M.Prasad NaiduMSc Medical Biochemistry,

Ph.D.Research Scholar

Our life is maintained by molecular Our life is maintained by molecular network systemsnetwork systems

Molecular network system in a cell

(From ExPASy Biochemical Pathways; http://www.expasy.org/cgi-bin/show_thumbnails.pl?2)

Proteins play key roles in a living Proteins play key roles in a living systemsystemThree examples of protein

functionsCatalysis:

Almost all chemical reactions in a living cell are catalyzed by protein enzymes.

Transport:Some proteins transports various substances, such as oxygen, ions, and so on.

Information transfer:For example, hormones.

Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones

Haemoglobin carries oxygen

Insulin controls the amount of sugar in the blood

Biology/Chemistry of Protein Structure

Primary

Secondary

Tertiary

Quaternary

Assembly

Folding

Packing

InteractionS T

R U

C T

U R

E P R O C E S S

Primary structure1.Primary structure denotes the number and sequence of aminoacids in the peptide chain and location of disulfide bonds,if present

2.The higher levels of organisation are decided by the primary structure.

3.The primary structure is maintained by the covalent peptide bond.

4.peptide bonds are not broken down by conditions that denature proteins,such as heating or high concentrations of urea.

5.Peptide bonds need prolonged exposure to a strong acid or base at elevated temperatures to hydralyse non enzymatically.

CHARECTERSTICS OF PEPTIDE BOND1.Partial double bond.It is rigid and planar.so

there is no freedom of rotation.2.The C-N bond is trans in nature because of

steric interference of the R-groups when in the cis position.

3.the distance is 1.32A*which is midway between single bond(1.49A*) and double bond (1.27 A*)

4.The side chains are free to rotate on either side of peptide bond.

5.The angles of rotation known as “Ramchandran angles”,determines the spatial orientation of peptide chain.

NUMBERING OF AMINOACIDSPSEUDOPEPTIDE;Eg: Glutathione (gamma glutamyl-cysteinyl-

glycine)FORMATION OF PEPTIDE BOND;Nameing of aminoacids in a

polypeptidechain;By changing the suffix” in” to “yl”Eg; NH2-Gly-Ala-Val-COOH glycyl-alanyl-valine

BRANCHED AND CIRCULAR PROTEINSGenerally ,primary structure is linear.Branched proteins are produced by

interchain disulfide bondEg:insulin

Circular protein: Eg; Gramicidin.

Clinical significance:A single aminoacid change (mutation) in the

linear sequence may have profound biological effects on the function.

Eg:Sickle cell anemia:HbS is produced by substitution of Valine in

place of Glutamic acid in the 6th position of beta chain of HbA.

Secondary structureSecondary structure denotes the

configurational relationship between residues which are about 3-4 aminoacids apart in the linear sequence.

It is maintained by Hydrogen bonds, Electrostatic bonds, Hydrophobic bonds, Van der waals forces.

1.Alpha helix1.Alpha helix is a spiral structure.Polypeptide

bonds form the back-bone core and the side chains of aminoacids extend outward to avoid interfering sterically with each other.

2.It is the most common and stable conformation for a polypeptide chain.

abundent in hemoglobin and myoglobin ---- globular and flexible molecule.

absent in chymotrypsin.

3.Present in keratins,fibrous proteins ------ major component of hair and skin--- rigidity is determined by number of disulfide bonds in it.

4.The structure is stabilized by hydrogen bonds between NH and C=O groups of the main chain.

5.Each turn is formed by3.6 residues.the distance between each aminoacid residue is 1.5 A*.

6.It is generally right handed because aminoacids found in proteins are of L-variety,which exclude left handedness.

Aminoacids that disrupts an alpha-helix;1.Proline and Hydroxy proline will not allow

the formation of alpha-helix because a) its secondary aminogroup is not

geometrically copatible with the right handed spiral of alpha-helix.

b)it inserts a kink in the chain,which interfers with the smooth,helical structure.

2.Large number of charged aminoacids also disrupt by forming ionic bonds or by electrostatically repelling each other.

3.aminoacids with bulky side chains ,such as tryptophan,valine,isoleucine,that branch at beta carbon,if present in large numbers---- also interferes.

