The three important structural features of proteins:

a. Primary (1o) – The amino acid sequence (coded by genes)

b. Secondary (2o) – The interaction of amino acids that are close together or far apart in the sequence

c. Tertiary (3o) – The interaction of amino acids that are far apart in sequence

In 2o and 3o the primary interaction is noncovalent

Some proteins have quaternary structure (4o): noncovalent interaction of multiple polypeptide chains (subunits)

Native structure (conformation) biological function

Peptide bonds link amino acids in proteins

Figure 4.1

Amino-terminus Carboxyl-terminus

Residue or side chain

Alanine Ala (A) Serine Ser (S)

DipeptideAla-Ser or AS

Peptide bonds link amino acids in proteinsPrimary sequence

Peptide bonds link amino acids in proteinsPrimary sequence has directionality

Important: the sequence Tyr-Gly-Gly-Phe-Leu is not the same as Leu-Phe-Gly-Gly-Tyr

Figure 4.2

Figure 4.3-the polypeptide backbone is richWith hydrogen bond donors and acceptors

How many amino acids are typically found in polypeptide chains?

1 amino acid molecular weight is ~110 g/mol or 110 Da (Daltons)

Proteins can be very large, hundreds of amino acids long

The enzyme HMG-CoA reductase

MLSRLFRMHGLFVASHPWEVIVGTVTLTICMMSMNMFTGNNKICGWNYECPKFEEDVLSSDIIILTITRCIAILYIYFQFQNLRQLGSKYILGIAGLFTIFSSFVFSTVVIHFLDKELTGLNEALPFFLLLIDLSRASTLAKFALSSNSQDEVRENIARGMAILGPTFTLDALVECLVIGVGTMSGVRQLEIMCCFGCMSVLANYFVFMTFFPACVSLVLELSRESREGRPIWQLSHFARVLEEEENKPNPVTQRVKMIMSLGLVLVHAHSRWIADPSPQNSTADTSKVSLGLDENVSKRIEPSVSLWQFYLSKMISMDIEQVITLSLALLLAVKYIFFEQTETESTLSLKNPITSPVVTQKKVPDNCCRREPMLVRNNQKCDSVEEETGINRERKVEVIKPLVAETDTPNRATFVVGNSSLLDTSSVLVTQEPEIELPREPRPNEECLQILGNAEKGAKFLSDAEIIQLVNAKHIPAYKLETLMETHERGVSIRRQLLSKKLSEPSSLQYLPYRDYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKEFQVPMATTEGCLVASTNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSAEVKAWLETSEGFAVIKEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGMNMISKGTEKALSKLHEYFPEMQILAVSGNYCTDKKPAAINWIEGRGKSVVCEAVIPAKVVREVLKTTTEAMIEVNINKNLVGSAMAGSIGGYNAHAANIVTAIYIACGQDAAQNVGSSNCITLMEASGPTNEDLYISCTMPSIEIGTVGGGTNLLPQQACLQMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALAAGHLVKSHMIHNRSKINLQDLQGACTKKTA

Practice Problem

Draw the chemical structure of the tripeptide Glu – Ser – Cys at pH 7.

Answer the following with regard to this tripeptide:

1. Indicate the charge present on any ionizable group(s).

2. Indicate, using an arrow, which covalent bond is the peptide bond.

3. What is the net, overall charge of this tripeptide at pH 7? __________

4. What is this peptide called using the one-letter code system for amino acids? ______

Double bond character of the peptide bond

Bond lengths revealC-N is between asingle and a doublebond. (Figure 4.7)

Trans and Cis conformations of a peptide groupFigure 4.8

Nearly all peptide groups in proteins are in the trans conformation

The N-Ca and Ca-CO bonds are not rigid and rotation is possibleFigure 4.9

Phi angle Psi angle

Ca

Are all angles “allowed”?

Ramachandran PlotFigure 4.10

The amino acid cysteine also stabilizes proteins through theformation of a disulfide bond.

