Secondary protein structure

Question 1

What are the most commonly observed secondary structural elements

Answer 1

a-helix (alpha helix) and b-strands (beta strands)

Question 2

What is the α-helix?

Answer 2

The α-helix is a coiled or spiral conformation in which every backbone carbonyl oxygen (C=O) group forms a hydrogen bond with the backbone amide (N-H) group of the amino acid four residues ahead of it in the helix.

Question 3

What direction can the a-helix turn?

Answer 3

The helix can turn right or left from N to C terminus, but right-handed helices are most often observed in nature, since this produces less clashes.

Question 4

Why is the α-helix stable?

Answer 4

Although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable.

Question 5

What is another name for the α-helix?

Answer 5

The α-helix is also known as 3.613 helix, since each turn of the helix has approximately 3.6 amino acids (measuring 5.4 Å) and a 13 member ring is formed by hydrogen bonding.

Question 6

What were the key developments in the modeling of the α-helix?

Answer 6

The two key developments in the modeling of the α-helix were: (1) the correct bond geometry, thanks to crystal structure determinations of amino acids and peptides, and (2) Pauling’s prediction of planar peptide bonds, and his relinquishing of the assumption of an integral number of residues per turn of the helix.

Question 7

How did Linus Pauling discover the α-helix?

Answer 7

In the early spring of 1948, while Pauling was sick in bed, he drew a polypeptide chain on a strip of paper and folded it into a helix, being careful to maintain the planar peptide bonds. After a few attempts, he produced a model with physically plausible hydrogen bonds. He then worked with Corey and Branson to confirm his model before publication.

Question 8

What was Linus Pauling’s contribution to the study of the α-helix?

Answer 8

Linus Pauling discovered the α-helix and made significant contributions to the study of its structure and stability. He was awarded his first Nobel Prize in 1954 for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances.

Question 9

What is a beta-sheet?

Answer 9

A beta-sheet is a protein structure formed by beta-strands, which are usually 5-10 amino acids in length and form an almost fully extended zig-zag conformation.

Question 10

How do beta-strands usually align to form a beta-sheet?

Answer 10

Two or more beta-strands usually align to form a beta-sheet.

Question 11

What are the two types of beta-sheets?

Answer 11

The two types of beta-sheets are parallel and anti-parallel.

Question 12

How are parallel beta-sheets arranged?

Answer 12

Parallel beta-sheets are arranged with beta-strands running in the same direction, from N-terminus to C-terminus.

Question 13

How are anti-parallel beta-sheets arranged?

Answer 13

Anti-parallel beta-sheets are arranged with successive strands of alternating directions, from N-terminus to C-terminus followed by C-terminus to N-terminus.

Question 14

What is a mixed beta-sheet?

Answer 14

A mixed beta-sheet contains both parallel and anti-parallel strands.

Question 15

What are loops in proteins?

Answer 15

Loops are regions in proteins that separate segments of α-helix and/or β-strands. They vary in length and shape and are typically rich in polar/charged amino acids. Loops are present on the surface of polypeptides and often form the active sites of enzymes or the antigen binding domains of antibodies. They participate or contribute directly to the polypeptide’s biological function.

Question 16

What is a β-turn?

Answer 16

A β-turn is a loop structure found in many polypeptides that achieves a 180 ̊ alteration in backbone direction over the course of 4 amino acid residues, and is most often found between two stretches of antiparallel β-strands.

Question 16

What is a β-turn?

Answer 16

A β-turn is a loop structure found in many polypeptides that achieves a 180 ̊ alteration in backbone direction over the course of 4 amino acid residues, and is most often found between two stretches of antiparallel β-strands.

Question 17

How is a β-turn stabilized?

Answer 17

The β-turn is stabilized in part by the formation of a hydrogen bond between the C=O of the first residue and NH of the fourth residue.

Question 18

What are domains in proteins?

Answer 18

Domains are composed of structural motifs, which are stretches of secondary structure linked via loops and arranged in a specific 3D conformation.

Question 19

How many types of domains are there?

Answer 19

There are three types of domains: alpha (α) domains, beta (β) domains, and alpha-beta (αβ) domains.

Question 20

What is the core structure of an α domain?

Answer 20

The core structure of an α domain is built exclusively from stretches of α-helix, with the four-helical bundle structure being the most common motif contributing to this.

Question 21

What is the core structure of a β domain?

Answer 21

The core structure of a β domain is comprised of antiparallel β-sheets, usually with two sheets packed against each other to form a distorted barrel-like structure.

Question 22

What are αβ domains?

Answer 22

αβ domains consist of combinations of β-α-β motifs that form parallel β-sheets surrounded by stretches of α-helix.

Question 23

What are the most common domain types found in proteins?

Answer 23

The most common domain types found in proteins are α, β, and αβ domains.

Question 24

What are some commonly observed structural motifs?

Answer 24

Some commonly observed structural motifs include: the helical bundle, the β-hairpin, the Greek key motif, the Jelly roll, the β-sandwich, and the β-barrels.

Question 25

What is the helical bundle motif?

Answer 25

The helical bundle motif consists of several stretches of α-helix separated by short bends or loops, and the α-helical elements are almost fully parallel or antiparallel to each other. The axis of the helical bundle can sometimes be twisted, giving it a twisted appearance. Different numbers of constituent helical stretches may also occur.

Question 26

What is the β-hairpin structural motif?

Answer 26

The β-hairpin is a simple structural motif consisting of two stretches of β secondary structure connected by a loop.

Question 27

What is the β-hairpin?

Answer 27

The β-hairpin is a simple structural motif consisting of two stretches of β secondary structure connected by a loop.

Question 28

What is the Greek key motif?

Answer 28

The Greek key motif consists of four adjacent antiparallel strands and their linking loops. It consists of three antiparallel strands connected by hairpins, while the fourth is adjacent to the first and linked to the third by a longer loop.

Question 29

What is the Jelly roll motif?

Answer 29

The Jelly roll motif is composed of two closely associated Greek key motifs forming a nearly fully closed barrel shape.

Question 30

What is the β-sandwich motif?

Answer 30

The β-sandwich motif consists of two β-sheets packed face to face against each other. It can also have variations, such as the αβα sandwich consisting of a layer of β-sheet packed tightly between two α-helical structures.

Question 31

What is the αβ domain?

Answer 31

The αβ domain is a type of protein domain consisting of combinations of β-α-β motifs that form parallel β-sheets surrounded by stretches of α-helix.

Question 32

What is a domain in protein structure?

Answer 32

A domain in protein structure is a distinct, compact, and independently folding unit of a polypeptide chain, usually composed of building blocks called structural motifs.

Question 33

What are β-barrels?

Answer 33

β-barrels are assemblages of stretches of β-strands, separated by loops and folded into a barrel-like structure.

Question 34

How are beta-strands typically arranged in beta-barrels?

Answer 34

Beta-strands in beta-barrels are typically arranged in an antiparallel fashion.

Question 35

What is the α/β barrel?

Answer 35

The α/β barrel is a variation of the β-barrel structure, which is composed of alternating α and β stretches.

Question 36

What is the orientation of hydrophobic and hydrophilic residues in porins and other membrane proteins containing β-barrels?

Answer 36

Hydrophobic residues are oriented toward the exterior, where they contact the surrounding lipids, and hydrophilic residues are oriented toward the interior pore.

Question 37

What are porins and what is their function?

Answer 37

Porins are transmembrane channels that are generally non-selective. They are found in the outer membrane of Gram-negative bacteria and allow the passive diffusion of small molecules across the membrane.