2.Beta pleated sheet:1.the surfaces of beta-sheets appear pleated”

----beta pleated sheets.2.it is formed by the polypeptide chain folding

back on itself.3.The polypeptide chains are fully extended.The

distance between adjacent aminoacids is 3.5 A*.4.It is stabilized by hydrogen bonds between

NH and C=O groups of neighboring polypeptide segments.

5.Strands run in same direction regard to the amino and carboxy terminal ends of poly peptide chain--------------- parallel.

Eg; Flavodoxin

6.Strands run in opposite direction --------------- antiparallel

Eg; Silk fibroin7.Both are present in Carbonic anhydrase.

3.Beta bends(reverse turns,Beta-turns):1. are formed by the abrupt U-turn folding of

chain.Intrachain disulfide bridges stabilize these bends.

2.it reverse the direction of a polypeptide chain to form a copact,globular shape.

3.they are usually present on the surface of protein molecules.

4. it usually composed of 4 aminoacids,among one is Proline -----causes kink”Glycine ----smallest

4.Non repetitive secondary structure:

1.small part of polypeptide chain forms loop or coil.

2. it is less regular structure than alpha helix and beta pleated sheets.

5.SUPER SECONDARY STRUCTURE(MOTIFS):

Produced by packing side chains from adjascent secondary structural elements close to each other.

Eg; Zinc finger motif– common .found in transcription factors.

COLLAGEN;It is a triple helix.Formed by mainlyProline – kinks because of its ring structureGlycine- fits in to the restricted spaces where

the three chains of the helix come together.

3.TERTIARY STRUCTURE1.Tertiary structure denotes three

dimensional structure of whole protein.2.It defines steric relationship of aminoacids

which are far apart from each other in linear sequence,but are close in three-dimensional aspect.

3.It is thermodynamically most stable.4.it refers to folding of domains and to the

final arrangement of domains in the polypeptide.

4. It is maintained by Hydrogen bonds, Electrostatic bonds, Hydrophobic bonds, Van der waals forces. 1.DOMAINS;1.These are fundamental functional and three

dimensional structural units of polypeptides.2.The core of domain is built from combinations

of super secondary structural elements (motifs).5.Domain is a compact globular unit of

protein.These are connected with relatively flexible areas of protein.

Eg; Phenyl alanine hydroxylase enzyme contains 3 domains,one regulatory,one catalytic and one protein-protein interaction domains.

2.Protein folding:1.Interactions between the side chains of

aminoacids determine how a long polypeptide chain folds into intricate three-dimensional shape of the functionalprotein.

2.interactions involving hydrogen bonds,hydrophobic bonds and disulfide bonds all exert an influence on the folding process.

3.ROLE OF CHAPERONS IN PROTEIN FOLDING;

1.CHAPERONES” are required for proper folding of many species of proteins.

2.chaperones-also known as heat shock”proteins- interact with the polypeptide at various stages during the folding process.

4.QUATERNARY STRUCTURE1.It denotes polypeptide subunits aggregate

to form one functional unit. . 2.It is maintained by Hydrogen bonds, Electrostatic bonds, Hydrophobic bonds, Van der waals forces.

3.Depending on the number of polypeptide chains,protein is termed as

1.monomer, 2.dimer, Eg;creatine kinase 3.tetramer. Eg;1.Hemoglobin, 2. Immunoglobulin.

PROTEIN MISFOLDING1.protein folding is trail and error process

that can sometimes result in improperly folded molecules.

2.misfolded proteins are usually tagged and degraded with in the cell.

3.if they accumulate causes diseases.Eg;1.Amyloidoses:

Seen in Alzeimers disease;It is a neuro degenerative disease

charecterised mainly by cognitive impairment.

B.PRION DISEASE;1.PRION PROTEIN IS A CAUSATIVE of

transmissible spongiform encephalopathies,Creutzfeldt-jakob disease in humans,Scrapie in sheep,Bovine spongiform encephalopathy in cattle.

SummarySummaryProteins are key players in our living systems.Proteins are polymers consisting of 20 kinds of

amino acids.Each protein folds into a unique three-dimensional

structure defined by its amino acid sequence.Protein structure has a hierarchical nature.Protein structure is closely related to its function.Protein structure prediction is a grand challenge

of computational biology.