proteins

Proteins

Peptides with >1000 amino acid residues

• most proteins are <2000 amino acid residues

Prosthetic groups

Peptides containing non amino acid components

6 classes of proteins with their prosthetic groups

1. Lipoproteins - lipids

2. Glycoproteins - carbohydrates

3. Phosphoproteins - phosphates

4. Hemoproteins - heme

5. Flavoproteins - flavin nucleotides

6. Metalloproteins - iron, zinc, calcium, molybdenum, copper

What does protein research involve

1. Protein purification

2. Protein analysis

• protein concentration, protein activity, amino acid sequence

Why is protein sequencing valuable information

Gives us info about

• strcuture of proteins, activity and mechanism of action

What are protein sequences determined by

1. Inferring from DNA sequences

2. Breaking down pure protein into small oligopeptide units small enough to be solved and then overlapping small oligopeptide sequences

Homologs

Alignments of closely related protein sequences

• can be orthologs (proteins shared between species of common descent) or paralogs (products of duplicated genes in a species)

Protein sequence data bases

Sequences of proteins are stored in databases

How can we determine homology

Protein sequences are highly conserved in evolution and we can compare them to determine homology, these data can be used to create phylogenetic trees which can be used to infer protein functions

4 levels of protein strcuture

1. Primary - sequence of amino acid residues

2. Secondary - arrangement of backbone atoms of the peptide

3. Tertiary - 3D strcuture of all atoms in a peptide (singular protein)

4. Quaternary - spatial arrangement of. All the peptide subunits (multiple proteins)

What level of protein strcuture has a specific peptide bond

Secondary, its peptide bond has partial double bond characters

• it doesnt freeely rotate and the atoms in the bond are all in the same plane

• Has either trans or cis conformation

Is cis or trans configurations more stable

Trans conformation is more energetically favourable because of steric interference of the side chains (side chains are separated and wont bump into each other)

Is cis or trans configurations more stable

Trans conformation is more energetically favourable because of steric interference of the side chains (side chains are separated and wont bump into each other)

In linked peptide bonds, which bonds can rotate

Alpha carbon - nitrogen bond and the alpha carbon to the carbon bond

• torsion angles of these bonds describe conformation of the polypeptide backbone

When are torsion angles pairs energetically impossible

When R groups are closer than their van der waal distance (overlap of electron orbitals)

• also known as steric hindrance

Ramachandran diagram

Diagrams showing the possibility of different combinations of theta (O) and phi (Y) for amino acid residues based on steric interactions

How to interpret the ramachandran diagram

• white area - forbidden combination

• Blue area - achievable for all amino acids except for Gly, Pro, Val, Ile

• Green area - achievable for all amino acids except for Gly and Pro

How does glycine have strong effects on secondary structures

• only has a H as an R group so which has high conformational entropy and flexibility, favours random coils or sharp turns instead

• Makes protein backbone more ‘floppy’ and doesnt really fold into helices or sheets

How does proline have a strong effect on secondary structure

Has side chains that loop back n bonds to its backbone nitrogen → forms rigid 5 member pyrrolidine ring (cyclic secondary amine structure)

• cant donate a hydrogen bond. To stabilize regular helical or sheet networks bc nitrogen lacks attatched hydrogen once bonded in a chain

• Cyclic pyrrolidine ring locks backbone phi torsion angle, limiting rotational freedom and it becomes too rigid to fit into standard alpha helices or beta strands

Alpha helices

• right handed helical coils

• has 3.6 residues per turn with 0.54nm pitch (5.4A)

• Usually 3 turns long

Structure of alpha helices

• Strong H bond between carbonyl oxygen of one residue and then N-H hydrogen four residues later

• atoms at the core of the helix are within van der waals contact

In alpha helices when are R groups residues considered close in proximity

When 3-4 residues apart which then dictates how strong it destabilizes or stabilizes to stay in the alpha helix configuration

4 types of potential Destabilizing interactions

1. Proline residues because they can’t adopt correct torsional angles due to cyclic strcuture

2. Glycine residues because theyre too flexible

3. When theres 2 adjacent bulky R groups (causes steric crowding)

4. When theres 2 similarly charged R groups due to ionic repulsion

• thus is usually not found in alpha helices

When do stabilizing interactions occur in alpha helix

When it has 2 adjacent, oppositely charged R groups due to ionic attractions

Beta sheets

Sheets of H bonded polypeptide chains

• can occur anti parallel or parallel configurations (anti parallel are more stable)

