Protein Structure

Prasetyo adi, drg, MS.

Why Studying Proteins?

They perform many vital functions : Catalysis of reactions enzymes Structural support collagen, keratin Transport hemoglobin, transferrin Movement actin, myosin Hormones insulin, growth hormone, etc. Storage glycogen, ferritin Protection antibodies (immunoglobulin) Transmission of signals Regulation control the expression of genes

Whats Protein?
Proteins are polymers of amino acids. Constructed from 20 different amino acids that are encoded in the DNA of the genome Protein can divide into 2 major types : - Fibrous protein insoluble in water, used mainly for structural purposes. Ex. keratin - Globular protein more or less soluble in water, used mainly for nonstructural purposes Ex. globulin

Overview of protein structure and function

Hierarchical Structure of Proteins

Protein is constructed by the polymerization of 20 different amino acids A protein chain folds into a unique shape that is stabilized by noncovalent interactions between regions in the linear sequence of amino acids. Only when a protein is in its correct threedimensional structure (conformation ), able to function efficiently. A key concept in understanding how proteins work is : protein function is derived from threedimensional structure, and three-dimensional structure is specified by amino acid sequence.

Structure of Amino Acids

Carbonyl

Carbonyl groups >C=O Hydroxyl groups -OH Amine groups -NH2 Alkyl/aryl groups or others -R

H R C NH2 C

OH

Amine

Hydroxyl

Characteristic of AA
Amphoteric can act either as an acid or base Zwitterions have a positive charge on one atom and a negative charge on another. Not only in H2O, but also in solid form.

AA is a (+) ion at low pH and a () ion at high pH Isoelectric point : pH at which all the molecules are in the zwitterionic form.

Buffer can neutralizes both acid and base All solid form protein has high boiling point. Ex : Glycine 262C

Physical and chemical properties

C=O, -OH, -NH2 groups polar -R/-Aryl groups polar/ non polar AA is a polar compound Soluble in H2O but insoluble in non polar and organic solvent (ether and benzene) A moderately weak acid and weak base

Classification of amino acids:

1.Essential / non essential Based on the synthesis by body Synthesis reaction : transamination a reaction catalyzed by enzymes in which an amino group of an amino acid is transferred into a-ketoglutaric acid. The pathways for the biosynthesis are diverse, common feature : C skeleton come from intermediate of glycolysis, pentosa phosphat pathway or citric acid cycle.

Essential amino acids:

AA that must be supplied from the diet.

Val, Trp, leu, Ile, lys, phe, Met, His

The need of each individual varied Deficiency of one AA negative nitrogen balance Phenilketonuria (lack of phenilhydroxilase: no tyr produced effect : accumulation of phenilpyruvic acid mental retardation.

Classification of amino acids:

2. R GROUPS NON POLAR / POLAR ACIDIC / BASIC

NON POLAR

GLYCINE
ALANINE

ISOLEUSINE
VALINE

PROLINE PHENYLALANINE LEUCINE METHIONINE SERINE CYSTEINE TIROSINE

POLAR / NETRAL

ASPARAGINE GLUTAMINE

THREONINE

TRYPTOPHAN

ACIDIC BASIC

GLUTAMIC ACID, ASPARTIC ACID LYSINE, ARGININE, HISTIDINE

Classification and characteristics of AA

20 AA are classified according to the polarities of the side chain (R groups) Protein folds to their native conformation in response to the tendency to remove their hydrophobic side chain from contact to water and to solvate the hydrophilic side chain. There are 3 groups AA : 1. with nonpolar R groups (G,A,V,L,I,M,P,F,W) 2. with uncharged polar R groups (S,T,N,Q,Y,C) 3. with charged polar R groups (K,R,H,D,E)

20 AA commonly found in proteins

Nonpolar R groups
Gly, Ala, Val, Leu, Ile,

Nonpolar R groups

Met, Pro, Phe, trp

Polar but neutral/uncharged R groups

Ser, Thr, Asn, Glu, Tyr, Cys.

Polar and basic R groups

Lys, Arg, his

Polar and acidic R groups

Asp, Glu

The hierarchial structure of protein

1.Primary structure : linier amino acid sequence 2.Secondary structure : helices, sheet and turns 3.Tertiary structure : side chain packing in the 3-D 4.Quarternary structure : association of subunits

Primary structure of a protein

The primary structure of a protein is simply the linear arrangement, or sequence, of the amino acid residues that compose it. A short chain of amino acids is linked by peptide bonds and having a defined sequence is called a peptide; longer chains are referred to as polypeptides. The size of a protein or a polypeptide is reported as its mass in daltons (a dalton is 1 atomic mass unit) or as its molecular weight (MW).

