A primer on the structure and function of proteins Protein is derived from the Greek “ proteios ”, for “of first rank” (Jöns J. Berzelius, 1838) 1
Examples of protein functionality: • Enzymatic catalysis • vast majority of reactions catalyzed by enzymes • Transport and Storage • enzymes have an enormous influence on reaction rates • Motion • biochemical reaction rate can be increase by > a million fold • Signaling and communication • enzymes control biochemical reactions ranging • Immunity from simple to complex (e.g., replication of a genome) • Control of gene expression Examples of protein functionality: • Enzymatic catalysis • transport of small, but critically important molecules is carried out by specific proteins. • Transport and Storage • examples: haemoglobins to transport oxygen; myoglobins to transport and store oxygen in muscle. • Motion • over time haemoglobin and myoglobin have evolved • Signaling and communication very precise, but divergent functions with respect to their role in oxygen transport within an organism. • Immunity • Control of gene expression 2
Examples of protein functionality: Examples include: muscle contraction, movement of • Enzymatic catalysis chromosomes during mitosis and meiosis, the propulsion of sperm by flagella. • Transport and Storage • Motion • Signaling and communication • Immunity • Control of gene expression Examples of protein functionality: • Enzymatic catalysis • proteins can receive molecular signals • proteins can transmit molecular signals • Transport and Storage • signals are transmitted within proteins by changes • Motion in 3D conformation. • proteins can “perceive” a change in an • Signaling and communication environment and “communicate” this change via a molecular signal. • Immunity • Control of gene expression 3
Examples of protein functionality: • Enzymatic catalysis • proteins critical to distinguishing “self” from “non-self” • recognize and bind foreign proteins • Transport and Storage • evolutionary conflict between pathogen and its host • Motion • leads to an evolutionary arms-race • Signaling and communication • Immunity • Control of gene expression Examples of protein functionality: Precise control of the level of gene expression is • Enzymatic catalysis essential to the proper growth and function of cells. The incredibly complex process of development • Transport and Storage from a fertilized egg to a multi-cellular organism such as a human being is under genetic control • Motion through the production (expression) and function of proteins such as transcription factors. • Signaling and communication • Immunity • Control of gene expression 4
Amino acids as building blocks of proteins (or how do we get all this functionality from just 20 monomers?) The number of possible A guess at the number of natural polypeptides is “nearly infinite”: polypeptides on earth: • polypeptide of 2 aa’s: 20 2 = 400 • 10 million species • polypeptide of 3 aa’s: 20 3 = 8000 • average genome of 5,000 genes • at least 5 x 10 10 proteins • most polypeptides: 50 – 2000 aa’s • polypeptide of 150 aa’s: 20 150 • estimated number of 3D folds: 650 – 10,000 • number of possible 3D conformations is >> number of polypeptides! • majority of proteins = 1,000 folds The distribution of natural folds is highly skewed. The usage of foldes could be subject to natural selection. 5
Polypeptides are built by using the peptide bond 20 amino acids are defined by 20 unique R-group side-chains 6
Overlapping physiochemical properties of amino acids Tiny Small P Polar C S-S A N G S I V Aliphatic Q C S-H L D T Negative E M Y K F H W R Charged Aromatic Hydrophobic Positive Scales of physiochemical properties are artificial 7
The structural hierarchy of a protein can be described at four levels Prosthetic group: any small, non polypeptide, molecule that is tightly bound to a protein • essential role in protein function • influence 3D fold • ex: Heme molecular of haemoglobin. Globin fold > 800 million years old • association can be covalent or non- covalent • not all proteins have prosthetic groups 8
Post-translational modifications : covalent modifications that affect the structure and function of proteins • Disulphide bridges • Polypeptide cleavage • Modification of amino acid side chains • Addition of carbohydrates • Addition of lipids The native conformation of insulin is NOT the one with the lowest free energy Enzymes convert preproinsulin into insulin: 1. Preproimsulin is cleaved by an enzyme almost immediately after the chain of 108 amino acids is synthesized. 2. Proinsulin is folded in such a way that the state of lowest free energy at this pont is the one in which the disulfide bridges can be formed. 3. Lastly, enzymes remove the C-chain to produce the insulin. By utilizing intermediate stages, the cell is able to for a stable conformation (insulin) that is not the one with the lowest free energy. Note: Free energy is a measure of the potential energy of a biological reaction. Free energy determines the direction of the reaction, with the reaction going in the direction of lower free energy. 9
30,000 genes of mice and men: 1. Effect of mutations in active sites, etc. 2. Mix and match regulatory elements 3. Alternative splicing 4. Post-translational modifications Protein functionality derives from 3D conformation: 1. Recognize and bind variety of molecules: i. Heme ii. Other native proteins iii. Forgeign proteins iv. RNA and DNA v. Etc. e.g., regulatory proteins binding directly with DNA 10
Protein functionality derives from 3D conformation: 2. Complimentary surfaces or clefts: i. Very precise 3D surfaces ii. Side chain interactions via physiochemical properties of side- chains Protein functionality derives from 3D conformation: 3. Precise orientation = increased catalytic power: i. Reaction rate increased > 1 million fold by enzymes ii. optimal distance iii. optimal orientation iv. Charged R-groups important in reactions 11
Protein functionality derives from 3D conformation: 3. Proteins transmit molecular signals: i. Allosteric control ii. Conformational changes iii. Hg uses this to “perceive” changes in its environment Cancer can be the result of an information transfer system “gone wrong” 12
Modularity of protein folds: Relationship between coding sequences, functional domains, and tertiary structure of beta globin Relationship between coding sequences, functional domains, and tertiary structure of beta globin Regulatory Signals Regulatory Signals Introns Introns Exon 1 Exon 1 DNA DNA Exon 2 Exon 2 Exon 3 Exon 3 Exon shuffling: Comparison of LDL receptor gene with the C9 complement and EGF genes. Comparison clearly indicates that the LDL receptor gene evolved via a gene fusion. event. 13
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