scholarly journals Characterization of Protein-Lipid Interactions in Biosystems Processes

2019 ◽  
pp. 93-99
Author(s):  
Dr. Chrysanthus Chukwuma Sr
Keyword(s):  
Membrane Proteins ◽  
Binding Sites ◽  
Systematic Investigation ◽  
Morphological Characterization ◽  
Protein Activity ◽  
Lipid Interactions ◽  
Cellular Processes ◽  
Normal Enzyme ◽  
Basic And Applied Research

Lipids correlate with membrane characteristics and functionalities as macromolecular constituentts in all cellular processes. Numerous aspects of lipid modulation of protein activity and structure are not completely understood and, thus a holistic systematic investigation activities will be pertinent. Protein-lipid interactions are the resultant impacts of membrane proteins on lipid physical states or vice versa. Encompassing research needs to be associated with strategies to elucidate whether proteins contain binding sites which are lipid specific, and that the protein-lipid complexes are ostensibly long-lived, on the time order necessary for the turnover of a normal enzyme. Biological membranes have since been determined as essential ingredients in an expansive array of cellular processes, such as photosynthesis, cell defence, signaling transduction, communication and motility. Therefore, they constitute multiple targets in both basic and applied research. Protein-lipid interactions are becoming increasingly relevant to the morphological characterization of membrane proteins as related to their functionalities. Excepting for simplified models, certain protein-lipid interactions specifically constitute remarkable challenges which require optimum experimental paradigm and design.

scholarly journals PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

2021 ◽  
Author(s):  
Wanling Song ◽  
Robin A. Corey ◽  
Bertie Ansell ◽  
Keith Cassidy ◽  
Michael Horrell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Objective Assessment ◽  
Source Distribution ◽  
Lipid Interactions ◽  
Dynamics Simulations ◽  
Python Package

Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these protein-lipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements whilst bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation datasets of multiple species of membrane proteins.

scholarly journals Genetic and Enzymatic Experiments relating to the Quaternary Structure of ß-Galactosidase

1974 ◽  
Vol 27 (3) ◽  
pp. 321 ◽  
Author(s):  
J Langridge
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Quaternary Structure ◽  
Substrate Binding ◽  
Isolation And Characterization ◽  
Normal Enzyme ◽  
Substrate Binding Sites ◽  
Polypeptide Sequences

The quaternary structure of f:!-galactosidase, which consists of four identical subunits, has been studied by the isolation and characterization of appropriate mutants of Escherichia coli. Of 146 mutants examined, 19 were found to have enzymes with reduced subunit association. These altered enzymes are especially sensitive to inactivation by urea which, at concentrations that do not affect the normal enzyme, causes dissociation into subunits. Mapping with overlapping deletions showed that the mutations affecting quaternary structure are not distributed continuously, but occur in five or six groups within the gene. The mapping indicates that polypeptide sequences involved in subunit association and in substrate binding are contiguous. A model for f:!-galactosidase structure is suggested in which substrate binding sites are provided by the clefts formed between subunits when they associate.

SUMO and ubiquitin paths converge

2010 ◽  
Vol 38 (1) ◽  
pp. 34-39 ◽  
Author(s):  
Amanda Denuc ◽  
Gemma Marfany
Keyword(s):  
Genome Stability ◽  
Cell Signalling ◽  
Covalent Attachment ◽  
Small Peptides ◽  
Protein Activity ◽  
Protein Protein Interaction ◽  
Cellular Processes ◽  
Reversible Covalent ◽  
And Function

One of the more rapidly expanding fields in cell signalling nowadays is the characterization of proteins conjugated to Ub (ubiquitin) or Ub-like peptides, such as SUMO (small Ub-related modifier). The reversible covalent attachment of these small peptides remodels the target protein, providing new protein–protein interaction interfaces, which can be dynamically regulated given a set of enzymes for conjugation and deconjugation. First, ubiquitination was thought to be merely relegated to the control of protein turnover and degradation, whereas the attachment of SUMO was involved in the regulation of protein activity and function. However, the boundaries between the protein fates related to these tag molecules are becoming more and more fuzzy, as either the differences between mono-, multi- and poly-modifications or the lysine residue used for growth of the poly-chains is being dissected. The Ub and SUMO pathways are no longer separated, and many examples of this cross-talk are found in the literature, involving different cellular processes ranging from DNA repair and genome stability, to the regulation of protein subcellular localization or enzyme activity. Here, we review several cases in which SUMOylation and ubiquitination intersect, showing also that the same protein can be conjugated to SUMO and Ub for antagonistic, synergistic or multiple outcomes, illustrating the intricacy of the cellular signalling networks. Ub and SUMO have met and are now applying for new regulatory roles in the cell.

scholarly journals Primary, Secondary Metabolites and Molecular Characterization of Hawthorn (Crataegus spp.) Genotypes

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1731
Author(s):  
Aysen Gurlen ◽  
Muttalip Gundogdu ◽  
Goksel Ozer ◽  
Sezai Ercisli ◽  
Boris Duralija
Keyword(s):  
Citric Acid ◽  
Binding Sites ◽  
Morphological Characterization ◽  
Resolving Power ◽  
Crataegus Monogyna ◽  
The World ◽  
Citric Acid Content ◽  
Polymorphic Bands ◽  
First Time

