scholarly journals A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure

2014 ◽  
Vol 11 (95) ◽  
pp. 20140249 ◽  
Author(s):  
Sam F. Greenbury ◽  
Iain G. Johnston ◽  
Ard A. Louis ◽  
Sebastian E. Ahnert
Keyword(s):  
Self Assembly ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Protein Complexes ◽  
Biological Evolution ◽  
Shape Space ◽  
The Self ◽  
Mutational Robustness ◽  
Self Assembling ◽  
Hp Lattice

The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here, we introduce a rich, intuitive and biologically realistic genotype–phenotype (GP) map that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a two-dimensional lattice and exhibits a number of properties: redundancy (genotypes vastly outnumber phenotypes), phenotype bias (genotypic redundancy varies greatly between phenotypes), genotype component disconnectivity (phenotypes consist of disconnected mutational networks) and shape space covering (most phenotypes can be reached in a small number of mutations). We also show that the mutational robustness of phenotypes scales very roughly logarithmically with phenotype redundancy and is positively correlated with phenotypic evolvability. Although our GP map describes the assembly of disconnected objects, it shares many properties with other popular GP maps for connected units, such as models for RNA secondary structure or the hydrophobic-polar (HP) lattice model for protein tertiary structure. The remarkable fact that these important properties similarly emerge from such different models suggests the possibility that universal features underlie a much wider class of biologically realistic GP maps.

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.

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 Lessons from equilibrium statistical physics regarding the assembly of protein complexes

2019 ◽  
Vol 117 (1) ◽  
pp. 114-120 ◽  
Author(s):  
Pablo Sartori ◽  
Stanislas Leibler
Keyword(s):  
Self Assembly ◽  
Statistical Physics ◽  
Liquid Mixture ◽  
Protein Complexes ◽  
Biological Evolution ◽  
Cellular Protein ◽  
Cellular Functions ◽  
Physical Constraints ◽  
Polypeptide Chains ◽  
Protein Complex Assembly

Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular functions are carried out not by long, isolated proteins, but rather by multiprotein complexes. Protein complexes themselves do not escape physical constraints, one of the most important being the difficulty of assembling reliably in the presence of cellular noise. In order to lay the foundation for a theory of reliable protein complex assembly, we study here an equilibrium thermodynamic model of self-assembly that exhibits 4 distinct assembly behaviors: diluted protein solution, liquid mixture, “chimeric assembly,” and “multifarious assembly.” In the latter regime, different protein complexes can coexist without forming erroneous chimeric structures. We show that 2 conditions have to be fulfilled to attain this regime: 1) The composition of the complexes needs to be sufficiently heterogeneous, and 2) the use of the set of components by the complexes has to be sparse. Our analysis of publicly available databases of protein complexes indicates that cellular protein systems might have indeed evolved so as to satisfy both of these conditions.

The self-assembly and secondary structure of peptide amphiphiles determine the membrane permeation activity

RSC Advances ◽  
2014 ◽  
Vol 4 (58) ◽  
pp. 30654-30657 ◽  
Author(s):  
Rie Wakabayashi ◽  
Yuko Abe ◽  
Noriho Kamiya ◽  
Masahiro Goto
Keyword(s):  
Secondary Structure ◽  
Membrane Permeability ◽  
Self Assembly ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Membrane Permeation ◽  
Related Peptide ◽  
Self Assembling

New GALA-related peptide amphiphiles were designed and the influence of their self-assembling propensity and the secondary structure on the membrane permeability was studied.

scholarly journals Self-assembly study of type I collagen extracted from male Wistar Hannover rat tail tendons

2020 ◽  
Vol 24 (1) ◽  
Author(s):  
Jeimmy González-Masís ◽  
Jorge M. Cubero-Sesin ◽  
Simón Guerrero ◽  
Sara González-Camacho ◽  
Yendry Regina Corrales-Ureña ◽  
...  
Keyword(s):  
Regenerative Medicine ◽  
Self Assembly ◽  
Type I Collagen ◽  
Ph Effect ◽  
The Self ◽  
Titration Calorimetry ◽  
Type I ◽  
Self Assembling ◽  
Functional Features ◽  
Rat Tail

Abstract Background Collagen, the most abundant protein in the animal kingdom, represents a promising biomaterial for regenerative medicine applications due to its structural diversity and self-assembling complexity. Despite collagen’s widely known structural and functional features, the thermodynamics behind its fibrillogenic self-assembling process is still to be fully understood. In this work we report on a series of spectroscopic, mechanical, morphological and thermodynamic characterizations of high purity type I collagen (with a D-pattern of 65 nm) extracted from Wistar Hannover rat tail. Our herein reported results can be of help to elucidate differences in self-assembly states of proteins using ITC to improve the design of energy responsive and dynamic materials for applications in tissue engineering and regenerative medicine. Methods Herein we report the systematic study on the self-assembling fibrillogenesis mechanism of type I collagen, we provide morphological and thermodynamic evidence associated to different self-assembly events using ITC titrations. We provide thorough characterization of the effect of pH, effect of salts and protein conformation on self-assembled collagen samples via several complementary biophysical techniques, including circular dichroism (CD), Fourier Transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic mechanical thermal analysis (DMTA) and thermogravimetric analysis (TGA). Results Emphasis was made on the use of isothermal titration calorimetry (ITC) for the thermodynamic monitoring of fibrillogenesis stages of the protein. An overall self-assembly enthalpy value of 3.27 ± 0.85 J/mol was found. Different stages of the self-assembly mechanism were identified, initial stages take place at pH values lower than the protein isoelectric point (pI), however, higher energy release events were recorded at collagen’s pI. Denatured collagen employed as a control exhibited higher energy absorption at its pI, suggesting different energy exchange mechanisms as a consequence of different aggregation routes. Graphical abstract

scholarly journals 2-Deoxyglucose-Modified Folate Derivative: Self-Assembling Nanoparticle Able to Load Cisplatin

