scholarly journals Structural analysis of nonapeptides derived from elastin

2019 ◽  
Author(s):  
B Hernandez ◽  
JM Crowet ◽  
J Thiery ◽  
SG Kruglik ◽  
N Belloy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cancer Progression ◽  
Specific Activity ◽  
Consensus Sequence ◽  
Sequence Motif ◽  
Specific Class ◽  
Receptor Complex ◽  
Type Ii ◽  
Structural Element ◽  
Elastin Receptor

AbstractElastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG which harbors the XGXXPG consensus pattern allowing interaction with the elastin receptor complex located at the surface of cells. Besides these elastokines, another class of peptides has been identified. This group of bioactive elastin peptides presents the XGXPGXGXG consensus sequence but the reason for their bioactivity remains unexplained. In order to better understand their nature and structure-function relationships, herein we searched the current databases for this nonapeptide motif and observed that the XGXPGXGXG elastin peptides define a specific group of tandemly repeated patterns. Further, we focused on four tandemly repeated human elastin nonapeptides, i.e. AGIPGLGVG, VGVPGLGVG, AGVPGLGVG and AGVPGFGAG. These peptides were analysed by means of optical spectroscopies and molecular dynamics. UV-circular dichroism and Raman spectra are consistent with a conformational equilibrium between β-turn, β-strand and random chain secondary elements in aqueous media. This equilibrium was found to be concentration-independent. Quantitative analysis of their conformations suggested that turns corresponded to half of the total population of structural elements while the remaining half was equally distributed between β-strand and unordered chains. These distributions were confirmed by molecular dynamics simulations. Altogether, our data suggest that these peptides harbor a type II β-turn located in their central part. We hypothesize that this structural element could explain their specific bioactivity.Statement of SignificanceElastin fragmentation products, the so-called elastin peptides, may exhibit a bioactivity towards normal and tumor cells. This phenomenon depends on the sequence motif they harbor. While XGXXPG sequences bioactivity is explained by the presence of a type VIII β-turn allowing interaction with the elastin receptor complex, the structural reasons for XGXPGXGXG specific activity remain unexplained. Using data mining, we show that elastin nonapeptides define a specific class of tandemly repeated features. Further, spectroscopic and numerical simulations methods suggest the presence of a type II β-turn in their conformation. This structural element could explain their bioactivity.

scholarly journals Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

2020 ◽  
Vol 11 (1) ◽  
pp. 282
Author(s):  
Yogeshwaran Krishnan ◽  
Mohammad Reza Ghaani ◽  
Arnaud Desmedt ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Guest Molecule ◽  
Arrhenius Equation ◽  
Dynamics Simulation ◽  
Type Ii ◽  
Large Cage ◽  
Guest Molecules ◽  
Simulation Time ◽  
Average Occupancy

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.

scholarly journals Mechanisms of Transforming Growth Factor-β Receptor Endocytosis and Intracellular Sorting Differ between Fibroblasts and Epithelial Cells

2001 ◽  
Vol 12 (3) ◽  
pp. 675-684 ◽  
Author(s):  
Jules J.E. Doré ◽  
Diying Yao ◽  
Maryanne Edens ◽  
Nandor Garamszegi ◽  
Elizabeth L. Sholl ◽  
...  
Keyword(s):  
Growth Factor ◽  
Epithelial Cells ◽  
Ligand Binding ◽  
Transforming Growth Factor ◽  
Point Mutations ◽  
Type I ◽  
Receptor Complex ◽  
Type Ii ◽  
Down Regulation ◽  
Β Receptor

Transforming growth factor-βs (TGF-β) are multifunctional proteins capable of either stimulating or inhibiting mitosis, depending on the cell type. These diverse cellular responses are caused by stimulating a single receptor complex composed of type I and type II receptors. Using a chimeric receptor model where the granulocyte/monocyte colony-stimulating factor receptor ligand binding domains are fused to the transmembrane and cytoplasmic signaling domains of the TGF-β type I and II receptors, we wished to describe the role(s) of specific amino acid residues in regulating ligand-mediated endocytosis and signaling in fibroblasts and epithelial cells. Specific point mutations were introduced at Y182, T200, and Y249 of the type I receptor and K277 and P525 of the type II receptor. Mutation of either Y182 or Y249, residues within two putative consensus tyrosine-based internalization motifs, had no effect on endocytosis or signaling. This is in contrast to mutation of T200 to valine, which resulted in ablation of signaling in both cell types, while only abolishing receptor down-regulation in fibroblasts. Moreover, in the absence of ligand, both fibroblasts and epithelial cells constitutively internalize and recycle the TGF-β receptor complex back to the plasma membrane. The data indicate fundamental differences between mesenchymal and epithelial cells in endocytic sorting and suggest that ligand binding diverts heteromeric receptors from the default recycling pool to a pathway mediating receptor down-regulation and signaling.

