Biochem - protein structure

What is the hierarchy of protein structure?

• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

What are Angstroms?

• Unit for length

• Equal to 10^-10 metres

What are Daltons?

• Unit of mass almost equal to the mass of a hydrogen atom

• Used to express mass on an atomic scale of objects - protein molecular weights

• 1 Da = 1 au

What are the five secondary structures possible in a polypeptide?

• a-helices

• B-sheets

• Reverse turns

• Loops

• Structural motifs

What is the structure of an a-helix?

• Rod-like structure

• Tightly coiled polypeptide chain forms the inner part of the tube

• Amino acid residue R-groups extend outwards in a helical array

• Both phi and psi angles are negative in a right-hand helix

What are the properties of a right-handed helix?

• Number of residues per turn is 3.6

• Pitch is 5.4 angstroms

• H-bonding stabilises the structure with almost optimal H-bond lengths

• Vary from 4 to >40 residues

How is the H-bonding organised in an a-helix?

• Peptide C=O group of a residue at n points at an N-H on a residue at n+4

• Three amino acid residues between the two groups that form a H-bond

How can an a-helix be viewed using plots?

• Use a helical wheel - convenient to view

• One turn in an a-helix is 3.6 residues long so each residue is plotted at 100 degrees around a circle

• Plots highlight the properties of the a-helices with regard to the type of amino acid residue R-groups

• a-helical content of proteins varies from 0-~100%

What is the structure of a B-sheet?

• Polypeptide chain is almost fully extended

• Phi angles are negative, psi values are positive

• Made from at least 2 linked polypeptide chains (typically 4/5)

• Strands can be parallel, antiparallel or mixed

• Have a rippled or pleated appearance

• Distance between adjacent amino acids is 3.5 angstroms, distance between two R groups is 7 angstroms

• B-strands are typically between 3-10 residues long

• Depicted as broad arrows pointing in the direction of the C-terminal

• An important structural element in many proteins

How does H-bonding stabilise the B-sheet?

• H-bonding occurs between the C=O of one strand and the N-H of an adjacent strand

• Pattern varies depending on whether strands are parallel or anti-parallel

What is the structure of reverse turns and how does H-bonding stabilise the structure?

• Also known as B-turns or hairpin turns

• H-bonding stabilises abrupt changes in direction of the polypeptide chains in B-sheets

• C=O group of residue i is H-bonded to the N-H group of residue i+3

What is the structure of loops and where are they found in a protein structure?

• Do not have a regular periodic structure

• Loop structures are often rigid and well defined

• Turns and loops are found on the surfaces of proteins and often participate in interactions with other proteins or molecules

What structural motifs can be present in proteins?

• Elements of a secondary structure will often link together into common combinations

• Form as mini-domains or ‘motifs’ that have some stability in their own right

• Helix-turn-helix motif

• Hairpin motif

• Greek key motif

• B-a-B motif

What are some vital statistics of proteins?

• Proteins are polypeptide chains that contain between 50-2000 amino acid residues

• Molecular weight of most proteins is between 5500-220,000Da

• Proteins are on the nanometre scale

• Widths typically range between 2-100nm

What are the bond lengths between amino acids?

• Amino acids are joined by peptide bonds to form polypeptide chains

• Peptide bonds have partial double bond character and is therefore stronger than a single bond with less flexibility - 1.32 angstroms long

What are the stereo configurations of peptide bonds?

• Planar due to partial double bond character

• Two configurations possible: cis or trans

• Trans configuration - two a-carbons are on opposite sides of the peptide bond

• Cis configuration - two a-carbons are on the same side of the peptide bond

• Almost all peptide bonds are trans

• R groups are on opposite sides of the chain to avoid steric clashes

What shapes can bonds within a residue form?

• Free rotation around the single bonds within a residue

• Phi is the angle of rotation around the atom between N and the a-carbon

• Psi is the angle of rotation around the atom between the a-carbon and the carbonyl carbon

• Phi and psi angles determine the path of the polypeptide chain

How can allowed steric combinations be viewed?

• Allowed values can be visualised on a two-dimensional plot (Ramachandran Plot)

• Rigidity of the peptide bond and restricted set of phi and psi angles limit the number of structures accessible to an unfolded polypeptide chain

• Will fold into regular structures

What are the tertiary structures of a protein?

• Overall fold of the whole protein

• Can be made up from any combination of a-helices, B-sheets and loops

• Active form of the protein or enzyme may require post-translational modification and/or binding of cofactors

What was the first all a-helix protein?

Myoglobin

What was the first all B-sheet protein?

Concanavalin

What are the common tertiary folds?

• Globin fold

• a/B barrel

• B barrel

What are domains within a protein?

Sections that fold independently

What is the quaternary structure of the protein?

• Groups of two or more protein chains

• Can be the same protein with two or more copies of the same monomer - homomultimer

• Different proteins can come together to make the mature protein - heteromultimers

What three models can be used to visualise proteins?

• Space-filling model

• Ribbon or cartoon diagram

• Wireframe/ball and stick diagram