Protein structure and function

BY SAKSHI AND RISHU MITTAL

DEFINATION OF PROTEIN
Proteins are large complex biological molecules which play many diverse roles in all organisms. Proteins make up a high percentage of the structure of living things. Every organism contains thousands of different kinds of proteins, each with its own unique three dimensional structure, which enables it to carry out a specific functions. Two amino acids (left) can combine to form a dipeptide by a condensation reaction between carboxyl group of one and the amino group of the other. He resulting bond linking the two amino acids is called a peptide bond.

From amino acids to protein:

N-terminus terminates by an amino group Peptide bond

Amino acid

C-terminus terminates by a carboxyl group

A peptide: Phe-Ser-Glu-Lys (F-S-E-K)

The Shape of proteins:

Occurs Spontaneously Native conformation

determined by different Levels of structure

Four Levels of Structure Determine the Shape of Proteins

Primary structure
The linear arrangement (sequence) of amino acids and the location of covalent (mostly disulfide) bonds within a polypeptide chain. Determined by the genetic code.

Secondary structure

local folding of a polypeptide chain into regular structures including the a helix, b sheet, and U-shaped turns and loops.

Tertiary structure
overall three-dimensional form of a polypeptide chain, which is stabilized by multiple non-covalent interactions between side chains.

Quaternary structure:
The number and relative positions of the polypeptide chains in multisubunit proteins. Not all protein have a quaternary structure.

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

Primary Structure of a protein:

determined by the nucleotide sequence of its gene

Bovine Insulin: the first sequenced protein

In 1953, Frederick Sanger determined the amino acid sequence of insulin, a protein hormone .

This work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence.
it demonstrated that insulin consists only of amino acids linked by peptide bonds between amino and -carboxyl groups. the complete amino acid sequences of more than 100,000 proteins are now known. Each protein has a unique, precisely defined amino acid sequence.

Primary Structure
C-peptide

Pro-insulin protein

Pro-insulin is produced in the Pancreatic islet cells

30/31

65/66 Human: Thr-Ser-Ile Cow: Ala-Ser-Val Pig: Thr-Ser-Ile Chiken: His-Asn-Thr

Insuline

C-peptide
+ C peptide

SECONDARY STRUCTURE
Stabilized by hydrogen bonds H- bonds are between CO and NH groups of peptide backbone H-bonds are either intra- or intermolecular 3 types : a-helix, b-sheet and triple-helix

Secondary structures:
a Helix: a helix conformation was discovered 50 years ago in a keratine abundant in hair nails, and horns b Sheet: discovered within a year of the discovery of a helix.Found in protein fibroin the major constituant of silk

The a helix:
result from hydrogen bonding, does not involve the side chain of the amino acid

bsheet:
result from hydrogen bonding, does not involve the side chain of the amino acid

Two type of b Sheet structures

An anti paralellel b sheet

A paralellel b sheet

TRIPLE HELIX
Limited to tropocollagen molecule Sequence motif of (Gly-X-Pro/Hypro)n3 left-handed helices wound together to give a right-handed superhelix Stable superhelix : glycines located on the central axis (small R group) of triple helix One interchain H-bond for each triplet of aas between NH of Gly and CO of X (or Proline) in the adjacent chain

Triple helix of Collagen

Tertiary structure: the 3D shape

The tertiary structure refers to the overall three dimensional shape of a polypeptide chain. Proteins are classified into two main groups on the basis of their tertiary structure: Fibrous Globular proteins. The precise 3D shape of the protein determines its function: every coil and twist, bump and indentation is important. The shape is maintained by various bonds including ionic bonds, hydrogen bonds, disulphide bonds and hydrophobic interactions (between non-polar groups in the protein). The tertiary structure of a protein depends on its primary structure.

FIBROUS PROTEINS
Fibrous proteins consist of parallel polypeptide chains cross-linked at intervals to form long fibres or sheets. Fibrous proteins are usually insoluble in water and physically tough, which suits them for their mainly structural functions. Fibrous proteins include collagen (a major constituent of tendons and bone) and keratin (the main component of hair).

Globular proteins
Globular proteins have usually a spherical shape. Many are folded so that their hydrophobic groups are on the inside of the molecule and the hydrophilic group face outwards, making these proteins soluble in water. Globular proteins include enzymes, antibodies and hormones (hemoglobin transport of oxygen and carbon dioxide; tubulin makes up microtubules

Similarly:
The tertiary structure for myoglobin is fairly well understood. Myoglobin has an alpha helix which then can be viewed as being enclosed in this blue sheath, the sheath doesn't exist but we can draw it that way. That helix folds back upon itself into what's referred to as the tertiary structure of myoglobin. Bonds between the side groups of the amino acid residues are responsible for holding together the tertiary structure of this protein.

Quaternery structure:
If protein is formed as a complex of more than one protein chain, the complete structure is designed as quaternery structure:

Generally formed by non-covalent interactions between subunits

Either as homo- or hetero-multimers

QUATERNARY STRUCTURE: ADVANTAGES

Oligomers (multimers) are more stable than dissociated subunits
They prolong life of protein in vivo

Active sites can be formed by residues from adjacent subunits/chains

A subunit may not constitute a complete active site

Error of synthesis is greater for longer polypeptide chains Subunit interactions : cooperativity/ allosteric effects

What forces determine the structure?

Primary structure - determined by covalent bonds Secondary, Tertiary, Quaternary structures all determined by weak forces
Weak forces - H-bonds, ionic interactions, van der Waals interactions, hydrophobic interactions

How protein structures are determined?

The majority of protein structures known to date have been solved with the experimental technique of X-ray crystallography, which typically provides data of high resolution but provides no timedependent information on the protein's conformational flexibility.

NMR (nuclear magnetic resonance spectroscopy), which provides somewhat lower-resolution data in general and is limited to relatively small proteins, but can provide time-dependent information about the motion of a protein in solution. More is known about the tertiary structural features of soluble globular proteins than about membrane proteins because the latter class is extremely difficult to study using these methods.

An X-ray diffraction image for the protein myoglobin.

The first protein crystal structure was of sperm whale myoglobin, as determined by Max Perutz and Sir John Cowdery Kendrew in 1958, which led to a Nobel Prize in Chemistry. The X-ray diffraction analysis of myoglobin was originally motivated by the observation of myoglobin crystals in dried pools of blood on the decks of whaling ships.

NMR is a field of structural biology, that applies nuclear magnetic resonance spectroscopy to investigating proteins
The field was pioneered by among others, Kurt Wthrich, who won the Nobel prize in 2002,

Pacific Northwest National Laboratory's high magnetic field (800 MHz) NMR spectrometer being loaded with a sample.

The NMR sample is prepared in a thin walled glass tube.

Protein NMR is performed on aqueous samples of highly purified protein. Sample consist of between 300 and 600 microlitres with a protein concentration in the range 0.1 3 millimoles. The source of the protein can be either natural or produced in an expression system using recombinant DNA techniques through genetic engineering.

Function of proteins
Enzymatic catalysis Transport and storage (the protein hemoglobin, albumins) Coordinated motion (actin and myosin). Mechanical support (collagen). Immune protection (antibodies) Generation and transmission of nerve impulses - some amino acids act as neurotransmitters, receptors for neurotransmitters, drugs, etc. are protein in nature. (the acetylcholine receptor), Control of growth and differentiation transcription factors Hormones growth factors ( insulin or thyroid stimulating hormone)

Proteins are the most important buffers in the body.

Why?
(a) Protein molecules possess basic and acidic groups which act as H+ acceptors or donors respectively if H+ is added or removed.