scholarly journals A Comparative Study on Interactions of Antimicrobial Peptides L- and D-phenylseptin with 1,2-dimyristoyl-sn-glycero-3-phosphocholine

2019 ◽  
Vol 9 (13) ◽  
pp. 2601 ◽  
Author(s):  
Batsaikhan Mijiddorj ◽  
Yuta Matsuo ◽  
Hisako Sato ◽  
Kazuyoshi Ueda ◽  
Izuru Kawamura
Keyword(s):  
Circular Dichroism ◽  
Antimicrobial Peptides ◽  
Lipid Bilayers ◽  
Binding Constants ◽  
Bound State ◽  
Dynamics Simulation ◽  
Membrane Bound ◽  
The Difference ◽  
Α Helix ◽  
Circular Dichroïsm

L-phenylseptin (L-Phes) and D-phenylseptin (D-Phes) are amphibian antimicrobial peptides isolated from the skin secretion of Hypsiboas punctatus. In the N-termini, L-Phes and D-Phes contain three consecutive phenylalanine residues, l-Phe-l-Phe-l-Phe and l-Phe-d-Phe-l-Phe, respectively. They are known to exhibit antimicrobial activity against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Xanthomonas axonopodis pv. Glycines. However, their mechanism of action and the role of the D-amino acid residue have not been elucidated yet. In this study, the interactions of both peptides with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were investigated by means of quartz crystal microbalance, circular dichroism, vibrational circular dichroism, 31P solid-state NMR, and molecular dynamics simulation. Both peptides have similar binding constants to the DMPC lipid bilayers, in the order of 106 M−1, and form an α-helix structure in the DMPC lipid bilayers. Both the peptides induce similar changes in the dynamics of DMPC lipids. Thus, in spite of the difference in the conformations caused by the chirality at the N-terminus, the peptides showed similar behavior in the membrane-bound state, experimentally and computationally.

Effect of Temperature and pH on the Secondary Structure and Denaturation Process of Jumbo Squid Hepatopancreas Cathepsin D.

2019 ◽  
Vol 26 (7) ◽  
pp. 532-541 ◽  
Author(s):  
Cadena-Cadena Francisco ◽  
Cárdenas-López José Luis ◽  
Ezquerra-Brauer Josafat Marina ◽  
Cinco-Moroyoqui Francisco Javier ◽  
López-Zavala Alonso Alexis ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Cathepsin D ◽  
Thermal Denaturation ◽  
Protein Denaturation ◽  
Marine Organisms ◽  
Effect Of Temperature ◽  
Jumbo Squid ◽  
Α Helix ◽  
Circular Dichroïsm

Background: Cathepsin D is a lysosomal enzyme that is found in all organisms acting in protein turnover, in humans it is present in some types of carcinomas, and it has a high activity in Parkinson's disease and a low activity in Alzheimer disease. In marine organisms, most of the research has been limited to corroborate the presence of this enzyme. It is known that cathepsin D of some marine organisms has a low thermostability and that it has the ability to have activity at very acidic pH. Cathepsin D of the Jumbo squid (Dosidicus gigas) hepatopancreas was purified and partially characterized. The secondary structure of these enzymes is highly conserved so the role of temperature and pH in the secondary structure and in protein denaturation is of great importance in the study of enzymes. The secondary structure of cathepsin D from jumbo squid hepatopancreas was determined by means of circular dichroism spectroscopy. Objective: In this article, our purpose was to determine the secondary structure of the enzyme and how it is affected by subjecting it to different temperature and pH conditions. Methods: Circular dichroism technique was used to measure the modifications of the secondary structure of cathepsin D when subjected to different treatments. The methodology consisted in dissecting the hepatopancreas of squid and freeze drying it. Then a crude extract was prepared by mixing 1: 1 hepatopancreas with assay buffer, the purification was in two steps; the first step consisted of using an ultrafiltration membrane with a molecular cut of 50 kDa, and the second step, a pepstatin agarose resin was used to purification the enzyme. Once the enzyme was purified, the purity was corroborated with SDS PAGE electrophoresis, isoelectric point and zymogram. Circular dichroism is carried out by placing the sample with a concentration of 0.125 mg / mL in a 3 mL quartz cell. The results were obtained in mdeg (millidegrees) and transformed to mean ellipticity per residue, using 111 g/mol molecular weight/residue as average. Secondary-structure estimation from the far-UV CD spectra was calculated using K2D Dichroweb software. Results: It was found that α helix decreases at temperatures above 50 °C and above pH 4. Heating the enzyme above 70°C maintains a low percentage of α helix and increases β sheet. Far-UV CD measurements of cathepsin D showed irreversible thermal denaturation. The process was strongly dependent on the heating rate, accompanied by a process of oligomerization of the protein that appears when the sample is heated, and maintained a certain time at this temperature. An amount typically between 3 and 4% α helix of their secondary structure remains unchanged. It is consistent with an unfolding process kinetically controlled due to the presence of an irreversible reaction. The secondary structure depends on pH, and a pH above 4 causes α helix structures to be modified. Conclusion: In conclusion, cathepsin D from jumbo squid hepatopancreas showed retaining up to 4% α helix at 80°C. The thermal denaturation of cathepsin D at pH 3.5 is under kinetic control and follows an irreversible model.

