SMILES

Bismillahirahmanirahim....

Alhamdulillah..today we learn about SMILES...dont be surprised with the title..we didnt learn how to smile but it is Simplified Molecular Input Line Entry System (SMILES). It is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. We are using ACD Chemsketch to complete our assignment.The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. There are four pages of molecular structures that we need to sketch. Let us take a look our work.

 < SLIDE 1 >

< SLIDE 2 > 

<SLIDE 3>

<SLIDE 4>

At last we SMILE after completing this assignment..=)....

For more information about SMILES,do click here..

http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system">	http://www.acdlabs.com/download/chemsk.html
http://jmol.sourceforge.net/>	http://www.daylight.com/dayhtml/smiles/smiles-intro.html

Protein Data Bank (PDB)

 Assalamualaikum...

Our assignment for today's lecture is about drawing protein structure.For your information, there are four protein structure namely primary,secondary,tertiary and quatenary structure. We are given task to draw these structure:

Clp P	Deg P
Thermolysin	Trypsin

We can get this software from http://www.rcsb.org ..Let's check it out...:)



1. ClpP

ClpP is ATP-dependent Clp Protease Proteolytic subunits is an enzyme that in humans is encoded by the ClpP genes.It is found in mitochondria and is widely distributed bacteria species.In several bacteria ,such as E.coli,protein tagged with the SsrA peptide(ANDENYALAA) encoded by tMRNA digested by Clp Protease.The protein encoded by this gene belongs to the peptide family S14 and hydrolyzes protein into small peptide in the presence of ATP and magnesium.The protein is transported into mitochondrial matrix and associated with inner mitochondria membrane.

2. DegP

The DegP (HtrA) protein, essential for the survival of Escherichia coli cells at elevated temperatures with homologues found in almost all organisms uniquely has both functions. Here we report a mechanism for DegP to activate both functions via formation of large cage-like 12- and 24-mers after binding to substrate proteins. Cryo-electron microscopic and biochemical studies revealed that both oligomers are consistently assembled by blocks of DegP trimers, via pairwise PDZ1PDZ2 interactions between neighboring trimers. Such interactions simultaneously eliminate the inhibitory effects of the PDZ2 domain. Additionally, both DegP oligomers were also observed in extracts of E. coli cells, strongly implicating their physiological importance.

 

3. Thermolysin

Thermolysin is a proteolytic enzyme obtained from the bacterium Bacillus thermoproteolyticus, which hydrolyses the N-terminal amide bonds of hydrophobic amino acid residues in proteins. It is used in studies of protein structure. It has a molecular weight of about 37,500 and contains zinc and calcium in its active configuration.

4. Trypsin

Trypsin is part of the digestive system and degrades proteins, making it an enzyme known as a protease. It is initially formed as a larger, inactive molecule in the pancreas and is transported to the small intestine, where it is activated to digest food molecules. This protease is also a regulator of many other digestive proteases. A lack of its production in the pancreas is a component of the disorder cystic fibrosis.