Chapter 4: Protein 3D Structure

Knowing amino acid sequences is important for several reasons:

1) amino acid sequences determine the three-dimensional structures of proteins. 2) knowledge of the sequence of a protein is usually essential to elucidating its function (e.g., the catalytic mechanism of an enzyme). 3) alterations in amino acid sequence can produce abnormal function and disease. Severe and sometimes fatal diseases, such as sickle-cell anemia and cystic fibrosis, can result from a change in a single amino acid within a protein. 4) the sequence of a protein reveals much about its evolutionary history. Proteins resemble one another in amino acid sequence only if they have a common ancestor. Consequently, molecular events in evolution can be traced from amino acid sequences; molecular paleontology is a flourishing area of research.

What are the rules governing the relation between an amino acid sequence and the three-dimensional structure of a protein? This question is very difficult to answer, but we know that certain characteristics of the peptide bond itself are important:

1) the peptide bond is essentially planar 2) the peptide bond has considerable double-bond character owing to resonance structures: the electrons resonate between a pure single bond and a pure double bond 3) the peptide bond is uncharged

The C—N distance in a peptide bond is typically _____ which is between

1.32 Å; the values expected for a C—N single bond (1.45 Å) and a C=N double bond (1.27 Å)

the lifetime of a peptide bond in aqueous solution in the absence of a catalyst approaches ____ years.

1000

The mean molecular weight of an amino acid residue is about ____ g mol−1, and so the molecular weights of most proteins are between ____ and ______ g mol−1.

110; 5500; 22000

Proteins are the embodiment of the transition from the _______ world of _______ _______ to the ___ world of _______ capable of diverse activities.

1D; DNA Sequences; 3D; molecules

Indeed, about _____ of all soluble proteins are composed of α helices connected by

25%; loops and turns of the polypeptide chain.

Primary structure determines the ______ _______ of a protein, and the three-dimensional structure determines the ______ ______

3D structure; protein's function

Most natural polypeptide chains contain between ____ and _____ amino acid residues and are commonly referred to as _____. The largest protein known is the

50; 2000; proteins; muscle protein titin

The double-bond character is also expressed in the length of the bond between the ____ and the ___ groups.

CO; NH

____ encodes the sequence of amino acids that constitute a protein.

DNA

Beta Sheets Are Stabilized by

Hydrogen Bonding Between Polypeptide Strands

Can a polypeptide chain fold into a regularly repeating structure?

In 1951, Linus Pauling and Robert Corey proposed that certain polypeptide chains have the ability to fold into two periodic structures called the α helix (alpha helix) and the β pleated sheet (beta pleated sheet). Subsequently, other structures such as turns and loops were identified. Alpha helices, β pleated sheets, and turns are formed by a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence, or primary structure. Such regular folded segments are called secondary structure.

Polypeptide Chains Can Change Direction by

Making Reverse Turns and Loops

The three-dimensional structure becomes more complex when the __ groups of amino acids that are far apart in the _______ structure bond with one another. This level of structure is called ______ ______ and is the highest level of structure that an individual _______ can attain.

R; primary; tertiary structure; polypeptide

_______ _______ helices are energetically more favorable because

Right-handed; there are fewer steric clashes between the side chains and the backbone.

Fibrous Proteins Provide

Structural Support for Cells and Tissues

Are all combinations of ϕ and ψ possible?

The Indian biophysicist Gopalasamudram Ramachandran recognized that many combinations are not found in nature because of steric clashes between atoms. He generated a two-dimensional plot, now called a Ramachandran plot, of the ϕ and ψ values of possible conformations

What is phi (ϕ)?

The angle of rotation about the bond between the nitrogen atom and the α-carbon atom

What is psi (ψ)?

The angle of rotation about the bond between the α-carbon atom and the carbonyl carbon atom

How is the α helix helical?

The side chains of the amino acids composing the structure extend outward in a helical array

Explain what this double-bond character prevents

This partial double-bond character prevents rotation about this bond and thus constrains the conformation of the peptide backbone.

What is secondary structure?

Three-dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain is called secondary structure.

______-quarters of the possible (ϕ, ψ) combinations are excluded simply by

Three; local steric clashes

Explain how the peptide bond is planar

Thus, for a pair of amino acids linked by a peptide bond, six atoms lie in the same plane: the α-carbon atom and CO group of the first amino acid and the NH group and α-carbon atom of the second amino acid

Two configurations are possible for a planar peptide bond:

Trans and cis

*Thus, in the pentapeptide Tyr-Gly-Gly-Phe-Leu (YGGFL), tyrosine is the amino-terminal (N-terminal) residue and leucine is the carboxyl-terminal (C-terminal) residue. The reverse sequence, Leu-Phe-Gly-Gly-Tyr (LFGGY), is a different pentapeptide, with different chemical properties. Note that the two peptides in question have the same _____ _____ composition but differ in _______ ______

amino acid, primary structure

Loops exposed to an aqueous environment are usually composed of

amino acids with hydrophilic R groups.