Conformation of membrane-bound proteins revealed by vacuum-ultraviolet circular-dichroism and linear-dichroism spectroscopy

2016 ◽  
Vol 84 (3) ◽  
pp. 349-359 ◽  
Author(s):  
Koichi Matsuo ◽  
Yasuyuki Maki ◽  
Hirofumi Namatame ◽  
Masaki Taniguchi ◽  
Kunihiko Gekko
Keyword(s):  
Circular Dichroism ◽  
Vacuum Ultraviolet ◽  
Linear Dichroism ◽  
Membrane Bound ◽  
Circular Dichroïsm

Citrate chelation as a potential mechanism against aluminum toxicity in cells: the role of calmodulin

1985 ◽  
Vol 63 (11) ◽  
pp. 1167-1175 ◽  
Author(s):  
Charles G. Suhayda ◽  
Alfred Haug
Keyword(s):  
Circular Dichroism ◽  
Conceptual Understanding ◽  
Aluminum Toxicity ◽  
Hydrophobic Surface ◽  
Native Structure ◽  
Calcium Calmodulin Dependent ◽  
Α Helix ◽  
Kinetics Of ◽  
Circular Dichroïsm

At a molar excess of [citrate]/[aluminum], this organic acid can protect calmodulin from aluminum binding if the metal is presented to the protein in stoichiometric micromolar quantities, as judged by fluorescence and circular dichroism spectroscopy. Similar citrate concentrations are also capable of fully restoring calmodulin's hydrophobic surface exposure to that of the native protein when calmodulin was initially damaged by aluminum binding. Fluoride anions are equally effective in restoring calmodulin's native structure as determined by fluorescence spectroscopy. Measurements of the kinetics of citrate-mediated aluminum removal also indicated that the metal ions are completely removed from calmodulin, consistent with results derived from atomic absorption experiments. On the other hand, results from circular dichroism studies indicated that citrate-mediated aluminum removal from calmodulin can only partially restore the α-helix content to that originally present in apocalmodulin or in calcium–calmodulin, dependent upon the absence or presence of calcium ions. The results that chelators like citrate can protect calmodulin from aluminum injury may provide a conceptual understanding of physiological observations regarding aluminum-tolerant plant species which are generally rich in certain organic acids.

scholarly journals BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy

2020 ◽  
pp. 175-189
Author(s):  
András Micsonai ◽  
Éva Bulyáki ◽  
József Kardos
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Classical Method ◽  
Cd Spectroscopy ◽  
Protein Fold ◽  
Cd Spectra ◽  
Secondary Structure Analysis ◽  
Β Sheets ◽  
Α Helix ◽  
Circular Dichroïsm

Abstract Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold. The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.