scholarly journals Torsional Characteristics of Carbon Nanotubes: Micropolar Elasticity Models and Molecular Dynamics Simulation

Nanomaterials ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 453
Author(s):  
Razie Izadi ◽  
Meral Tuna ◽  
Patrizia Trovalusci ◽  
Esmaeal Ghavanloo
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Scale Effects ◽  
Couple Stress Theory ◽  
Dynamics Simulation ◽  
Local Theory ◽  
Beam Model ◽  
Specific Class ◽  
Micropolar Theory ◽  
Material Parameters

Efficient application of carbon nanotubes (CNTs) in nano-devices and nano-materials requires comprehensive understanding of their mechanical properties. As observations suggest size dependent behaviour, non-classical theories preserving the memory of body’s internal structure via additional material parameters offer great potential when a continuum modelling is to be preferred. In the present study, micropolar theory of elasticity is adopted due to its peculiar character allowing for incorporation of scale effects through additional kinematic descriptors and work-conjugated stress measures. An optimisation approach is presented to provide unified material parameters for two specific class of single-walled carbon nanotubes (e.g., armchair and zigzag) by minimizing the difference between the apparent shear modulus obtained from molecular dynamics (MD) simulation and micropolar beam model considering both solid and tubular cross-sections. The results clearly reveal that micropolar theory is more suitable compared to internally constraint couple stress theory, due to the essentiality of having skew-symmetric stress and strain measures, as well as to the classical local theory (Cauchy of Grade 1), which cannot accounts for scale effects. To the best of authors’ knowledge, this is the first time that unified material parameters of CNTs are derived through a combined MD-micropolar continuum theory.

scholarly journals Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers

Brain ◽  
2014 ◽  
Vol 137 (11) ◽  
pp. 2938-2950 ◽  
Author(s):  
Axel Freischmidt ◽  
Kathrin Müller ◽  
Lisa Zondler ◽  
Patrick Weydt ◽  
Alexander E. Volk ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Expression Profiles ◽  
Consensus Sequence ◽  
Disease Onset ◽  
Therapeutic Targets ◽  
Familial Amyotrophic Lateral Sclerosis ◽  
Sequence Motif ◽  
Mutation Carriers ◽  
Disease Modifying ◽  
Lateral Sclerosis

Abstract Knowledge about the nature of pathomolecular alterations preceding onset of symptoms in amyotrophic lateral sclerosis is largely lacking. It could not only pave the way for the discovery of valuable therapeutic targets but might also govern future concepts of pre-manifest disease modifying treatments. MicroRNAs are central regulators of transcriptome plasticity and participate in pathogenic cascades and/or mirror cellular adaptation to insults. We obtained comprehensive expression profiles of microRNAs in the serum of patients with familial amyotrophic lateral sclerosis, asymptomatic mutation carriers and healthy control subjects. We observed a strikingly homogenous microRNA profile in patients with familial amyotrophic lateral sclerosis that was largely independent from the underlying disease gene. Moreover, we identified 24 significantly downregulated microRNAs in pre-manifest amyotrophic lateral sclerosis mutation carriers up to two decades or more before the estimated time window of disease onset; 91.7% of the downregulated microRNAs in mutation carriers overlapped with the patients with familial amyotrophic lateral sclerosis. Bioinformatic analysis revealed a consensus sequence motif present in the vast majority of downregulated microRNAs identified in this study. Our data thus suggest specific common denominators regarding molecular pathogenesis of different amyotrophic lateral sclerosis genes. We describe the earliest pathomolecular alterations in amyotrophic lateral sclerosis mutation carriers known to date, which provide a basis for the discovery of novel therapeutic targets and strongly argue for studies evaluating presymptomatic disease-modifying treatment in amyotrophic lateral sclerosis.

scholarly journals Type II transmembrane serine proteases as potential targets for cancer therapy

