Protein Structure and Function

Proteins

• Have many functions in the cell– Enzymes– Structural– Transport– Motor– Storage– Signaling– Receptors– Gene regulation– Special functions

Shape = Amino Acid Sequence

• Proteins are made of 20 amino acids linked by peptide bonds

• Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond

• The side chain or R group is not part of the backbone or the peptide bond

Polypeptide Backbone

Figure 3-2 Molecular Biology of the Cell (© Garland Science 2008)

Amino Acids

Hydrophilic Hydrophobic

Protein Folding

• The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions

• Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape

Figure 3-4 Molecular Biology of the Cell (© Garland Science 2008)

Non-covalent Bonds in Proteins

Figure 3-5 Molecular Biology of the Cell (© Garland Science 2008)

Globular Proteins

• The side chains will help determine the conformation in an aqueous solution

Hydrogen Bonds in Proteins

• H-bonds form between 1) atoms involved in the peptide bond; 2) peptide bond atoms and R groups; 3) R groups

Protein Folding

• Proteins shape is determined by the sequence of the amino acids

• The final shape is called the conformation and has the lowest free energy possible

• Denaturation is the process of unfolding the protein– Can be down with heat, pH or chemical

compounds– In the chemical compound, can remove and

have the protein renature or refold

Figure 3-6a Molecular Biology of the Cell (© Garland Science 2008)

Refolding

• Molecular chaperones are small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner

Protein Folding

• 2 regular folding patterns have been identified – formed between the bonds of the peptide backbone

• -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns)

• -sheet – protein folds back on itself as in a ribbon –globular protein

Figure 3-7a,b,c Molecular Biology of the Cell (© Garland Science 2008)

-helix

Figure 3-7d,e,f Molecular Biology of the Cell (© Garland Science 2008)

-sheet

Figure 3-8 Molecular Biology of the Cell (© Garland Science 2008)

• Core of many proteins is the sheet

• Form rigid structures with the H-bond

• Can be of 2 types– Anti-parallel – run in an

opposite direction of its neighbor (A)

– Parallel – run in the same direction with longer looping sections between them (B)

Sheets

Figure 3-9 Molecular Biology of the Cell (© Garland Science 2008)

• Formed by a H-bond between every 4th peptide bond – C=O to N-H

• Usually in proteins that span a membrane

• The helix can either coil to the right or the left

• Can also coil around each other – coiled-coil shape – a framework for structural proteins such as nails and skin

Helix

Levels of Organization

• PrimaryPrimary structure– Amino acid sequence of the protein

• SecondarySecondary structure– H bonds in the peptide chain backbone

• -helix and -sheets

• TertiaryTertiary structure– Non-covalent interactions between the R groups

within the protein• QuanternaryQuanternary structure

– Interaction between 2 polypeptide chains

Protein Structure

Domains

• A domaindomain is a basic structural unit of a protein structure – distinct from those that make up the conformations

• Part of protein that can fold into a stable structure independently

• Different domains can impart different functions to proteins

• Proteins can have one to many domains depending on protein size

Domains

Useful Proteins

• There are thousands and thousands of different combinations of amino acids that can make up proteins and that would increase if each one had multiple shapes

• Proteins usually have only one useful conformation because otherwise it would not be efficient use of the energy available to the system

• Natural selection has eliminated proteins that do not perform a specific function in the cell

Figure 3-12 Molecular Biology of the Cell (© Garland Science 2008)

Protein Families

• Have similarities in amino acid sequence and 3-D structure• Have similar functions such as breakdown proteins but do it

differently

Proteins – Multiple Peptides

• Non-covalent bonds can form interactions between individual polypeptide chains– Binding site – where proteins interact with one

another– Subunit – each polypeptide chain of large protein– Dimer – protein made of 2 subunits

• Can be same subunit or different subunits

Single Subunit Proteins

Different Subunit Proteins

• Hemoglobin–2 globin

subunits–2 globin

subunits

Protein Assemblies

• Proteins can form very large assemblies

• Can form long chains if the protein has 2 binding sites – link together as a helix or a ring

• Actin fibers in muscles and cytoskeleton – is made from thousands of actin molecules as a helical fiber

Types of Proteins

• Globular ProteinsGlobular Proteins – most of what we have dealt with so far– Compact shape like a ball with irregular

surfaces– Enzymes are globular

• Fibrous ProteinsFibrous Proteins – usually span a long distance in the cell– 3-D structure is usually long and rod shaped

Important Fibrous Proteins• Intermediate filaments of the cytoskeleton

– Structural scaffold inside the cell• Keratin in hair, horns and nails

• Extracellular matrix – Bind cells together to make tissues– Secreted from cells and assemble in long fibers

• Collagen – fiber with a glycine every third amino acid in the protein

• Elastin – unstructured fibers that gives tissue an elastic characteristic

Collagen and Elastin

Stabilizing Cross-Links

• Cross linkages can be between 2 parts of a protein or between 2 subunits

• Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine

Proteins at Work

• The conformation of a protein gives it a unique function

• To work proteins must interact with other molecules, usually 1 or a few molecules from the thousands to 1 protein

• Ligand – the molecule that a protein can bind• Binding site – part of the protein that interacts

with the ligand– Consists of a cavity formed by a specific arrangement

of amino acids

Figure 3-36 Molecular Biology of the Cell (© Garland Science 2008)