Magnetic Structure of Multilayers from Soft-X-Ray Magnetic Circular Dichroism

1994 ◽  
Vol 375 ◽  
Author(s):  
C. T. Chen ◽  
Y. U. Idzerda ◽  
C.-C. Kao ◽  
L. H. Tjeng ◽  
H.-J. Lin ◽  
...  
Keyword(s):  
Thin Films ◽  
Circular Dichroism ◽  
Magnetic Circular Dichroism ◽  
Magnetic Thin Films ◽  
X Rays ◽  
X Ray ◽  
Specific Manner ◽  
Left And Right ◽  
The Difference ◽  
Circular Dichroïsm

AbstractSoft-x-ray magnetic circular dichroism (MCD) is the difference between the absorptivity or reflectivity of left and right circularly polarized soft-x-rays at the magnetically interesting L2,3- edges of 3d transition metals or the M4,5-edges of the 4f rare earth elements. Thanks to its large absorption cross-section and strong MCD effect, this technique has become a powerful new means for probing, in an element- and site-specific manner, the magnetic properties of ultra-thin films and multilayers. Soft-x-ray MCD experiments, recently conducted at the Dragon beamline, are utilized to demonstrate the recent progress in this technique and its applications in the research of magnetic thin films.

scholarly journals In Silico Study of the Mechanism of Binding of the N-Terminal Region of α Synuclein to Synaptic-Like Membranes

Life ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 98 ◽  
Author(s):  
Carlos Navarro-Paya ◽  
Maximo Sanz-Hernandez ◽  
Alfonso De Simone
Keyword(s):  
Lipid Bilayers ◽  
Conformational Transition ◽  
Md Simulations ◽  
Bound State ◽  
Terminal Region ◽  
Coarse Grained ◽  
Biological Behavior ◽  
In Silico Study ◽  
Membrane Bound ◽  
Presynaptic Protein

The membrane binding by α-synuclein (αS), a presynaptic protein whose aggregation is strongly linked with Parkinson’s disease, influences its biological behavior under functional and pathological conditions. This interaction requires a conformational transition from a disordered-unbound to a partially helical membrane-bound state of the protein. In the present study, we used enhanced coarse-grained MD simulations to characterize the sequence and conformational determinants of the binding to synaptic-like vesicles by the N-terminal region of αS. This region is the membrane anchor and is of crucial importance for the properties of the physiological monomeric state of αS as well as for its aberrant aggregates. These results identify the key factors that play a role in the binding of αS with synaptic lipid bilayers in both membrane-tethered and membrane-locked conformational states.

Calculation of the circular dichroism spectrum of cyclo(l-tyr-l-tyr) based on a molecular dynamics simulation

1994 ◽  
Vol 49 (2) ◽  
pp. 141-152 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Joachim Grötzinger ◽  
Bernd Kramer ◽  
Peter Krüger ◽  
Axel Wollmer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
Circular Dichroism Spectrum ◽  
Dynamics Simulation ◽  
Circular Dichroïsm

Circular Dichroism Analysis of Native and Reaggregated Mycoplasma Membranes

1973 ◽  
Vol 51 (5) ◽  
pp. 632-636 ◽  
Author(s):  
Shlomo Rottem ◽  
Leonard Hayflick
Keyword(s):  
Circular Dichroism ◽  
Membrane Proteins ◽  
Sodium Dodecyl Sulfate ◽  
Lipid Composition ◽  
Sodium Dodecyl ◽  
Growth Cycle ◽  
Membrane Material ◽  
Α Helix ◽  
Low Amplitude ◽  
Circular Dichroïsm

Circular dichroism analyses of Acholeplasma laidlawii membranes solubilized by sodium dodecyl sulfate showed a typical α-helix spectrum. The estimated α-helix content was of the order of 35% calculated from the ellipticity at 208 nm of membranes solubilized by 20 mM SDS. Reaggregation of the solubilized membrane material to a membrane-like structure resulted in a distorted spectrum with low amplitude and red-shifted extrema like that of the native membranes. Throughout the growth cycle the circular dichroism spectra of membrane proteins remained the same despite the marked differences in membrane densities. The optical activity of the membranes was not affected by changing the lipid composition or extraction of over 90% of the lipids, although the latter resulted in marked destabilization of the proteins.

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