Protein function and Enzyme kinetics

Lecture 5

Proteins and Enzymes

The structure of proteins

How proteins functions

Proteins as enzymes

How to think about amino acids

Substitutions: Alanine generally prefers to substitute with other small amino acid, Pro, Gly, Ser.

Role in structure: Alanine is arguably the most boring amino acid. It is not particularly hydrophobic and is non-polar. However, it contains a normal C-beta carbon, meaning that it is generally as hindered as other amino acids with respect to the conforomations that the backbone can adopt. For this reason, it is not surprising to see Alanine present in just about all non-critical protein contexts.

Role in function: The Alanine side chain is very non-reactive, and is thus rarely directly involved in protein function. However it can play a role in substrate recognition or specificity, particularly in interactions with other non-reactive atoms such as carbon.

Tyrosine

Substitutions: As Tyrosine is an aromatic, partially hydrophobic, amino acid, it prefers substitution with other amino acids of the same type (see above). It particularly prefers to exchange with Phenylalanine, which differs only in that it lacks the hydroxyl group in the ortho position on the benzene ring.

Role in function: Unlike the very similar Phenylalanine, Tyrosine contains a reactive hydroxyl group, thus making it much more likely to be involved in interactions with non protein atoms. Like other aromatic amino acids, Tyrosine can be involved in interactions with non-protein ligands that themselves contain aromatic groups via stacking interactions.

A common role for Tyrosines (and Serines and Threonines) within intracellular proteins is phosphorylation. Protein kinases frequently attach phosphates to Tyrosines in order to fascilitate the signal transduction process. Note that in this context, Tyrosine will rarely substitute for Serine or Threonine, since the enzymes that catalyse the reactions (i.e. the protein kinases) are highly specific (i.e. Tyrosine kinases generally do not work on Serines/Threonines and vice versa)

Cysteine

Substitutions: Cysteine shows no preference generally for substituting with any other amino acid, though it can tolerate substitutions with other small amino acids. Largely the above preferences can be accounted for by the extremely varied roles that Cysteines play in proteins (see below). The substitutions preferences shown above are derived by analysis of all Cysteines, in all contexts, meaning that what are really quite varied preferences are averaged and blurred; the result being quite meaningless.

Role in structure: The role of Cysteines in structure is very dependent on the cellular location of the protein in which they are contained. Within extracellular proteins, cysteines are frequently involved in disulphide bonds, where pairs of cysteines are oxidised to form a covalent bond. These bonds serve mostly to stabilise the protein structure, and the structure of many extracellular proteins is almost entirely determined by the topology of multiple disulphide bonds

Cystine andGlutathione

Slide 18

The peptide bond

Slide 20

Slide 21

Slide 22

Slide 23

Slide 24

Slide 25

Lock and key

Specific interactions at active site

Slide 28

Slide 29

Slide 30

How do proteins function?

Structural: Actin is an example it is a major component of the cells architecture as well as the contractile apparatus

Carriers: Hemoglobin is an example. It functions to carry O₂ to tissue and eliminate CO₂

Regulatory: Transcription factors bind to DNA a control the level of mRNA that is produced

Transport: EGFR-epithelial growth factor receptor. Binds EGF and signals for cell growth.

Binders: Immunoglobulin proteins or antibodies- bind to foreign proteins and destroy infectious agents.

