lecture 10 - the structure of proteins

8/18/2019 Lecture 10 - The Structure of Proteins

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The Structure of Proteins

Head of Medusa Caravaggio, 1599


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Proteins are polymers of Amino acids

Last day we considered the structure and chemical characteristics of amino acids.

Today we will examine how they polymerize together and form higher order structure.

H3N – C – C

O

O-

H

R

–

–+ The

zwitterionic form of

an amino acid

C = the alpha (α) Carbon


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H3N – C – C

O

O

-

H

R1

–

–+

N – C – C

O

O

-

H

R2

–

–+

H3N – C – C

O

H

H

R1

= –

–+

+ – H

H

N – C – CO

O-

H

R2

–

–H –

– + H2O

Amino acid polymerization

• the peptide bond forms via a condensation or dehydration reaction.

the peptide bond


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A more accurate depiction from your textbook:

• it depicts the COO- charge as de-localized over the entire group

• both the H atom and R groups are opposite of the carbonyl O atom to avoid stericclash


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The Primary (1o) Structure of Proteins

• primary structure of protein refers to the sequence of amino acids in the protein, as

specified by the gene sequence encoding the protein

• most proteins consist of between 50 to 2000 amino acids

• the largest known protein is titin, a muscle protein consisting of 27,000 amino acids

• amino acid polymers of less than 50 amino acids are often called peptides though

there is no strict cut off between the terms peptide and protein

• the α Carbon of each amino acid can always be recognized since the R group

is attached

• the peptide bond occurs between the carbonyl group of the first amino acid and the

amine group of the next amino acid


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Identify the α Carbon and the Side chain (R group) of each amino acid in this

five amino acid peptide.

Locate each peptide bond in the peptide.

Note that every peptide or protein begins with the amino group of the first

amino acid and ends with the carboxyl group of the last amino acid.

Thus we refer to the start of a protein as the Amino terminus or N-terminus

and the end of a protein as the Carboxyl terminus or C-terminus


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The Nature of the Peptide Bond

the structure of the amino acid chain about the peptide bond is planar and rigid

free to

rotate

free to

rotate

Planar

Rigid


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Why the peptide bond is rigid

• the peptide bond has a resonance structure shared with the carbonyl group

• as with all resonance bonds, they are neither single or double bonds, but ahybrid between the two. Since the peptide bond is not a pure single bond,

free rotation is not possible.


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free to

rotate

free to

rotate

Planar

Rigid

But, proteins have a very complex and convoluted structure and this is due to

the bonds that can rotate somewhat freely


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peptide bonds

φ (phi) bond rotation after peptide bond

ψ (psi) bond rotation before peptide bond

peptide bonds

The bonds before and after the peptide bond can rotate

these are the bonds that flank the alpha Carbon of each amino acid


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Nelson p144

φ=-180o, ψ=+180o

φ=-0o, ψ=+180o φ=-180o, ψ=+0o

Permissible

Not Permissible

The phi and psi bonds have rotational freedom, but not unlimited freedom


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A Ramachandran Plot shows the permissible phi (ψ) and

psi (φ) bond angles allowed in polypeptide backbone

beta strand

alpha helix

the range of permissible bond

angle combinations reflect

the secondary structures wesee in proteins

i.e. alpha helices and beta strands


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Nelson p103

The phi and psi bond angles

define the overall secondary andtertiary structure of a protein

If we know the angle of every bond

in a protein, we know its exact structure

The Secondary (2o) Structure of Proteins


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The Secondary (2o) Structure of Proteins

• the polypeptide chain can adopt several higher order structures

• because of the permissible phi and psi bond angles within amino acids,

the polypeptide or protein backbone can form a (not unlimited) range ofconformations.

• Hydrogen bonding between functional groups on the amino acids result

in the formation of regular structures (SECONDARY STRUCTURES) that help

determine the overall structure of the protein.

• due to the combination of possible bond angles coupled with Hydrogen bonding

effects, certain amino acid segments spontaneously form secondary structures

• secondary structures include the:

Alpha (α) HelixBeta (β) Sheet

Turns and Loops

• some proteins are made up of only α-helices or only β-sheets while others are

mixtures of both secondary structure types. Loops and turns often connect

helices or sheets together.


