Protein Structure and Function: The 3D Structure of Proteins (The Living Cell)

• Carrier functions

• Metabolic functions

• Form parts of the Cellular machinery

• Make up structural scaffold

• Organelle and Cell communication

Yes

+ The basic building blocks of proteins are amino acids+ Amino acids have a generalised structure

• Tetrahedral arrangement of atoms with the alpha carbon at its centre

• Carboxyl and amine groups attached to a central carbon

• A variable side chain represent by R confers the specific physicochemical properties

• And a Hydrogen

• Amine and Carboxyl groups readily ionise

• Acidic and basic groups - AA are in equilibrium with the surrounding environment

-A type of chemical bond formed by the electrostatic attraction of oppositely charged ions.

D and L

2. D-isomer (dextro or right):

The amino group (NH2) is on the right side in a Fischer projection.

D-amino acids are less common in nature and are not typically found in proteins, although some exceptions exist.

1. L-isomer (levo or left):

The amino group (NH2) is on the left side in a Fischer projection.

Most naturally occurring amino acids in proteins are in the L-configuration

-Asymmetric

-Chiral (exception is Glycine, where R is a hydrogen)

-Peptide

-Condensation

-Releasing H2O

•Each repeating unit of the polypeptide chain is termed a residue

•Each residue consists of an invariable unit comprising

• Alpha carbon, C’=O and NH, group

•The variable side chain R is usually arranged in a trans conformation

• 0.1% peptide bonds have a less energetically favourable cis arrangement

• Covalent bonds forming polypeptide chain – i.e. order of aminoacid residues in the polymer

• Regular folded form stabilised by hydrogen bonding, e.g. alpha helices, beta sheets and beta turns

• Overall 3D structure, stabilised by non-covalent bonds and forces, and sometimes by intra-chain covalent bonds

• Organisation of polypeptides into assemblies, stabilised by non-covalent bonds and forces (as for Tertiary) and sometimes interchain covalent bonds

•beta sheets (are formed from hydrogen bonding) between adjacent beta strands, either in antiparallel or parallel arrangement

•beta strands are connected by loops or short turns, depending upon their arrangement

• Right handed helix

• stabilized by H-bonds

• H-bonds are 4 residues apart between residue 1 and 5

• 3.6 residues per turn or 0.54 nm per turn

-folded polypeptides that combine to form the mature protein.

• Heme of Haemoglobin,

• Nicotinamide adenine diphosphate (NAD)

• Flavin adenine dinucleotide (FAD)

- Organic cofactors are sometimes called coenzymes, but other proteins might include ions- e.g. Zn2+ Mg2+ Ca2

Globular

-Hydrophobic Core (Residues): Globular proteins have a compact structure with a hydrophobic core, where nonpolar amino acid side chains cluster together to minimize contact with water.

-Hydrophilic Surface (Residues): The exterior surface of globular proteins is hydrophilic, allowing them to interact favourably with the surrounding aqueous environment

Examples:

Some Water soluble proteins:

• May assemble into filaments (e.g. actin) or tubes (e.g. tubulin) or coiled-coils (cortexillin)

• Membrane spanning regions have externally located hydrophobic residues that interact with the membrane lipids.

• They may have hydrophilic central channels.

1)If they are CHARGED!

• May be subdivided into acidic or basic (alternatively positive or negative)

+Acidic = -ve charge

+Basic = +ve charge

2)Charged amino acids are also polar in nature

3)Sometimes the sulphur containing amino acids are a separate group

4)Glycine is sometimes considered Nonpolar, sometimes it’s a separate group

5)Histidine is sometimes also considered as a charged basic amino acid

– Carboxyl groups COO- ⇾ charged or acidic

– Amine groups NH3+ → charged or basic

– 2o (secondary) Amine NH and Carbonyl C=O groups →polar

– Hydroxyl OH → polar

– Hydrocarbon → Non-polar Hydrophobic

• The rotational freedom within a polypeptide is found around alpha carbon, NOT the peptide bond

The equation for ΔG is:

ΔG=ΔH−TΔS

where:

ΔH is the change in enthalpy (heat absorbed or released during the reaction),

T is the temperature in Kelvin,

ΔS is the change in entropy.