Actin and myosin: the contractile apparatus

Skeletal Muscle Cells

Skeletal Muscle Structure

Muscle cells are formed by fusion of myoblasts

Myofibrils are parallel arrays of long cylinders packed in the muscle cell

Sarcomeres are symmetric repeating units from z-line to z-line in the myofibril

Thick filaments are myosin filaments

Thin filaments are actin filaments

Structure of Myosin

More myosin structure

Arrangement of Myosin Molecules in Thick Filaments

bipolar polymer of myosin

myosin tails align and point to center of sarcomere

myosin heads arranged in a helical pattern pointing away from center

myosin heads reach out from the thick filaments to contact the actin filaments

contain ~300 molecules of myosin

Myosin filament

Thin Filaments

actin filaments in the sarcomere are of fixed length

actin filaments are cross-linked by a-actinin at Z-line

both ends of actin filaments are capped

barbed ends are embedded at the Z-line

tropomyosin and troponins bind along each filament

Structure of actin filament

Actin in detail

Actin structure

Folding of the actin molecule is represented by ribbon tracing of the a-carbon atoms. N and C correspond to the amino- and carboxyl-terminals, respectively. The letters followed by numbers represent amino acids in the polypeptide chain. A hypothetical vertical line divides the actin molecule into two domains "large", left side, and "small", right side. ATP and Ca2+ are located between the two domains. These two domains can be subdivided further into two subdomains each, the small domain being composed of subdomains 1 and 2, and the 2 has significantly less mass than the other three subdomains and this is the reason of dividing actin into small and large domains). The four subdomains are held together and stabilized mainly by salt bridges and hydrogen bonds to the phosphate groups of the bound ATP and to its associated Ca2+ localized in the center of the molecule.

Actin domains

1. Where does it polymerize with actin?

2. Where does it interact with troponin and tropomyosin?

3. Where does it interact with myosin?

4. How could we answer this question?

Structure of a Sarcomere

Muscle Contraction

Stabilization of the Alignment of Thick and Thin Filaments

Crystal Structure of Myosin Head and Lever Arm

Regulation of Non-muscle Myosin II Assembly

Muscle continue

Myosin Superfamily

Three examples of the diverse structures of members of the myosin superfamily

In vitro Motility Assay

1. Attach myosin S1 on the cover slip

2. Add fluorescently tagged actin filament

3. Addition of ATP initiates the movement of the filaments

4. Also done by coating cover slip with actin filaments and use fluorescently tagged myosin motor domain

In vitro motility assay

Proteins as enzymes

There are 6 major classes of enzymes:

    1.Oxidoreductases, which are involved in oxidation, reduction, and electron or proton transfer reactions;

   2.Transferases, catalyzing reactions in which groups are transferred;

   3.Hydrolases that cleave various covalent bonds by hydrolysis;

   4.Lyases catalyze reactions forming or breaking double bonds;

   5.Isomerases catalyze isomerization reactions;

   6.Ligases join constituents together covalently.

Enzymes fall into classes based on function

There are 6 major classes of enzymes:

1.Oxidoreductases which are involved in oxidation, reduction, and electron or proton transfer reactions;

   2.Transferases, catalysing reactions in which groups are transferred;

   3.Hydrolases which cleave various covalent bonds by hydrolysis; 4

4.Lyases catalyse reactions forming or breaking double bonds;

5.Isomerases catalyse isomerisation reactions;

   6.Ligases join substituents together covalently.

Enzyme Kinetics

Enzymes are protein catalysts that, like all catalysts, speed up the rate of a chemical reaction without being used up in the process.

Enzyme reaction rates are determined by several factors.

the concentration of substrate molecules (the more of them available, the quicker the enzyme molecules collide and bind with them). The concentration of substrate is designated [S] and is expressed in unit of molarity.

the temperature. As the temperature rises, molecular motion - and hence collisions between enzyme and substrate - speed up. But as enzymes are proteins, there is an upper limit beyond which the enzyme becomes denatured and ineffective.

Enzymes cont.

the presence of inhibitors.

competitive inhibitors are molecules that bind to the same site as the substrate - preventing the substrate from binding as they do so - but are not changed by the enzyme.

noncompetitive inhibitors are molecules that bind to some other site on the enzyme reducing its catalytic power.

pH. The conformation of a protein is influenced by pH and as enzyme activity is crucially dependent on its conformation, its activity is likewise affected.

How we determine how fast an enzyme works

We set up a series of tubes containing graded concentrations of substrate, [S] . At time zero, we add a fixed amount of the enzyme preparation.

Over the next few minutes, we measure the concentration of product formed. If the product absorbs light, we can easily do this in a spectrophotometer.

Early in the run, when the amount of substrate is in substantial excess to the amount of enzyme, the rate we observe is the initial velocity of Vi.

Mechaelis Menton kinetics

Plotting Vi as a function of [S], we find that

At low values of [S], the initial velocity,Vi, rises almost linearly with increasing [S].

But as [S] increases, the gains in Vi level off (forming a rectangular hyperbola).

The asymptote represents the maximum velocity of the reaction, designated Vmax

The substrate concentration that produces a Vi that is one-half of Vmax is designated the Michaelis-Menten constant, Km(named after the scientists who developed the study of enzyme kinetics).

Km is (roughly) an inverse measure of the affinity or strength of binding between the enzyme and its substrate. The lower the Km, the greater the affinity (so the lower the concentration of substrate needed to achieve a given rate).