Peptide bond
Peptide bond joins amino acids AA are linked by peptide bonds to form polypeptide chains. Bond at both ends

The modified chain AA has different biological activity as the original chain Sickle cell anemia 4 5 6 7 8 9

Normal Hb -Thr-Pro-Glu-Glu-Lys-Al Sickle cell Hb -Thr-Pro-Val-Glu-Lys-Al-

Protein structure - bonding

5 bonds or forces determine structure Peptide bond Hydrogen bond Disulfide bond Ionic bond Hydrophobic force

Secondary structure
The second level in the hierarchy of protein structure consists of the various spatial arrangements resulting from the folding of localized parts of a polypeptide chain. When stabilizing hydrogen bonds form between certain residues, parts of the backbone fold into one or more well-defined periodic structures: the alpha (a) helix, the beta (b) sheet, or a short U-shaped turn.

The secondary structure

a helix
the shape is maintained by intramolecular H bonds between backbone C=O and HN groups. Ex. a keratin

b sheet and turn the shape is maintained by intermolecular H bonds between C=O and N-H groups in backbone. Polypeptide run parallel or antiparallel R groups directed above and below backbone Ex. Silk fibroin a b pleated sheet

Tertiary structure
Three dimensional folding and coiling of polypeptide into globular 3-D structure Secondary structures fold and pack together to form tertiary

structure
Usually globular shape Caused by additional chemical interactions among side chains Disulfide bonds Ionic bonds Hydrogen bonds Hydrophobic force

Disulfide bond
Covalent bond between sulfur atoms on two cysteine amino acids

ionic bond
Ions on R groups form salt bridges through ionic bonds

hydrophobic forces
Close attraction of non-

polar R groups through

dispersion forces Very weak but collective interactions over large area stabilise structure Repel polar and charged molecules/particles

Protein stability
Peptide bonds Disulfide bonds Hydrogen bonds Hydrophobic forces Salt bridge/ Electrostatic forces

During the denaturation process of protein,, H bond, hydrophobic and electrostratic forces break but not peptide bond and disulfide bond.

Quaternary structure
The polypeptide subunits associate in a geometrically specific manner Arrangement of multiple tertiary structures into single functional complex Usually the functional unit of a protein, especially for enzymes

hemoglobin
Structure: tetramer

Protein Structure

Protein folding
Protein spontaneously fold into their native conformations under physiological conditions. Proteins primary structure dictates its three dimentional structure Cell has error-checking processes that eliminate incorrectly synthesized or folded proteins. Incorrectly folded proteins usually lack biological activity and, in some cases, may be associated with disease. Protein misfolding is suppressed by two distinct mechanisms : - cells have systems that reduce the chances for misfolded proteins to form. - any misfolded proteins are degraded by a specialized cellular garbage-disposal system.

Protein folding
Folding of proteins in vivo is promoted by Chaperones Chaperones are located in every cellular compartment, bind a wide range of proteins, and function in the general protein-folding mechanism of cells. Two general families of chaperones are : Molecular chaperones, which bind and stabilize unfolded or partly folded proteins preventing proteins from aggregating and being degraded Chaperonins, directly facilitate the folding of proteins

Protein denaturation Any physical or chemical agent that destroys the stabilizing protein structure by altering the balance of the weak nonbonding forces that maintain the native conformation.

Condition/agents of protein denaturation

1. high Temperature
Heat cleaves H bond, destroys a-helices structure, changes the optical rotation, viscosity and UV absorbtion. ex. Collagen-triple helix dissapear random coil conformation (gelatin)

2. pH variation
Affect the salt bridge and H bond. Alter ionization states of AA side chainchanges protein charge distribution.

3. detergents
interfering hydrophobic interactions.

4. chemical compound
Break H bonds and cause the unfolding of globular protein. Ex. Urea or guanidine chloride Reducing agent breaks S-S- disulfide bond. Ex. beta-mercaptoethanol

5. high concentration of water-soluble organic substances.

Interfere the hydrophobic forces Ex. Aliphatic alcohol