The sign of ΔG determines the spontaneity of a reaction:

If ΔG is negative, the reaction is spontaneous (exergonic), releasing energy.

If ΔG is positive, the reaction is non-spontaneous (endergonic), requiring an input of energy.

If ΔG is zero, the system is at equilibrium.

-Non-covalent bonds have 1/20th strength of covalent bonds

-However...the overall contribution of non-covalent bonds are significant because non-covalent bonds are far larger

1. Charge or electrostatic attractions

• falls off exponentially as distance increases, affected by electrostatic environment (aqueous environment)

2. Hydrogen bonds

•(transient bonds, similar in some respects to covalent bonds)

3. Van der Waals attractions – dipole These weak forces occur between two atoms• determined by their fluctuating charge

• Van der Waals forces are induced by proximity of molecules

4. hydrophobic interactions

• (water is a polar molecule) hydrophobic interactions minimise disruption of water network – i.e. the fourth weak force Non-covalent bonds and forces

-Disulphide bonds form between the side chains of two cysteine residues

• Bonds form in an oxidative reaction

• The SH groups from each cysteine cross-link.

• Usually occurs in distant parts of the primary sequence but adjacent in the three-dimensional structure.

• Can form on the same (intra-chain) or different (interchain) polypeptide chains, e.g. insulin left

• The function of the misfolded protein is almost always lost or reduced

• Misfolded proteins tend to self-associate and form aggregates

• Huntingtin Htt (Huntington’s)

• Amyloid-beta Ab (Alzheimer’s)

• prion protein (PrPSc) Creutzfeldt–Jakob disease and variant CJD

• alpha-synuclein (Parkinson’s disease)

• Serum amyloid A (AA amyloidosis)

• islet amyloid polypeptide IAPP (Type 2 Diabetes) and many more

• Other misfolded proteins result in cellular processing that lead to their degradation

• Cystic fibrosis

1. somatic mutations in the gene sequence, leading to the production of a protein unable to adopt the native folding

2. errors in transcription or translation leading to the production ofmodified proteins unable to properly fold

3. Failure of the folding machinery

4. mistakes of the post-translational modifications or in trafficking ofproteins

5. Structural modification produced by environmental changes

6. induction of protein misfolding by seeding and cross-seeding by other proteins

This hypothesis proposes that the aggregation and accumulation of Aβ (Amyloid beta) peptides, particularly in the form of amyloid fibrils, play a central role in the development and progression of Alzheimer's disease

In Alzheimer's Disease:

•The 40 amino acid β-Amyloid (Aβ) peptide accumulates.

•Misfolding of β-Amyloid (Aβ) results in a flat arrangement forming a beta sheet.

•Polymerization forms fibrils of misfolded protein known as amyloid fibrils.

•Stacked beta sheets of β-Amyloid (Aβ) are stabilized by side chains that interdigitate (weave together)

Common Mutation:

In Cystic fibrosis, the prevalent mutation is the deletion of Phenylalanine at residue 508 of the CFTR (Transmembrane conductance regulator) gene.

DF508del Mutation and Misfolding:

The DF508del mutation leads to the misfolding of the CFTR protein, occurring while the protein is still within the ER.

Recognition by Cellular Machinery:

The misfolded CFTR protein is recognized by the cellular machinery responsible for identifying and processing misfolded proteins.

Ubiquitination and Proteasomal Degradation:

-This results in ubiquitination, trafficking to the proteasome and degradation

Seeding: Process where misfolded proteins act as templates, inducing the misfolding of normal proteins.

Cross-Seeding: Involves misfolded proteins from one type encouraging the misfolding of a different protein type, potentially amplifying the protein misfolding cascade.