In this study, the molecular, biochemical and agro-morphological characterization of genotypes belonging to hawthorn species collected from Bolu province of Turkey was performed. Inter-priming binding sites (iPBS) markers based on retrotransposons were used for the first time in the molecular properties of hawthorn genotypes in the world. The marker system provided very useful information for revealing the genetic variation of the genotypes. Six iPBS markers amplified 68 fragments, of which 65 were polymorphic (95.59%) with an average of 10.83 polymorphic bands per primer. The polymorphism and resolving power per primers ranged from 0.12 to 0.42 and from 0.78 to 8.11 with the average being 0.32 and 5.95, respectively. Pomological properties of Crataegus tanacetifolia, such as fruit pomology and core weight were determined to higher than those of Crataegus monogyna. Citric acid was determined as the most predominant organic acid, followed by malic and succinic acid in the genotypes of both species. The highest citric acid content (26.745 mg 100 g−1) was noted for 14BL09 genotype. The vit. C content was recorded ranging from 2.681 to 9.621 mg 100 g−1. Catechin, chlorogenic, caffeic and rutin contents were varied between 4.140–51.393 mg, 2.254–42.361 mg, 0.624–4.407 mg, and 1.241–10.029 mg per 100 g of fruits, respectively. As a result, it has been determined that twenty-five genotypes belonging to different hawthorn species are important genetic resources to be evaluated in horticultural breeding studies in terms of their physical and biochemical contents.

Charge Effect on the Quantum Dots-Peptide Self-Assembly Using Fluorescence Coupled Capillary Electrophoresis

2016 ◽  
Vol 16 (4) ◽  
pp. 4035-4039 ◽  
Author(s):  
Jianhao Wang ◽  
Jingyan Li ◽  
Yiwan Teng ◽  
Yanhua Bi ◽  
Wei Hu ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Capillary Electrophoresis ◽  
Self Assembly ◽  
Binding Sites ◽  
Systematic Investigation ◽  
Assembly Process ◽  
Charge Effect ◽  
Metal Affinity ◽  
Assembly Kinetics

We present a molecular characterization of metal-affinity driven self-assembly between CdSe–ZnS quantum dots and a series of hexahistidine peptides with different charges. In particular, we utilized fluorescence coupled capillary electrophoresis to test the self-assembly process of quantum dots with peptides in solution. Four peptides with different charges can be efficiently separated by fluorescence coupled capillary electrophoresis. The migration time appeared to be influenced by the charges of the peptide. In addition, the kinetics of self-assembly process of quantum dots with one of the peptides manifested a bi-phasic kinetics followed by a saturating stage. This work revealed that there exist two types of binding sites on the surface of quantum dots for peptide 1: one type termed “high priority” binding site and a “low priority” site which is occupied after the first binding sites are fully occupied. The total self-assembly process finishes in solution within 80 s. Our work represents the systematic investigation of the details of self-assembly kinetics utilizing high-resolution fluorescence coupled capillary electrophoresis. The charge effect of peptide coating quantum dots provides a new way of preparing bioprobes.

Morphological Characterization of Mycobacteriophage R1

1974 ◽  
Vol 32 ◽  
pp. 254-255
Author(s):  
B. L. Soloff ◽  
T. A. Rado
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Growth Phase ◽  
Minimal Medium ◽  
Morphological Characterization ◽  
Logarithmic Growth Phase ◽  
Complete Lysis ◽  
Lysogenic Culture ◽  
Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

Morphological Characterization of Rhinacanthus Species of Sri Lanka

Planta Medica ◽  
2010 ◽  
Vol 76 (05) ◽  
Author(s):  
APPR Amarasinghe ◽  
RP Karunagoda ◽  
DSA Wijesundara
Keyword(s):  
Sri Lanka ◽  
Morphological Characterization

Characterization of Thromboxane A2/Prostaglandin H2 Receptors in Porcine Coronary Artery -The Inhibitory Effect of a Novel Dibenzoxepin Derivative, KW-3635

1992 ◽  
Vol 67 (05) ◽  
pp. 582-584 ◽  
Author(s):  
Ichiro Miki ◽  
Akio Ishii
Keyword(s):  
Coronary Artery ◽  
Binding Sites ◽  
Thromboxane A2 ◽  
Inhibitory Effect ◽  
Scatchard Analysis ◽  
Single Class ◽  
Porcine Coronary Artery ◽  
Equilibrium Binding ◽  
H2 Receptors

SummaryWe characterized the thromboxane A2/prostaglandin H2 receptors in porcine coronary artery. The binding of [3H]SQ 29,548, a thromboxane A2 antagonist, to coronary arterial membranes was saturable and displaceable. Scatchard analysis of equilibrium binding showed a single class of high affinity binding sites with a dissociation constant of 18.5 ±1.0 nM and the maximum binding of 80.7 ± 5.2 fmol/mg protein. [3H]SQ 29,548 binding was concentration-dependently inhibited by thromboxane A2 antagonists such as SQ 29,548, BM13505 and BM13177 or the thromboxane A2 agonists such as U46619 and U44069. KW-3635, a novel dibenzoxepin derivative, concentration-dependently inhibited the [3H]SQ 29,548 binding to thromboxane A2/prosta-glandin H2 receptors in coronary artery with an inhibition constant of 6.0 ± 0.69 nM (mean ± S.E.M.).

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