Peptide and Protein Structure and Function

Peptide and ProteinStructure and FunctionHarliansyah, Ph.DDept. Biochemistry School of Medicine University of YARSI2013

Peptide bondAmino acidC-terminus terminates by a carboxyl groupN-terminus terminates by an amino groupA peptide: Phe-Ser-Glu-Lys (F-S-E-K)From amino acids to protein:2Formation of a peptide bond:Dipeptide = 2 A.ATripeptide = 3 A.AOligopeptide = 20 A.A.Proteins >50 amino acidsAmino acid with free a-amino group is the amino-terminal or N-terminal residueAmino acid with free a-carboxyl group is the carboxyl-terminal or C-terminal residueThree letter code Met-Gly-Glu-Thr-Arg-HisSingle letter code M-G-E-T-R-HEach amino acid residue is called by replacing -ine or -ate with yl = carboxyl - hydroxyl (acyl) glycine glycyl glutamate glutamyl asparagine, glutamine, cysteine asparaginyl, glutaminyl, cysteinyl.

Naming of PeptidesFor naming peptides, the AA suffixes ine (glycine), - an (tryptophan) ate (glutamate) are changed to yl with the exception of C terminal AA.

A tripeptide composed of an N terminal glutamate, a cysteine and a C terminal glycine is called:glutamyl cysteinyl - glycineCharacteristics of Peptide BondsRigidPlanarPartial double bond in characterGenerally exists in transconfigurationBoth _C = O and _NH2 groups of peptide bonds are polarInvolved in hydrogen bond formationPeptides of Physiologic ImportanceGlutamine- a tripeptide composed of 3 AA - gamma glutamyl cysteinyl glycine - wildly distributed in nature - exists in reduced or oxidized states

Functions:a) As a coenzyme for certain enzymes asprostaglandinPGE2 synthaseglycoxylaseb) Prevents the oxidation of sulfhydryl groups of several proteins to disulfide groupsc) In association with glutathione reductase participates in the formation of correct disulfide bonds in several protiensd) In erythrocytes- maintains RBC membrane structure and integrity- protects hemoglobin from getting oxidized by agents such as H2O2e) Involved in the transport of AA in the intestine and kidney tubules via delta glutamyl cycle or Meister cycle

f) Involved in the detoxification process

g) Toxic amounts of peroxidases and free radicals produced in the cells are scavanged by glutathione peroxidase ( a selenium containing enzyme).2. Thyrotropin Releasing Hormone (TRH)- a tripeptide secreted by hypothalamusFunction:Stimulates pituitary gland to release thyrotropic hormone

3. Oxytocin- contains 9 AA (nonapeptide)- hormone secreted by posterior pituitary glandFunction:Causes contraction of the uterus4. Vasopressin (ADH antidiuretic hormone)- also a nonapeptide- produced by posterior pituitary glandFunction:Stimulates kidneys to retain water and thus increases the blood pressure

5. Angiotensins- Angiotensin 1 a decapeptide (10AA) which is converted to angiotensin II (8AA)Function: For the release of aldosterone from adrenal gland6. Methionine Enkephalin- a pentapeptide found in the brain and has opiate like function.Function:It inhibits the sense of a pain.

7. Bradykinin and Kallidin- nona and decapeptides respectively- produced from plasma proteins by snake venom enzymesFunction:Powerful vasodilators8. Peptide Antibiotics- Antibiotics such as Gramicidin, Bacitracin, tyrocidin and Actinomysin peptide in nature

9. Substance P- a decapeptide- acts as neurotransmitter

10. Gastrointestinal Hormones- Gastrin, Secretin & etc.- gastrointestinal peptides serving as hormones

Tertiary structure overall three-dimensional form of a polypeptide chain, which is stabilized by multiple non-covalent interactions between side chains.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.Quaternary structure: The number and relative positions of the polypeptide chains in multisubunit proteins. Not all protein have a quaternary structure.Four Levels of Structure Determine the Shape of Proteins14

C-peptide

Human: Thr-Ser-IleCow: Ala-Ser-ValPig: Thr-Ser-Ile

Chiken: His-Asn-Thr Pro-insulin proteinInsuline

+ C peptideC-peptidePro-insulin is produced in the Pancreatic islet cellsPrimary Structure65/6630/3116Amino acid substitution in proteins from different speciesConservativeSubstitution of an amino acid by another amino acid of similar polarity (Val for Ile in position 10 of insulin)Non conservativeSubstitution involving replacement of an amino acid by another of different polarity (sickle cell anemia, 6th position of hemoglobin replace from a glutamic acid to a valine induce precipitation of hemoglobin in red blood cells)Invariant residuesAmino acid found at the same position in different species(critical for for the sructure or function of the protein)17

Stabilized by hydrogen bonds H- bonds are between CO and NH groups of peptide backboneH-bonds are either intra- or inter- molecular3 types : a-helix, b-sheet and triple-helix

sheet:result from hydrogen bonding, does not involve the side chain of the amino acid19

The a helix: result from hydrogen bonding, does not involve the side chain of the amino acid20TERTIARY STRUCTURER-group interactions result in 3D structures of globular proteinsTypes of interactions : H-, ionic- (salt linkage), hydrophobic- and disulphide- bondHydrophilic R groups on surface while hydrophobic R groups buried inside of moleculeWide variety of 3o structures: since large variation in protein sizes and amino acid sequences21

The role of side chain in the shape of proteinsWhere is water?HydrophobicHydrophilic22

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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

24Protein domains:

Any part of a protein that can fold independently into a compact, stable structure. A domain usually contains between 40 and 350 amino acids.