• has pleated sheets to maximize H bonding stabilization

Beta bends

Are turning points within a beta sheet that causes abrupt changes in direction of the polypeptide backbone

• are a result from strong H bonds between carbonyl oxygen of. One residue and the N-H hydrogen 3 residues later

What is residue 2 in beta sheets in type 1 and type 2

Proline in both

What is residue 3 in type 2 beta sheets

Glycine

Fibrous proteins

Structures had stiff, elongated, fibrous regions.

• play structural role in organisims

• Made by cells and then extruded into the extracellular matrix

Globular proteins

Structure have compact, highly folded globular regions

What protein is alpha keratin

Fibrous protein

• has right handed alpha helical structure, 2 right handed alpha helices twist around each other to form a left handed coiled coil

• Rich in Cys, fibers cross link using disulfide bonds

Structure of keratin

1. Sequence has 7 residue pseudorepeat where every first and fourth amino acid residue are hydrophobic → creates hydrophobic strip on the surface of the alpha helix

2. 2 helices coil to shield the hydrophobic strip in aqueous cellular environments

Quaternary strcuture of keratin fibers

• has higher levels of quaternary structure

• The first is a left handed coiled coil

alpha Keratin

Tough insoluable protein with varying hardness and flexibility

• found in skin, hair, nails and horns

• Main part of the epidermis

Dimer

2 alpha helix chains

Protofilament

N- and C- termini of a coiled coil interact to form along fiber (protofilament)

Protofibril

2 protofilaments

Microfibril

4 protofilbrils

Macrofibrils / intermediate filament

Formed through the association of microfibrils

What is the rigidity of alpha keratin fibers affected by

Degrees of disulphide cross linking

Why do we need sulphur in our diets

Because of all the cysteine present in keratin

What are hair and nails made of

Packed dead cells of alpha keratin

what makes up 25% o the protein in the human body

Collagen

Collagen

Strong, insoluable, fibrous protein with high tensile strength

• Its the stress bearing component of bone, cartilage, tendon, and the fibrous matrices of skin and blood vessels (ties things together)

Structure of collagen

Has left handed helical (collagen helix) secondary structure with around 3 residues per turn, the three helices twist around each other to form a right handed super helical structure (triple helix)

What are the sequence of the three residue pseudorepeat in collagen

Gly - x - y

• X is usually proline

• Y is a non standard amino acid

  • 4-hydroxyproline (hyp)

  • 3-hydroxyproline

  • 5-hydroxylysine (hyl)

What prevents the formation of alpha helix and beta sheets in collagen

High amounts of proline

Interior of collagens triple helix

• Packed tight with atoms

• Only Gly projects R groups into the interior

• N-H hydrogen of Gly makes strong H bond with the carbonyl oxygen of the proline residue in neighbouring collagen polypeptide chains

Assembly of collagen molecule

Can be staggered arrays where molecules are covalently crosslinked using all the -OH groups on the modified R groups

• creates rigid rope like strcuture

Scurvy

Disease resulting from malfunctioning collagen

• deficiency in vitamin C in the diet resulting in failure of prolyl hydroxyl ash to make 4-hydroyproline (hyp)

• Results in skin lesions, fragile blood vessels, poor wound healing, teeth fall out and death from maternal haemorrhaging

Why do we call the British limeys

Cause of scurvy - they had a poor diet that didnt have a lot Of vitamin C (humans cant make vitamin C)

Lathyrism

Disease from malfunctioning of collagen

• Eating the toxin beta-aminopropionitrile (from specific peas) results in failure of lysyl oxidase to covalently cross link collagen molecules

• Results in abnormal bones, joints and large blood vessels

Osteogenesis imperfecta (brittle bone disease)

Inherited disease causing malfunction of collagen

• genetic mutation that changes primary sequence of type 1 collagen resulting in structural distortions in the collagen triple helix structure

• Severity varies with nature and mutation position

Ehlers danlos syndromes

Inherited diseases causing malfunction of collagen

• Collection of collagen disorders caused by collagen deficiencies or abnormal activity of collagen processing enzymes

• Results in hyper extensible joints and skin