaro Takahashi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
The Self ◽  
Supramolecular Polymer ◽  
Fine Tune ◽  
Acid Unit

The choice of the amino acid unit in benzenetrispeptide-PEO conjugates allows to fine-tune the self-assembly strength and to control the resulting solution morphologies in water.

scholarly journals Understanding the self-assembly of TCNQ on Cu(111): a combined study based on scanning tunnelling microscopy experiments and density functional theory simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (18) ◽  
pp. 15071-15079 ◽  
Author(s):  
Daniele Stradi ◽  
Bogdana Borca ◽  
Sara Barja ◽  
Manuela Garnica ◽  
Cristina Díaz ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Self Assembly ◽  
Density Functional ◽  
Scanning Tunnelling Microscopy ◽  
The Self ◽  
Functional Theory ◽  
Scanning Tunnelling ◽  
Tunnelling Microscopy ◽  
Deposition Conditions

Two polymorphic structures of TCNQ on Cu(111) can be formed by varying the deposition conditions.

Enzyme–substrate interactions promote the self-assembly of amino acid derivatives into supramolecular hydrogels

2016 ◽  
Vol 4 (5) ◽  
pp. 844-851 ◽  
Author(s):  
Yanyan Xie ◽  
Renliang Huang ◽  
Wei Qi ◽  
Yuefei Wang ◽  
Rongxin Su ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
The Self ◽  
Amino Acid Derivatives ◽  
Amino Acid Esters ◽  
Substrate Interactions ◽  
Substrate Interaction ◽  
Enzyme Substrate ◽  
Acid Esters

The first example of enzyme-substrate interaction-promoted self-assembly was reported for the synthesis of supramolecular hydrogels from Fmoc-amino acids and amino acid esters in the presence of α-chymotrypsin.

scholarly journals Self-assembly of amino acids toward functional biomaterials

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.

Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

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.

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Self-assembling behaviour of a modified aromatic amino acid in competitive medium

Soft Matter ◽  
2020 ◽  
Vol 16 (28) ◽  
pp. 6599-6607 ◽  
Author(s):  
Pijush Singh ◽  
Souvik Misra ◽  
Nayim Sepay ◽  
Sanjoy Mondal ◽  
Debes Ray ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acid ◽  
Photophysical Properties ◽  
Solvent Mixture ◽  
The Self ◽  
Solvent Ratio ◽  
Self Assembling

The self-assembly and photophysical properties of 4-nitrophenylalanine (4NP) are changed with the alteration of solvent and final self-assembly state of 4NP in competitive solvent mixture and are dictated by the solvent ratio.

Sign in / Sign up

Export Citation Format

Share Document