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The Alpha Helix

• alpha helices are segments of amino acids in proteins that form a helical structure

•

average length of 10 amino acids though may be shorter or longer

• there are about 3.6 amino acids per turn of the helix

• every fourth amino acid interacts via Hydrogen bonding

• not all amino acids participate in alpha helix formation, the geometry or the

size of the side-chains of some amino acids make them unsuitable for

alpha helix formation

Primary sequence and predicted secondary structure of a small 79 amino acid protein

VDGQFEQKKKQKDETYDIEHLIACFSPMIRKKLSNTSYQEREDLEQELKIKMFEKADMLLCQDVPGFWEFILYMVDENS

CN


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Nelson p149

Views of the Alpha Helix

Hydrogen bondingSide-chains on outside of helix

H-bonding every 4 residues

1 2 3 4 5


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A protein composed of all alpha helices

Th B Sh


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The Beta Sheet

• an important secondary structure in many proteins

•

composed of adjacent beta strands in anti-parallel or parallel arrangements

• beta strands are segments of amino acids in a fully extended sequence rather

then coiled as in an alpha helix.

each amino acid binds

to opposite residue

each amino acid binds

to two opposite residues

blue =amino nitrogen

green = side chain

red = oxygen

black = carbon


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Many Beta strands can associate in mixed orientations to form beta sheets

stabilized by intra-molecular H bonding

in all beta strands/sheets, note the orientation of the side chains


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Beta sheets are usually depicted as flat arrows

Anti-parallel arrangement

Parallel arrangement

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=KrOvFqa3LYYPlM&tbnid=lLJArvKxQWFmzM:&ved=0CAUQjRw&url=http://www.thestudentroom.co.uk/showthread.php?t=2178072&page=2&ei=ebE_Utf0OOqE2QWAzoBQ&bvm=bv.52434380,d.b2I&psig=AFQjCNF92kaxaFxvglLvG6fsJgFq5JmtBw&ust=1379992236678763


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The arrangement of beta strands in some proteins


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Turns and Loops

structured or unstructured segments of amino acids

often join other secondary structures together

Proline and Glycine often participate in forming turns (nearly 180o change in direction

of polypeptide backbone)

Proline at either one ofthese positions will mediate

a Turn

Ala Pro

proline forces a turn

in the backbone


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Nothing (almost nothing) is random about protein structure.

Amino acid segments of the protein adopt specific secondary structures not by chance

but because of the characteristics of the amino acid participants


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Tertiary Structure of Proteins

• proteins may be very small or large (thousands of amino acids long)

• amino acids form segments of secondary structure (α helices and β sheets)

• tertiary structure arises when these secondary structure segments associate in

specific and precise ways to form a 3-D compact structure

•

there is little or no “open space” within the interior of a protein

• interior is usually hydrophobic and water is excluded from interior

• forces that stabilize the tertiary structure

-charge interactions (e.g. between the + and - charged amino acids)

-H-bonding between polar groups

-van der Waals interactions between hydrophobic amino acid side chains

-the hydrophobic effect

-disulfide bonds between cysteine side-chains

S I t ti th t t bili th t ti t t


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Some Interactions that stabilize the tertiary structure

of Proteins

Charge-charge (ionic) Interactions

3. Induced dipole-induced dipole. Randomfluctuations in electron distribution in one

molecule sets up temporary dipole. This induces

dipole in adjacent molecule, resulting in

interaction. Weak but very important to the

cohesiveness of everything.

Also known as London Dispersion Forces.

van der Waals Interactions

S I t ti th t t bili th t ti t t


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Disulfide bond formation

Some Interactions that stabilize the tertiary structure

of Proteins

Disulfide bonds can be intra- or inter molecular

Th T i S f i


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Nelson p175

The Tertiary Structure of some proteins

Proteins are not usually “open structures”


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Primary sequence and predicted secondary structure of a small 79 amino acid protein

VDGQFEQKKKQKDETYDIEHLIACFSPMIRKKLSNTSYQEREDLEQELKIKMFEKADMLLCQDVPGFWEFILYMVDENS

CN

Proteins are not usually open structures


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Some Proteins fold into multiple tertiary structures called DOMAINS

each domain may possess a unique enzymatic function

that may be quite functional even if separated from the

rest of the protein


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Discrete regions of a protein, or a domain in a protein, with special functional

significance are called MOTIFS.

The Helix-turn-Helix motif is

often found in proteins that

bind double-stranded DNA

The Quaternary Structure of Proteins


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The Quaternary Structure of Proteins

• proteins fold into tertiary structures that are often active and do work

• sometimes separate proteins interact with other proteins to form multi-subunit

proteins

• sometimes proteins associate with themselves to form

homodimers 2 subunits or with other proteins (heterodimers)

homotrimers 3 subunitshomotetramers 4 subunits

etc.

• sometimes very different proteins assemble into multi-subunit complexes

e.g. DNA polymerase required for DNA replication is made up of many

different proteins that interact with each other to form a

complex

-only together do they form an active enzyme

• all the usual molecular interaction types are involved in these formations

Hi h d bli f t i (di t i t )


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Nelson p183

Higher order assemblies of proteins (dimers, trimers, etc.)


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Quaternary structure of RNA polymerase

this is the enzyme that

synthesizes mRNA during

transcription - the first step

in gene expression.

it is made up of several different

proteins.

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This Lecture

Stryer 8th Chapter 2 Protein Composition and Structure pg 27-57

Next Lecture

Stryer 8th Chapter 3 Exploring Proteins and Proteomes pg 66-79

lecture 10 - the structure of proteins

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