Plotting out our data it might look like this.

Lineweaver-Burke plot

Competitive inhibitors

Enzymes can be inhibited competitively, when the substrate and inhibitor compete for binding to the same active site or noncompetitively, when the inhibitor binds somewhere else on the enzyme molecule reducing its efficiency.

The distinction can be determined by plotting enzyme activity with and without the inhibitor present.

Competitive Inhibition

In the presence of a competitive inhibitor, it takes a higher substrate concentration to achieve the same velocities that

were reached in its absence. So while Vmax can still be reached if sufficient substrate is available, one-half Vmax requires a higher [S] than before and thus Km is larger.

Non-competitive inhibitor

With noncompetitive inhibition, enzyme molecules that have been bound by the inhibitor are taken out of the game so enzyme rate (velocity) is reduced for all values of [S], including Vmax and one-half Vmax but

Km remains unchanged because the active site of those enzyme molecules that have not been inhibited is unchanged.

Competitive/noncompetitive inhibitor

Effect of inhibitors


	The structure of proteins
	How proteins functions
	Proteins as enzymes


	Substitutions: Alanine generally prefers to substitute with other small amino acid, Pro, Gly, Ser.
	Role in structure: Alanine is arguably the most boring amino acid. It is not particularly hydrophobic and is non-polar. However, it contains a normal C-beta carbon, meaning that it is generally as hindered as other amino acids with respect to the conforomations that the backbone can adopt. For this reason, it is not surprising to see Alanine present in just about all non-critical protein contexts.
	Role in function: The Alanine side chain is very non-reactive, and is thus rarely directly involved in protein function. However it can play a role in substrate recognition or specificity, particularly in interactions with other non-reactive atoms such as carbon.


	Substitutions: As Tyrosine is an aromatic, partially hydrophobic, amino acid, it prefers substitution with other amino acids of the same type (see above). It particularly prefers to exchange with Phenylalanine, which differs only in that it lacks the hydroxyl group in the ortho position on the benzene ring.
	Role in function: Unlike the very similar Phenylalanine, Tyrosine contains a reactive hydroxyl group, thus making it much more likely to be involved in interactions with non protein atoms. Like other aromatic amino acids, Tyrosine can be involved in interactions with non-protein ligands that themselves contain aromatic groups via stacking interactions.
	A common role for Tyrosines (and Serines and Threonines) within intracellular proteins is phosphorylation. Protein kinases frequently attach phosphates to Tyrosines in order to fascilitate the signal transduction process. Note that in this context, Tyrosine will rarely substitute for Serine or Threonine, since the enzymes that catalyse the reactions (i.e. the protein kinases) are highly specific (i.e. Tyrosine kinases generally do not work on Serines/Threonines and vice versa)


	Substitutions: Cysteine shows no preference generally for substituting with any other amino acid, though it can tolerate substitutions with other small amino acids. Largely the above preferences can be accounted for by the extremely varied roles that Cysteines play in proteins (see below). The substitutions preferences shown above are derived by analysis of all Cysteines, in all contexts, meaning that what are really quite varied preferences are averaged and blurred; the result being quite meaningless.
	Role in structure: The role of Cysteines in structure is very dependent on the cellular location of the protein in which they are contained. Within extracellular proteins, cysteines are frequently involved in disulphide bonds, where pairs of cysteines are oxidised to form a covalent bond. These bonds serve mostly to stabilise the protein structure, and the structure of many extracellular proteins is almost entirely determined by the topology of multiple disulphide bonds


	Structural: Actin is an example it is a major component of the cells architecture as well as the contractile apparatus
	Carriers: Hemoglobin is an example. It functions to carry O₂ to tissue and eliminate CO₂
	Regulatory: Transcription factors bind to DNA a control the level of mRNA that is produced
	Transport: EGFR-epithelial growth factor receptor. Binds EGF and signals for cell growth.
	Binders: Immunoglobulin proteins or antibodies- bind to foreign proteins and destroy infectious agents.