A domain is the modular unit from which many larger proteins are constructed.

The different domain of protein are often associated with different functions.25

Protein domains Cytochrome b562A single domain protein involved in electron transport in mitochondriaThe NAD-binding domain of the enzyme lactic dehydrogenaseThe variable domain of an immunoglobulin26Classes of protein1 - Structural protein : Keratin, Collagen (give support to cells)2 - Dynamic protein : Hormone, enzyme (for catalytic purpose)

- Based on the structure, protein can be divided to :* Fibrin : Blood clotting * Fibrous : Myosin (from muscle)* Globular : Half sphere form/structure eg. Enzyme- Size : Varied - depending on functions- 1 amino acid = 110 Daltons - Most protein are highly foldedFibrous and Globular Proteins

- 4 different forces stabilize the tertiary structure of globular proteini. Hydrogen bonding between R groups of residues in adjacent loops of the chainii. Ionic attraction between oppositely charged R groupsiii. Hydrophobic interactionsiv. Covalent cross-linkages (via intrachain cystein residues)

Function of proteinsProteins are the most important buffers in the body. 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 factorsHormonesgrowth factors ( insulin or thyroid stimulating hormone)Why?Protein molecules possess basic and acidic groups which act as H+ acceptors or donors respectively if H+ is added or removed.

31Proteins are the most important buffers in the body. They are mainly intracellular and include haemoglobin.

The plasma proteins are buffers but the absolute amount is small compared to intracellular protein.

Protein molecules possess basic and acidic groups which act as H+ acceptors or donors respectively if H+ is added or removed.Many proteins (thousands!) present in blood plasmaProteins contain weakly acidic (glutamate, aspartate) and basic (lysine, arginine, histidine) side chains (or R groups)At neutral pH, only histidine residues (containing imidazole R group with pKa ~ 6.0) in proteins can act as a buffer component Haemoglobin with 38 histidine/tetramer is a good bufferN-terminal groups of proteins (pKa ~ 8.0) can also act as a buffer component32Proteins play crucial roles in almost every biological process. They are responsible in one form or another for a variety of physiological functions including

Enzymatic catalysis Transport and storage

Coordinated motion Mechanical support Immune protection

Generation and transmission of nerve impulses Control of growth and differentiation33Enzyme Catalysis

Transport and storage - small molecules are often carried by proteins in the physiological setting (for example, the protein hemoglobin is responsible for the transport of oxygen to tissues). Many drug molecules are partially bound to serum albumins in the plasma.

3-dimensional structure of hemoglobin. The four subunits are shown in red and yellow, and the heme groups in green.The binding of oxygen is affected by molecules such as carbon monoxide (CO) (for example from tobacco smoking, cars and furnaces).

CO competes with oxygen at the heme binding site. Hemoglobin binding affinity for CO is 200 times greater than its affinity for oxygen, meaning that small amounts of CO dramatically reduces hemoglobin's ability to transport oxygen. When hemoglobin combines with CO, it forms a very bright red compound called carboxyhemoglobin.

When inspired air contains CO levels as low as 0.02%, headache and nausea occur; if the CO concentration is increased to 0.1%, unconsciousness will follow. In heavy smokers, up to 20% of the oxygen-active sites can be blocked by CO.35Coordinated motion - muscle is mostly protein, and muscle contraction is mediated by the sliding motion of two protein filaments, actin and myosin.

Platelet before activationActivated plateletActivated platelet at a later stage than C)Platelet activation is a controlled sequence of actin filament:

SeveringUncappingElongatingCross linking

That creates a dramatic shape change in the platelet36Mechanical support - skin and bone are strengthened by the protein collagen.

Abnormal collagen synthesis or structure causes dysfunction of

cardiovascular organs, bone, skin, joints eyes

Refer to Devlin Clinical correlation 3.4 p12137Immune protection - antibodies are protein structures that are responsible for reacting with specific foreign substances in the body.

38Generation and transmission of nerve impulses -

Some amino acids act as neurotransmitters, which transmit electrical signals from one nerve cell to another. In addition, receptors for neurotransmitters, drugs, etc. are protein in nature.

An example of this is the acetylcholine receptor, which is a protein structure that is embedded in postsynaptic neurons.

GABA: gamma Amino butyric acidSynthesised from glutamate

GABA acts at inhibitory synapses in the brain. GABA acts by binding to specific receptors in the plasma membrane of both pre- and postsynaptic neurons. Neurotransmetter

39Control of growth and differentiation -

proteins can be critical to the control of growth, cell differentiation and expression of DNA.

For example, repressor proteins may bind to specific segments of DNA, preventing expression and thus the formation of the product of that DNA segment.

Also, many hormones and growth factors that regulate cell function, such as insulin or thyroid stimulating hormone are proteins.

Insuline40

Membrane transport proteins41

Shape and function43

DiseaseExemple:Neurodegenerative diseasesDisease and protein folding:4445

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