2016 ◽  
Vol 397 (9) ◽  
pp. 815-826 ◽  
Author(s):  
Andrew S. Murray ◽  
Fausto A. Varela ◽  
Karin List
Keyword(s):  
Cancer Progression ◽  
Serine Proteases ◽  
Molecular Mechanisms ◽  
Inflammatory Cells ◽  
Activity Levels ◽  
Type Ii ◽  
Neoplastic Progression ◽  
Treatment Regimens ◽  
Proinflammatory Mediators ◽  
Transmembrane Serine Protease

Abstract Carcinogenesis is accompanied by increased protein and activity levels of extracellular cell-surface proteases that are capable of modifying the tumor microenvironment by directly cleaving the extracellular matrix, as well as activating growth factors and proinflammatory mediators involved in proliferation and invasion of cancer cells, and recruitment of inflammatory cells. These complex processes ultimately potentiate neoplastic progression leading to local tumor cell invasion, entry into the vasculature, and metastasis to distal sites. Several members of the type II transmembrane serine protease (TTSP) family have been shown to play critical roles in cancer progression. In this review the knowledge collected over the past two decades about the molecular mechanisms underlying the pro-cancerous properties of selected TTSPs will be summarized. Furthermore, we will discuss how these insights may facilitate the translation into clinical settings in the future by specifically targeting TTSPs as part of novel cancer treatment regimens.

Olf-1-binding site: characterization of an olfactory neuron-specific promoter motif

1993 ◽  
Vol 13 (5) ◽  
pp. 3002-3014
Author(s):  
K Kudrycki ◽  
C Stein-Izsak ◽  
C Behn ◽  
M Grillo ◽  
R Akeson ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Consensus Sequence ◽  
Binding Motif ◽  
Sequence Motif ◽  
Olfactory Neuron ◽  
Sequence Motifs ◽  
Mobility Shift ◽  
Specific Expression ◽  
Mobility Shift Assay

We report characterization of several domains within the 5' flanking region of the olfactory marker protein (OMP) gene that may participate in regulating transcription of this and other olfactory neuron-specific genes. Analysis by electrophoretic mobility shift assay and DNase I footprinting identifies two regions that contain a novel sequence motif. Interactions between this motif and nuclear proteins were detected only with nuclear protein extracts derived from olfactory neuroepithelium, and this activity is more abundant in olfactory epithelium enriched in immature neurons. We have designated a factor(s) involved in this binding as Olf-1. The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG. Studies with transgenic mice indicate that a 0.3-kb fragment of the OMP gene containing one Olf-1 motif is sufficient for olfactory tissue-specific expression of the reporter gene. Some of the other identified sequence motifs also interact specifically with olfactory nuclear protein extracts. We propose that Olf-1 is a novel, olfactory neuron-specific trans-acting factor involved in the cell-specific expression of OMP.

Purification and Partial Amino Acid Sequence of Pentocin 31-1, an Anti-Listeria Bacteriocin Produced by Lactobacillus pentosus 31-1

2009 ◽  
Vol 72 (12) ◽  
pp. 2524-2529 ◽  
Author(s):  
JINLAN ZHANG ◽  
GUORONG LIU ◽  
NAN SHANG ◽  
WANPENG CHENG ◽  
SHANGWU CHEN ◽  
...  
Keyword(s):  
Molecular Mass ◽  
Specific Activity ◽  
Consensus Sequence ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Mass Spectrometry Analysis ◽  
Gel Chromatography ◽  
Original Activity ◽  
Lactobacillus Pentosus ◽  
Spectrometry Analysis

Pentocin 31-1, an anti-Listeria bacteriocin produced by Lactobacillus pentosus 31-1 from the traditional Chinese fermented Xuan-Wei ham, was successfully purified by the pH-mediated cell adsorption-desorption method and then purified by gel chromatography with Sephadex G-10. The purification resulted in a 1,381.9-fold increase in specific activity with a yield of 76.8% of the original activity. Using Tricine–sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), the molecular mass of the purified peptide was found to be between 3,500 and 6,400 Da, and bacteriocin activity was confirmed by overlayer techniques. When subjected to mass spectrometry analysis, the protein was highly pure and its molecular mass was 5,592.225 Da. The partial N-terminal sequence of pentocin 31-1 was the following: NH2-VIADYGNGVRXATLL. Compared with the sequence of other bacteriocins, pentocin 31-1 has the consensus sequence YGNGV in its N-terminal region, and therefore it belongs to the class IIa of bacteriocins.

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