Monthly Archives: January 2015

Sarcosine (part five)

Sarcosine in a N-methylglycine.

Structure of a N-methylglycine:

Untitled

It’s an intermediate in glycine synthesis and degradation as you can look on this schema:

Antimicrobial peptides

It’s an good antibacterial and anti fungal too. Able to form a bidentate complexe according to a carboxyl ion and can coordinates several metals, for instance Zn.

Some complexes containing Sn and Zn are very soluble in lipids. Consequently, these complexes can easily enter into the cell.

Lot of studies are made about Sarcosine and it function and confirm this.

Antimicrobial peptides (Part fourth)

The plant sources leaf extract are shown to be very effective against extracoccus faecals. It’s a major microbe recovered from root canal.

Proline-riche Bacterinine against Gram-ves

They can enter bacteria cells without damaging the membrane. It uses Sbm-A, a bacteria proton which permits to create a drive transporter into cells.

This polypeptide contains several combinaisons of amino acids, one of them contains:

– Ten residues Proline

– Two arginine residues

This polypeptide is the best combinaison (1).

PAF-26 is a de NOVO designed hexapeptide antifungial.

It contains two motifs N-terminal with cationic region and a C-reminal hydrophobic region.

It’s a dynamic antifungial mode of affection involving electrostatic interactions with the cells of the membrane . The internalisation is possible and it kills the cell. The mode of killing is not clear nowadays.

Current researches on PAF-26 are made like:

  • Analyzed by live cell imaging
  • Attached a fluorescent tag

(1) Sadler & al. Biochemistry, 2002,41, 48

Antimicrobial peptides-complements (Part three)

Complement system is made about 30 proteins which are circulating in the blood plasma.

These proteins are produced by the liver and my monocytes.

Most of them are inactive. They are cleaved by a protease then converted into an active protease.

In order that serve as a substate of a prior component  or as an enzyme to activate a subsequent component.

So, sequential activation produces an expanding cascada activity.

They provide an effector mechanism to enhance the specific antibody-antigen interactions. Antibodies play the role of “finger” the target, on the contrary, a complement destroys it.

Antimicrobial peptides (Second part)

Antimicrobial peptides

Antimicrobial peptides from saliva

They are in major secretion-submandibular gland:

Sublingual and parotid glands.

Minor salivary glands-lingual, buccal and labials glands.

– Lysozyme and lactotransferrin from both major and minor salivary glands

Salivary lysozyme is able to hydrolyze beta (1-4) bonds between a N-actelmuramic acid and a N-acetylglucosamine in the peptidoglycan layer of the bacterial cell wall.

→ Lysozyme protects us from ever-present danger of bacterial infection.

It is a small enzyme which attacks the protective cell walls go bacteria. It can breaks carbohydrate chains, destroying the structural integrity of the cell wall.

The bacteria burst under their own internal pression (1).

Also, Transferrin-cationic peptides have a great function. They bind iron thus hindering bacterial growth.

→ Lactotransferrin is found in the secondary granules of neutrophils.

The protein is a major iron-binding protein.

In fact, Iron (III) is no soluble, and it is incorporates by transferrin which cross the membrane layer and reducts into iron (II) . Thanks to a proton gradient into an endosome membrane , the pH decreases from 7 to 5,6 and ATP is hydrolyzed into ADP and Pi.  Consequently, Iron (II) is able to be stocked into ferritine.

This protein demonstrates a broad spectrum of properties, including (2) :

  1. Regulation of iron homeostasis
  2. Regulation of cellular growth
  3. Differentiation and protection against cancer development and metastasis.

(1) http://www.rscb.org

(2) sinobiological.com

Antimicrobial peptides (First part)

We can defined antimicrobial peptides as a polypeptide antimicrobial substance.

More than hundreds of these peptides are identified in fungi, insects, humans too and they contained between twelve and fifty amino acids whose the majority are hydrophobic.

Their role is very important. Indeed, they innate defense mechanism.