By convention, the _____ end is taken to be the beginning of a polypeptide chain, and so the sequence of amino acids in a polypeptide chain is written starting with the _____-terminal residue (or terminus).

amino; amino

The β pleated sheet (more simply, the β sheet) differs markedly from the rodlike α helix in

appearance and bond structure. Instead of a single polypeptide strand, the β sheet is composed of two or more polypeptide chains called β strands. A β strand is almost fully extended rather than being tightly coiled as in the α helix. The distance between adjacent amino acids along a β strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an α helix. Unlike α helices, β sheets can consist of sections of a polypeptide that are not near one another.

A polypeptide chain consists of a constant _____ shown and variable _____ _____

backbone (main chain); side chains

However, many proteins require more than one _____ to function. Such proteins display ______ structure, which can be as simple as a functional protein consisting of two identical polypeptide chains or as complex as one consisting of dozens of different polypeptide chains.

chain; quaternary

If viewed down the axis of a helix (N terminus to C terminus), the chain turns in ______ ______ and it has a ______ _________ screw sense. If turning is counterclockwise, the screw sense is _______ _______

clockwise direction; right-handed; left-handed.

The Alpha Helix Is a ______ Structure Stabilized by _____ ______ ______

coiled; Intrachain Hydrogen Bonds

Most proteins have ________ _______ shapes, requiring

compact, globular; reversals in the direction of their polypeptide chains.

Polypeptide Chains Are Flexible Yet __________ Restricted

conformationally

The two helices in α-keratin are

cross-linked by weak interactions such as van der Waals forces and ionic interactions.

The resulting unit of two linked cysteines is called _____. Disulfide bonds can form between ............ , or they can link

cystine; cysteine residues in the same polypeptide chain; two separate chains together.

We can also refer to the mass of a protein in units of ______; a dalton is a

daltons; unit of mass very nearly equal to that of a hydrogen atom.

Torsion angles are sometimes called _______ angles.

dihedral

In addition, the two helices may be linked by

disulfide bonds formed by neighboring cysteine residues.

In some proteins, the linear polypeptide chain is covalently cross-linked. The most common cross-links are ______ ______, formed by

disulfide bonds; the oxidation of a pair of cysteine residues

Thus, except for amino acids near the ___ of an α helix, all the main-chain CO and NH groups are hydrogen bonded.

ends

What are almost entirely built from β sheets?

fatty-acid-binding proteins, which are important for lipid metabolism

Beta sheets can be almost _____, but most adopt a somewhat _____ shape

flat; twisted

Functioning proteins, however, are not simply long polymers of amino acids. These polymers

fold to form discrete three-dimensional structures with specific biochemical functions.

Hence, the biosynthesis of peptide bonds requires an input of

free energy

Proteins Have Unique Amino Acid Sequences Specified by

genes

Explain what Frederick Sanger did in 1953

he determined the amino acid sequence of insulin, a protein hormone. This work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence consisting only of L amino acids linked by peptide bonds. Sanger's accomplishment stimulated other scientists to carry out sequence studies of a wide variety of proteins. The complete amino acid sequences of millions of proteins are now known.

The polypeptide backbone is rich in _____ _____ potential. Each residue contains a ______ _____ which is a good ______ _____ ______ , and with the exception of proline, an amino group (N—H), which is a good hydrogen-bond donor. These groups interact with each other and with the functional groups of side chains to _____ particular structures.

hydrogen bonding; carbonyl group (C=O); hydrogen-bond acceptor; stabilize

The α helix is stabilized by

hydrogen bonds between the NH and CO groups of the main chain. The CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence.

Proline also is an α helix breaker because

it lacks an NH group and because its ring structure prevents it from assuming the ϕ value to fit into an α helix.

A polypeptide chain has directionality, sometimes called polarity, because

its ends are different: an α-amino group is at one end, and an α-carboxyl group is at the other.

A β sheet is formed by

linking two or more β strands lying next to one another through hydrogen bonds.

Fibrous proteins form _____ fibers that serve a structural role. Although some of these proteins have regions of complex three-dimensional structure, for the most part, the three-dimensional structure of fibrous proteins is relatively simple, consisting of

long; extensive stretches of secondary structure.

Torsion angle, which is a .......... is usually taken to lie between

measure of rotation about a bond; -180 and +180 degrees.