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1084 ◽  
Author(s):  
Shaoming Jin ◽  
Zhongyao Du ◽  
Pengjie Wang ◽  
Huiyuan Guo ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Folic Acid ◽  
Self Assembly ◽  
Water Solubility ◽  
Pure Water ◽  
The Self ◽  
Molar Ratio ◽  
Antineoplastic Drugs ◽  
Self Assembling ◽  
Bonding Interaction ◽  
Nano Drug Delivery

Folic acid has been widely introduced into nano-drug delivery systems to give nanoparticle-targeted characteristics. However, the poor water solubility of folic acid may hinder the exploitation of its ability to load antineoplastic drugs. In the present study, we designed a new folate derivative (FA-2-DG) synthesized from folic acid and 2-Deoxyglucose (2-DG). The aim of this study was to evaluate the self-assembly characteristics of FA-2-DG, and its ability of loading cisplatin. The critical micelle concentration was 7.94 × 10−6 mol L−1. Fourier transform infrared spectroscopy indicated that hydrogen bonding interaction is a main driving force for the self–assembly of FA-2-DG. The particle was stable in pure water or 0.5% bovine serum albumin dispersions. By forming a coordination bond, the particles assembled from FA-2-DG can load cisplatin. The loading efficiency was maximal when the molar ratio of FA-2-DG to cisplatin was 2:1.

scholarly journals Tunable Supramolecular Chirogenesis in the Self-Assembling of Amphiphilic Porphyrin Triggered by Chiral Amines

2020 ◽  
Vol 21 (22) ◽  
pp. 8557
Author(s):  
Marco Savioli ◽  
Manuela Stefanelli ◽  
Gabriele Magna ◽  
Francesca Zurlo ◽  
Maria Federica Caso ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Effect ◽  
The Self ◽  
Chiral Amines ◽  
Solvent Mixtures ◽  
Fractal Structures ◽  
Chiral Amine ◽  
Supramolecular Chirality ◽  
Self Assembling ◽  
Aqueous Solvent

Supramolecular chirality is one of the most important issues in different branches of science and technology, as stereoselective molecular recognition, catalysis, and sensors. In this paper, we report on the self-assembly of amphiphilic porphyrin derivatives possessing a chiral information on the periphery of the macrocycle (i.e., D- or L-proline moieties), in the presence of chiral amines as co-solute, such as chiral benzylamine derivatives. The aggregation process, steered by hydrophobic effect, has been studied in aqueous solvent mixtures by combined spectroscopic and topographic techniques. The results obtained pointed out a dramatic effect of these ligands on the morphology and on the supramolecular chirality of the final self-assembled structures. Scanning electron microscopy topography, as well as fluorescence microscopy studies revealed the formation of rod-like structures of micrometric size, different from the fractal structures formerly observed when the self-assembly process is carried out in the absence of chiral amine co-solutes. On the other hand, comparative experiments with an achiral porphyrin analogue strongly suggested that the presence of the prolinate moiety is mandatory for the achievement of the observed highly organized suprastructures. The results obtained would be of importance for unraveling the intimate mechanisms operating in the selection of the homochirality, and for the preparation of sensitive materials for the detection of chiral analytes, with tunable stereoselectivity and morphology.

scholarly journals Molecular Determinants for the Self-Assembly of Elastin Peptides

2014 ◽  
Vol 2014 ◽  
pp. 1-4
Author(s):  
Brigida Bochicchio ◽  
Maria Rosaria Armenante ◽  
Maria Antonietta Crudele ◽  
Antonietta Pepe
Keyword(s):  
Molecular Structure ◽  
Mechanical Properties ◽  
Self Assembly ◽  
Terminal Region ◽  
The Self ◽  
Experimental Conditions ◽  
Self Assembling ◽  
Terminal Fragment ◽  
Aggregation Pattern ◽  
Molecular Determinants

Elastin and elastin-related peptides have great potential in the biomaterial field, because of their peculiar mechanical properties and spontaneous self-assembling behavior. Depending on their sequences and under appropriate experimental conditions, they are able to self-assemble in different fiber morphologies, including amyloid-like fibers. In this work, we will review recent data on elastin peptides derived from exon 30-coded domain of human tropoelastin. This domain has been shown to be fundamental for the correct assembly of elastin. However, the N-terminal region forms amyloid-like fibers, while the C-terminal fragment forms elastin-like fibers. A rationale for the varied aggregation pattern has been sought in the molecular structure of the peptides. Minimal differences in the sequences, adopting alternative conformations, are shown to be responsible for the observed data.

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