Intra-mitochondrial self-assembly to overcome the intracellular enzymatic degradation of l-peptides

2020 ◽  
Vol 56 (46) ◽  
pp. 6265-6268 ◽  
Author(s):  
M. T. Jeena ◽  
Seokyoung Lee ◽  
Ayan Kumar Barui ◽  
Seongeon Jin ◽  
Yuri Cho ◽  
...  
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Enzymatic Degradation ◽  
Therapeutic Efficiency

The design of peptide-based therapeutics is generally based on the replacement of l-amino acids with d-isomers to obtain improved therapeutic efficiency.

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.

Noncanonical Amino Acids for Hypoxia-Responsive Peptide Self-Assembly and Fluorescence

2021 ◽  
Author(s):  
Binbin Hu ◽  
Na Song ◽  
Yawei Cao ◽  
Mingming Li ◽  
Xin Liu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Noncanonical Amino Acids

Self-assembly of aromatic amino acids: a molecular dynamics study

2018 ◽  
Vol 20 (48) ◽  
pp. 30525-30536 ◽  
Author(s):  
Sahin Uyaver ◽  
Helen W. Hernandez ◽  
M. Gokhan Habiboglu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Self Assembly ◽  
Aromatic Amino Acids

Common structures identified in the assembly of aromatic amino acids and their mixtures include the four-fold tube (a and b) and the zig-zag structure (c and d).

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 Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Minwoo Yang ◽  
Woon Ju Song
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Protein Structures ◽  
Functional Materials ◽  
Building Blocks ◽  
Unnatural Amino Acid ◽  
Metal Coordination ◽  
Specific Chemical ◽  
Natural Building ◽  
Kinetics Of

AbstractProteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties of unnatural chelating amino acids as the sufficient and dominant driving force for diverse protein self-assembly. Bipyridine-alanine is genetically incorporated into a D3 homohexamer. Depending on the position of the unnatural amino acid, 1-directional, crystalline and noncrystalline 2-directional, combinatory, and hierarchical architectures are effectively created upon the addition of metal ions. The length and shape of the structures is tunable by altering conditions related to thermodynamics and kinetics of metal-coordination and subsequent reactions. The crystalline 1-directional and 2-directional biomaterials retain their native enzymatic activities with increased thermal stability, suggesting that introducing chelating ligands provides a specific chemical basis to synthesize diverse protein-based functional materials while retaining their native structures and functions.

scholarly journals THE PROPERTIES AND THE ENZYMATIC DEGRADATION OF DESOXYRIBONUCLEOPROTEIN FROM LIVER CELL NUCLEI

1958 ◽  
Vol 41 (3) ◽  
pp. 595-608 ◽  
Author(s):  
Kenneth J. Monty ◽  
Alexander L. Dounce
Keyword(s):  
Amino Acids ◽  
Cell Nucleus ◽  
Liver Cell ◽  
Enzymatic Degradation ◽  
Short Peptides ◽  
Chromosomal Protein ◽  
X Rays ◽  
Cell Nuclei ◽  
Desoxyribonucleic Acid ◽  
Mode Of Attachment

The isolation and properties of a desoxyribonucleoprotein of the rat liver cell nucleus are described. This material consists of DNA (desoxyribonucleic acid) bound to the residual chromosomal protein by what appear to be covalent linkages. Lipide is present, but can be removed by extraction in lipide solvents prior to isolation of the nucleoprotein, without much change in the physical properties of the latter. The nucleoprotein in question forms elastic, recoilable gels in molar saline at pH 7.0 or in water at pH 8.0 to 10.0 or even higher, which are similar to those that can be obtained from whole nuclei. The effects of x-rays, heat, and enzymes on the nucleoprotein are discussed, and the composition of the protein component is investigated. The latter contains an "occult" protein that can be liberated by heating in 0.1 N HCl. A study of the enzymatic degradation of the desoxyribonucleoprotein has been made, with the aim of attempting the isolation of small polynucleotide fragments attached to amino acids or short peptides that might be useful in characterizing the mode of attachment of the desoxyribonucleic acid to the protein in the desoxyribonucleoprotein. Evidence is presented indicating that such products can be isolated through the use of electrophoresis on paper.

ChemInform Abstract: Non-Standard Amino Acids and Peptides: From Self-Assembly to Nanomaterials

ChemInform ◽  
2016 ◽  
Vol 47 (52) ◽  
Author(s):  
Francesca Clerici ◽  
Emanuela Erba ◽  
Maria Luisa Gelmi ◽  
Sara Pellegrino
Keyword(s):  
Amino Acids ◽  
Self Assembly

scholarly journals Aza-Amino Acids Disrupt β-Sheet Secondary Structures

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1919 ◽  
Author(s):  
Michael A. McMechen ◽  
Evan L. Willis ◽  
Preston C. Gourville ◽  
Caroline Proulx
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Secondary Structures ◽  
Model Peptide ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Conformational Constraints ◽  
Bonding Properties ◽  
Β Sheet ◽  
Hairpin Formation

Cα to N substitution in aza-amino acids imposes local conformational constraints, changes in hydrogen bonding properties, and leads to adaptive chirality at the nitrogen atom. These properties can be exploited in mimicry and stabilization of peptide secondary structures and self-assembly. Here, the effect of a single aza-amino acid incorporation located in the upper β-strand at a hydrogen-bonded (HB) site of a β-hairpin model peptide (H-Arg-Tyr-Val-Glu-Val-d-Pro-Gly-Orn-Lys-Ile-Leu-Gln-NH2) is reported. Specifically, analogs in which valine3 was substituted for aza-valine3 or aza-glycine3 were synthesized, and their β-hairpin stabilities were examined using Nuclear Magnetic Resonance (NMR) spectroscopy. The azapeptide analogs were found to destabilize β-hairpin formation compared to the parent peptide. The aza-valine3 residue was more disruptive of β-hairpin geometry than its aza-glycine3 counterpart.

scholarly journals The Formation and Self-Assembly of Long Prebiotic Oligomers Produced by the Condensation of Unactivated Amino Acids on Oxide Surfaces

2014 ◽  
Vol 126 (18) ◽  
pp. 4759-4762 ◽  
Author(s):  
Gianmario Martra ◽  
Chiara Deiana ◽  
Yuriy Sakhno ◽  
Ilvis Barberis ◽  
Marco Fabbiani ◽  
...  
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Oxide Surfaces
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