Many proteins that span biological _______ also contain α helices.

membranes

In two β strands that lie next to each other, the last amino acid of one strand and the first amino acid of the adjacent strand are not necessarily

neighbors in the amino acid sequence.

Peptides made of small numbers of amino acids are called

oligopeptides or simply peptides.

Adjacent chains in a β sheet can run in

opposite directions (antiparallel β sheet) where hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure OR in the same direction (parallel β sheet) where hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

The formation of a disulfide bond between two cysteine residues is an _______ reaction.

oxidation

The linkage joining amino acids in a protein is called a

peptide bond (also called an amide bond)

by the peptide bond being uncharged, this allows

polymers of amino acids linked by peptide bonds to form tightly packed globular structures that would otherwise be inhibited by charge repulsion.

A series of amino acids joined by peptide bonds form a _________ _______, and each amino acid unit in a polypeptide is called a _____

polypeptide chain; residue

A clockwise rotation about either bond as viewed toward the α-carbon atom corresponds to a _____ value.

positive

Proteins are complicated three-dimensional molecules, but their three-dimensional structure depends simply on their ______ _______

primary structure

The amino acid sequence is called the _______ ________, and proteins typically consist of __ to ____ amino acids.

primary structure; 50, 300

In contrast with the peptide bond, the bonds between the amino group and the α-carbon atom and between the α-carbon atom and the carbonyl group are _____ _____ _____. The two adjacent rigid peptide units may ______ about these bonds, taking on ______ ______.

pure single bonds; rotate; various orientations

Many of these reversals are accomplished by common structural elements called

reverse turns and loops

The screw sense of a helix can be In schematic representations of proteins,

right-handed (clockwise) or left-handed (counterclockwise).

Essentially all α helices found in proteins are

right-handed.

Each residue is related to the next one by a ____, also called ______, of _____ along the helix axis and a rotation of ________ _____ which gives _____ amino acid residues per turn of helix

rise; translation; 1.5 Å; 100 degrees; 3.6

α helix

rodlike structure with a tightly coiled backbone.

The structure of each amino acid in a polypeptide can be adjusted by

rotation about two single bonds.

In contrast, amino acids spaced two apart in the sequence are

situated on opposite sides of the helix and so are unlikely to make contact.

Thus, amino acids spaced three and four apart in the sequence are

spatially quite close to one another in an α helix

Nonetheless, peptide bonds are quite ____ kinetically because

stable; the rate of hydrolysis is extremely slow

Remarkably, the final three-dimensional structure of a protein is determined simply by

the amino acid sequence of the protein.

Screw sense refers to

the direction in which a helical structure rotates with respect to its axis.

What is the pitch of the α helix?

the length of one complete turn along the helix axis and is equal to the product of the translation (1.5 Å) and the number of residues per turn (3.6), or 5.4 Å.

What is primary structure

the linear polymers formed by linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid.

A different type of helix is present in collagen:

the most abundant mammalian protein. Collagen is the main fibrous component of skin, bone, tendon, cartilage, and teeth. It contains three helical polypeptide chains, each nearly 1000 residues long. Glycine appears at every third residue in the amino acid sequence, and the sequence glycine-proline-proline recurs frequently

The ϕ and ψ angles determine

the path of the polypeptide chain.

In the trans configuration,

the two α-carbon atoms are on opposite sides of the peptide bond.

Serine, aspartate, and asparagine also tend to disrupt α helices because

their side chains contain hydrogen-bond donors or acceptors in close proximity to the main chain, where they compete for main-chain NH and CO groups.

In the cis configuration,

these groups are on the same side of the peptide bond.

The rotations about these bonds can be specified by ______ _______

torsion angles

Almost all peptide bonds in proteins are _____. This preference for _____ over ____ can be explained by the fact that there are

trans; trans, cis; steric clashes between R groups in the cis configuration but not in the trans configuration

α helices are depicted as

twisted ribbons or rods

This freedom of rotation about _____ bonds of each amino acid allows proteins to

two; fold in many different ways.

Branching at the β-carbon atom, as in _______, _______, ________

valine, threonine, and isoleucine; tends to destabilize α helices because of steric clashes.

The formation of a dipeptide from two amino acids is accompanied by the loss of a

water molecule

α-Keratin

which is the primary component of wool and hair, consists of two right-handed α helices intertwined to form a type of left-handed superhelix called a coiled coil. α-Keratin is a member of a superfamily of proteins referred to as coiled-coil proteins

What is titin

which serves as a scaffold for the assembly of the contractile proteins of muscle. Titin consists of almost 27,000 amino acids.

Not all amino acids can be readily accommodated in an

α helix

The first of Pauling and Corey's proposed secondary structures was the

α helix

Special types of helices are present in two common fibrous proteins,

α-keratin and collagen