Figure 4.4

Insulin

Figure 4.5

Secondary structureof proteins

Alpha helix

Pitch is ~5.4 Å or 3.6 AAs

The coil in the alpha helix allows for Hydrogen bondingFigure 4.12

The stability of the alphahelix is dependent uponthe residues attached.

Gly and Pro are notprevalent in most a-helix

The alpha helix cansometimes be amphipathic.

Amphipathic a-helices are oftenFound on the surface of proteins

hydrophilic

hydrophobic

A dehydrogenase globular protein

Secondary Structure – the Beta (b) sheet or Beta strand

Figure 4.15- the peptide chain is more elongated than In the alpha helix.

Secondary Structure – the Beta (b) sheet or Beta strandAntiparallel

N

C

Secondary Structure – the Beta (b) sheet or Beta strandParallel

C

C

Figure 4.17- both types of b-sheets are possible in one protein.

C

C

N

Figure 4.18 b-sheets can be found with a twist

The beta sheet.

Side chains alternatefrom one side to another

The ability for polypeptidesto reverse direction requiresreverse turns and/or loops

Figure 4.19

A protein involved inFatty acid metabolism

Reverse Turns and loopsFigure 4.20

Type I b turn

Hydrogen bonding

Tertiary Structure of Proteins

Supersecondarystructures oftencalled “motifs”

Figure 4.27

Tertiary Structure of Proteins

Domains area combinationof motifs

Figure 4.28

Protein found on surface of someImmune system cells

Tertiary structureof proteins

Domains in Pyruvate kinasethis protein has 3 domains

a-Keratin: A fibrous protein with extensive secondary structure

Figure 4.21-A coiled coil protein

Collagen-25% to 35% total protein in mammals

-Fibrous protein found in vertebrate connective tissue (skin, bone, teeth)

- Triple helix structureStrength is greater than steelof equal cross section

-only 3 amino acids per turn

Figure 4.24. A superhelical structure

Collagen is35% Glycine21% Proline + Hydroxyproline

The repeating unit is Gly – X – Y

X is usually ProY is usually Hyp

triple helix is packed with Glycines (red)

4-hydroxyproline For every Gly-X-Y, there is one interchainHydrogen bond (between chains).

Read Clinical Insight (pg 55)– OsteogenesisImperfecta and Scurvy

Figure 4.25 - Myoglobin (153 amino acids)

Globular Proteins- very compact and water solubleWHY?

Figure 4.26 - Distribution of amino acids in myoglobin

Charged amino acids(blue)

Hydrophobic amino acids(yellow)

Surface Interior

Quaternary Structure-multiple polypeptide strandsIntermingle though noncovalent interactions.

Figure 4.29A dimer of two subunits (polypeptides)

Figure 4.30 Hemoglobin: a tetramer protein

This protein has primary, secondarytertiary and quaternary structures

How do proteinsfold and unfold?

The information for proteins to fold is contained in the amino acid sequence.

Can proteins fold by themselves or do they need help?

Is there a way in which we can predict from the primary sequence how a protein will fold??

First, we must denature a protein and see if itwill spontaneously refold to the native structure

How can we denature proteins?a. Reducing agents

2-mercaptoethanol break disulfide bondsb. heatc. acids or basesd. heavy metals (good Lewis acidsbind to cysteine)e. chaotropic agent-Urea (help weaken hydrogen bonding and

eventually disrupt hydrophobic core.)

Figure 4.31 – 4 cystine residues in bovine ribonuclease A

Anfinsen’s protein folding Experiment.Figure 4-32

Denature Protein with b-mercaptoethanol and Urea.

Anfinsen result after removal of urea and most of the b-mercaptoethanol

Enzyme slowly regains activity!!

Native conformation is re-established

Conclusion: primary sequence specifies conformation

Figure 4.35 Energy well of cooperative folding

Protein folding is very fast! ~ largeProteins may take ~ hrs, but smallerProteins may fold in one step.

Read Clinical InsightAmyloid fibrils and priondiseases (pg 61)

Assignment

Read Chapter 4Read Chapter 6

Topics not covered:Chapter 5