Ligand Binding

Formation of Binding Site

• The binding site forms when amino acids from within the protein come together in the folding

• The remaining sequences may play a role in regulating the protein’s activity

Antibody Family

• A family of proteins that can be created to bind to almost any molecule

• AntibodiesAntibodies (immunoglobulins) are made in response to a foreign molecule ie. bacteria, virus, pollen… called the antigenantigen

• Bind together tightly and therefore inactivates the antigen or marks it for destruction

Antibodies

• Y-shaped molecules with 2 binding sites at the upper ends of the Y

• The loops of polypeptides on the end of the binding site are what imparts the recognition of the antigen

• Changes in the sequence of the loops make the antibody recognize different antigens - specificity

Figure 3-41 Molecular Biology of the Cell (© Garland Science 2008)

Antibodies

Binding Strength• Can be measured directly• Antibodies and antigens are mixing around in a

solution, eventually they will bump into each other in a way that the antigen sticks to the antibody, eventually they will separate due to the motion in the molecules

• This process continues until the equilibrium equilibrium is reached – number sticking is constant and number leaving is constant

• This can be determined for any protein and its ligandligand

Enzymes as Catalysts

• Enzymes are proteins that bind to their ligand as the 1st step in a process

• An enzyme’s ligand is called a substratesubstrate– May be 1 or more molecules

• Output of the reaction is called the product• Enzymes can repeat these steps many times and

rapidly, called catalysts• Many different kinds – see table 5-2, p 168

Enzymes at Work• Lysozyme is an important enzyme that protects us

from bacteria by making holes in the bacterial cell wall and causing it to break

• Lysozyme adds H2O to the glycosidic bond in the cell wall

• Lysozyme holds the polysaccharide in a position that allows the H2O to break the bond – this is the transition statetransition state – state between substrate and product

• Active siteActive site is a special binding site in enzymes where the chemical reaction takes place

Figure 3-50a Molecular Biology of the Cell (© Garland Science 2008)

Lysozyme

• Non-covalent bonds hold the polysaccharide in the active site until the reaction occurs

Figure 3-52 Molecular Biology of the Cell (© Garland Science 2008)

Features of Enzyme Catalysis

Prosthetic Groups

• Occasionally the sequence of the protein is not enough for the function of the protein

• Some proteins require a non-protein molecule to enhance the performance of the protein – Hemoglobin requires heme (iron containing

compound) to carry the O2

• When a prosthetic groupprosthetic group is required by an enzyme it is called a co-enzymeco-enzyme– Usually a metal or vitamin

• These groups may be covalently or non-covalently linked to the protein

Regulation of Enzymes

• Regulation of enzymatic pathways prevent the deletion of substrate

• Regulation happens at the level of the enzyme in a pathway

• Feedback inhibition is when the end product regulates the enzyme early in the pathway

Feedback Regulation

• Negative feedbackNegative feedback – pathway is inhibited by accumulation of final product

• Positive feedbackPositive feedback – a regulatory molecule stimulates the activity of the enzyme, usually between 2 pathways– ADP levels cause the

activation of the glycolysis pathway to make more ATP

Allostery• Conformational coupling of 2 widely separated

binding sites must be responsible for regulation – active site recognizes substrate and 2nd site recognizes the regulatory molecule

• Protein regulated this way undergoes allosteric transition or a conformational change

• Protein regulated in this manner is an allosteric protein

Allosteric Regulation

• Method of regulation is also used in other proteins besides enzymes– Receptors, structural and motor proteins

Allosteric Regulation

• Enzyme is only partially active with sugar only but much more active with sugar and ADP present

Phosphorylation

• Some proteins are regulated by the addition of a PO4 group that allows for the attraction of + charged side chains causing a conformation change

• Reversible protein phosphorylations regulate many eukaryotic cell functions turning things on and off

• Protein kinaseskinases add the PO4 and protein phosphatasephosphatase remove them

Phosphorylation/Dephosphorylation

• Kinases capable of putting the PO4 on 3 different amino acid residues– Have a –OH group on R

group• Serine• Threonine• Tyrosine

• Phosphatases that remove the PO4 may be specific for 1 or 2 reactions or many be non-specific

GTP-Binding Proteins (GTPases)

• GTP does not release its PO4 group but rather the guanine part binds tightly to the protein and the protein is active

• Hydrolysis of the GTP to GDP (by the protein itself) and now the protein is inactive

• Also a family of proteins usually involved in cell signaling switching proteins on and off

Figure 3-71 Molecular Biology of the Cell (© Garland Science 2008)

Molecular Switches

Figure 3-75 Molecular Biology of the Cell (© Garland Science 2008)

Molecular Switches

Figure 3-76 Molecular Biology of the Cell (© Garland Science 2008)

Motor Proteins

• Proteins can move in the cell, say up and down a DNA strand but with very little uniformity– Adding ligands to change the

conformation is not enough to regulate this process

• The hydrolysis of ATP can direct the the movement as well as make it unidirectional– The motor proteins that move

things along the actin filaments or myosin

Protein Machines

• Complexes of 10 or more proteins that work together such as DNA replication, RNA or protein synthesis, trans-membrane signaling etc.

• Usually driven by ATP or GTP hydrolysis

• THANK YOU • GOODLUCK FOR YOUR EXAMS