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Protein bonding(antigens)

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Protein bonding(antigens)

Postby mortonman1 » Tue May 25, 2010 3:16 am

How do two proteins bond together? More specifically, two antigens. As in CD's and MHC proteins in immunology studies. I want to understand how exactly a B cell or T cell bond with the antigen to the virus gp. i understand the general process but i want to know molecular bonding between two polypeptide chains, not two amino acids bonding to form a polypeptide chain. Thanks a lot for any answers
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Postby biobitch » Tue May 25, 2010 4:37 am

There are four levels of structure found in polypeptides and proteins. The primary structure of a polypeptide of protein determines its secondary, tertiary, and quaternary structures

Primary Structure

The primary structure of polypeptides and proteins is the sequence of amino acids in the polypeptide chain with reference to the locations of any disulfide bonds. The primary structure may be thought of as a complete description of all of the covalent bonding in a polypeptide chain or protein.

The most common way to denote a primary structure is to write the amino acid sequence using the standard three-letter abbreviations for the amino acids. For example:

gly-gly-ser-ala

is the primary structure for a polypeptide composed of glycine, glycine, serine, and alanine, in that order, from the N-terminal amino acid (glycine) to the C-terminal amino acid (alanine).

Secondary Structure

Secondary structure is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule. Hydrogen bonding plays an important role in stabilizing these folding patterns. The two main secondary structures are the alpha helix and the anti-parallel beta-pleated sheet. There are other periodic conformations, but the α-helix and β-pleated sheet are the most stable. A single polypeptide or protein may contain multiple secondary structures.

An α-helix is a right-handed or clockwise spiral in which each peptide bond is in the trans conformation and is planar. The amine group of each peptide bond runs generally upward and parallel to the axis of the helix; the carbonyl group points generally downward.

The β-pleated sheet consists of extended polypeptide chains with neighboring chains extending anti-parallel to each other. As with the α-helix, each peptide bond is trans and planar. The amine and carbonyl groups of peptide bonds point toward each other and in the same plane, so hydrogen bonding can occur between adjacent polypeptide chains.

The helix is stabilized by hydrogen bonding between amine and carbonyl groups of the same polypeptide chain. The pleated sheet is stabilized by hydrogen bonds between the amine groups of one chain and the carbonyl groups of an adjacent chain.


Tertiary Structure

The tertiary structure of a polypeptide or protein is the three-dimensional arrangement of the atoms within a single polypeptide chain. For a polypeptide consisting of a single conformational folding pattern (e.g., an alpha helix only), the secondary and tertiary structure may be one and the same. Also, for a protein composed of a single polypeptide molecule, tertiary structure is the highest level of structure that is attained.

Tertiary structure is largely maintained by disulfide bonds. Disulfide bonds are formed between the side chains of cysteine by oxidation of two thiol groups (SH) to form a disulfide bond (S-S), also sometimes called a disulfide bridge.


Quaternary Structure

Quaternary structure is used to describe proteins composed of multiple subunits (multiple polypeptide molecules, each called a 'monomer'). Most proteins with a molecular weight greater than 50,000 consist of two or more noncovalently-linked monomers. The arrangement of the monomers in the three-dimensional protein is the quaternary structure. The most common example used to illustrate quaternary structure is the hemoglobin protein. Hemoglobin's quaternary structure is the package of its monomeric subunits. Hemoglobin is composed of four monomers. There are two α-chains, each with 141 amino acids, and two β-chains, each with 146 amino acids. Because there are two different subunits, hemoglobin exhibits heteroquaternary structure. If all of the monomers in a protein are identical, there is homoquaternary structure.

Hydrophobic interaction is the main stabilizing force for subunits in quaternary structure. When a single monomer folds into a three-dimensional shape to expose its polar side chains to an aqueous environment and to shield its nonpolar side chains, there are still some hydrophobic sections on the exposed surface. Two or more monomers will assemble so that their exposed hydrophobic sections are in contact.

I hope that helps?
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Postby mortonman1 » Tue May 25, 2010 6:17 am

ya that does a little but unfortuantely i knew most of it. i want to know how two proteins bind together. almost like how a glycerol and a fatty acid join through hydrolysis to make fat or whatever. i need to know how two proteins bond, and stay together. Im mainly wondering because in immunology the gycoprotein on T cells(antigen) bind to the pathogen. These two antigens somehow bind then cell mediated response begins? thats really what i need to know. thanks for answers again
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Postby kolean » Tue May 25, 2010 5:07 pm

Antigen-Antibody binding is not covalent. It has to do with chemical noncovalent bonding/binding. Here is a picture that shows the "pocket" of the antibody Fab fragment with an antigen (epitope):
http://www.pnas.org/content/102/14/4984/F3.large.jpg
and a space filling model:
http://www.google.com/imgres?imgurl=htt ... ZvsNcC3jDk
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Postby mortonman1 » Wed May 26, 2010 3:51 am

okay thanks. ill ask my biology teacher how exactly to disect those diagrams. i asked this question because my teacher doesn't know the answer by the way, so you don't think you answered when my teacher could have. thanks!
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Postby oikagri » Wed Jul 14, 2010 6:51 am

can i get d diagrammetic representation of proteins? :D :lol:
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Postby JackBean » Tue Jul 20, 2010 7:01 am

what's diagrammetic? :roll:
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re:

Postby surendran » Thu Jul 22, 2010 4:38 pm

oikagri wrote:can i get d diagrammetic representation of proteins? :D :lol:


yes,you can get the diagramatic representation of proteins.for it,first you should open any bioinformatics tools like ncbi,swiss pdb on the internet and then type your specific protein name and click search.
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Re:

Postby surendran » Thu Jul 22, 2010 4:40 pm

JackBean wrote:what's diagrammetic? :roll:


diagramatic is the structural information of any thing.that structure or image or picture will explain the whole process of the desired job.
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