The classification is known in biology : we can find Beta sheet with S-S bonds between cysteine amino acide, alpha helices, or loop structures.

As mentioned before, the antimicrobial peptides have very important functions:

  • They participate in the innate immune system

  • They protect a host of possible invasive microbial infections

  • Innate immune response to adaptative immune system

These peptides can be found in cells-neutrophils, in body fluids-complement proteins. In body secretion such as tears or saliva. Also, in intestinal mucus layer,…

Antimicrobial peptides broad activity vs bacteria, protozoa, viruses HSV-1 & HSV-2, cytotoxic against some cancer cells.

Pareth cells-terminally differentiated, specialized secretory cells located at the base of the crypts of Lierberkühn in the small intestine. They secrete antimicrobials to regulate micro biome:

They secrete granules containing defensine / cryptdins and lysozyme into the lumen. And they maintain gastro-intestinal barrier. For example, they disfunction in intestinal inflammation: we can see this case in the Crohn’s disease for example.

Immunobioly, 7th ed. Janeway and Travers. 2008

I’m Charlie

We are all ravaged about the murder attempt yesterday over Charly’s Hebdo.

Why these twelve designers of the newspaper are killed? Because they drew, they wrote, because we have our freedom of expression.

This act won’t be tolerated, and today it’s all our country which is injured.

Among these people, there were also policemen, or guest.

Charb,

Cabu,

George Wolinski,

Tignous,

Honoré,

Mustapha Ourrad,

Elsa Cayat,

Frédéric Boisseau,

Michelle Renaud,

Franck Brinsolaro,

Ahmed Merabet

All in our heart.” I’m charlie “

Physical methods used in mineral bio-chemistry

I. Scale of time
In biology, to understand the nature of the metallic centre which contains a transition metal, it is often useful to obtain some informations about electronics states and magnetic states. Properties correlated with the coordination number and the molecular geometry of the metal center. These properties have an influence on the reactions which might happens in this environment. So, electronics ans magnetic phenomenas are the base of a lot spectroscopic techniques.
For kinetics studies, we must choose the appropriate technique.
II. Method using RX
A. RX Diffraction

One thing very important is in RX the wavelength which is about the order of the interatomic system: 1 A. 
This method is crucial for the determination of molecular structure.
For these, on a crystal organized comes an incident beam of RX which is diffracted and go until a screen where we can see diffraction tasks. Each tasks will be appropriate to an atom thanks to a CIF file.

The angular position of the diffracted beams is a function of the geometry about the unit cell
characteristic of the crystalized substance. 
Intensity of the diffracted beam is function of the element nature: more there are electrons, more the intensity increases , also about the position of the atomes in this unit cell.

B. XANES and EXAFS

These two methods are based on the absorption of RX.

-XANES means X Ray absorption near edge structure: informations about the local order: we can identify the metal by excitation of electron towards an empty orbital. Look at the energy level of the beginning of the absorption we can obtain the state oxidation of the molecular ion also information about the electronic structure.
-EXAFS means Extended X ray absorption fine structure and allows the gain of the environment of the compounds and about the coordination number of the metal because the electrons meet the coordinated ligands .
Disadvantages: the distance must be low (4A) and we have an inaccuracy on the nature of coordinated ligands about + or - 1 e-.

III. PRE

This is the same technique of RMN but for paramagnetic metals. RMN is used for diamagnetic metals. The aspect of the signal gives the aspect of the coordination environment of the metal.
We can obtain a factor "g" and we have three situations:
1) x=y=z, we have only one valor of g, the geometry is cubic.
2) x=y but z is different. The symmetry is axial and we have two valors for g
3) the three components are different , the symmetry is rhombic and there are three g.
"g" is very important, allowing to calcul the number of electron :
if g=2 for example , we know that (2S+1=g=2) and s=1/2, so there is one electron alone.

IV) NMR

This is the technique of choice for characterized diamagnetic compounds

V) Mossbauer

This spectroscopy is very known for compounds with iron II. We obtain thanks to the shift the oxidation state of iron.