	Muscle cells are formed by fusion of myoblasts
	Myofibrils are parallel arrays of long cylinders packed in the muscle cell
	Sarcomeres are symmetric repeating units from z-line to z-line in the myofibril
	Thick filaments are myosin filaments
	Thin filaments are actin filaments


	bipolar polymer of myosin
	myosin tails align and point to center of sarcomere
	myosin heads arranged in a helical pattern pointing away from center
	myosin heads reach out from the thick filaments to contact the actin filaments
	contain ~300 molecules of myosin




	actin filaments in the sarcomere are of fixed length
	actin filaments are cross-linked by a-actinin at Z-line
	both ends of actin filaments are capped
	barbed ends are embedded at the Z-line
	tropomyosin and troponins bind along each filament


	1. Where does it polymerize with actin?
	2. Where does it interact with troponin and tropomyosin?
	3. Where does it interact with myosin?
	4. How could we answer this question?



	1. Attach myosin S1 on the cover slip
	2. Add fluorescently tagged actin filament
	3. Addition of ATP initiates the movement of the filaments
	4. Also done by coating cover slip with actin filaments and use fluorescently tagged myosin motor domain


	There are 6 major classes of enzymes:
	1.Oxidoreductases, which are involved in oxidation, reduction, and electron or proton transfer reactions;
	2.Transferases, catalyzing reactions in which groups are transferred;
	3.Hydrolases that cleave various covalent bonds by hydrolysis;
	4.Lyases catalyze reactions forming or breaking double bonds;
	5.Isomerases catalyze isomerization reactions;
	6.Ligases join constituents together covalently.


	There are 6 major classes of enzymes:

	1.Oxidoreductases which are involved in oxidation, reduction, and electron or proton transfer reactions;
	2.Transferases, catalysing reactions in which groups are transferred;
	3.Hydrolases which cleave various covalent bonds by hydrolysis; 4
	4.Lyases catalyse reactions forming or breaking double bonds;
	5.Isomerases catalyse isomerisation reactions;
	6.Ligases join substituents together covalently.


	Enzymes are protein catalysts that, like all catalysts, speed up the rate of a chemical reaction without being used up in the process.


	the concentration of substrate molecules (the more of them available, the quicker the enzyme molecules collide and bind with them). The concentration of substrate is designated [S] and is expressed in unit of molarity.
	the temperature. As the temperature rises, molecular motion - and hence collisions between enzyme and substrate - speed up. But as enzymes are proteins, there is an upper limit beyond which the enzyme becomes denatured and ineffective.


	the presence of inhibitors.
		competitive inhibitors are molecules that bind to the same site as the substrate - preventing the substrate from binding as they do so - but are not changed by the enzyme.
		noncompetitive inhibitors are molecules that bind to some other site on the enzyme reducing its catalytic power.
	pH. The conformation of a protein is influenced by pH and as enzyme activity is crucially dependent on its conformation, its activity is likewise affected.


	We set up a series of tubes containing graded concentrations of substrate, [S] . At time zero, we add a fixed amount of the enzyme preparation.
	Over the next few minutes, we measure the concentration of product formed. If the product absorbs light, we can easily do this in a spectrophotometer.
	Early in the run, when the amount of substrate is in substantial excess to the amount of enzyme, the rate we observe is the initial velocity of Vi.


	Plotting Vi as a function of [S], we find that
	At low values of [S], the initial velocity,Vi, rises almost linearly with increasing [S].
	But as [S] increases, the gains in Vi level off (forming a rectangular hyperbola).
	The asymptote represents the maximum velocity of the reaction, designated Vmax
	The substrate concentration that produces a Vi that is one-half of Vmax is designated the Michaelis-Menten constant, Km(named after the scientists who developed the study of enzyme kinetics).
	Km is (roughly) an inverse measure of the affinity or strength of binding between the enzyme and its substrate. The lower the Km, the greater the affinity (so the lower the concentration of substrate needed to achieve a given rate).


	Enzymes can be inhibited competitively, when the substrate and inhibitor compete for binding to the same active site or noncompetitively, when the inhibitor binds somewhere else on the enzyme molecule reducing its efficiency.
	The distinction can be determined by plotting enzyme activity with and without the inhibitor present.
	Competitive Inhibition
	In the presence of a competitive inhibitor, it takes a higher substrate concentration to achieve the same velocities that
	were reached in its absence. So while Vmax can still be reached if sufficient substrate is available, one-half Vmax requires a higher [S] than before and thus Km is larger.


	With noncompetitive inhibition, enzyme molecules that have been bound by the inhibitor are taken out of the game so enzyme rate (velocity) is reduced for all values of [S], including Vmax and one-half Vmax but
	Km remains unchanged because the active site of those enzyme molecules that have not been inhibited is unchanged.