Protein FOLDING

proteins Proteins are composed of amino acids linked with peptide bond The way or sequence b y different amino acids are linked together makes the primary structure of a protein.

Peptide bond formation This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water.

Properties of Peptide bond Joins amino acids 40% double bond character Caused by resonance Results in shorter bond length Double bond disallows rotation

Biochemist’s peptide unit – from N to C – all main chain atoms within the unit lie in the same residue Structural biologist’s peptide unit – from Cα to next Cα - all main chain atoms within the unit lie in a plane

Torsion Angles A torsion angles is defined by 4 atoms; the carboxylic carbon, C1 the alpha carbon, C2 or C-alpha; and the amide group nitrogen, N. THREE repeating torsion angles along the peptide backbone chain are; phi (φ) N-Ca Single bond psi (ψ) Ca-CO Single bond omega (ω) C-N Partial double bond Dihedral angle— A measure of the rotation about a bond, usually taken to lie between -180° and +180°. Dihedral angles are sometimes called torsion angles

Rotations about Dihedral angles

Peptide bond has resonance structures Peptide bond has resonance structures --> partial double bond character Peptide bond is a partial double bond, so backbone can only rotate around Psi (ψ) and phi (φ) bonds. Planar

Peptide Bonds Are Planar The OMEGA angle tends to be planar (0 or 180o) due to delocalization of the carbonyl pi electrons & the nitrogen lone pair. Due to the partial double bond character of the peptide bond; six atoms (Cα, C, O, N, H, and Cα) lie in a plane in a pair of linked amino acids - there is no rotation about the peptide bond (peptide). 

Trans is generally favored over cis: Generally, the two Cα groups in a trans configuration experience minimum steric interaction (cis/trans) than when in cis. Because of the partly double nature of the peptide bond, ω is always close to 180o for trans- peptides or 0o for cis- peptides (±30o in exterme cases) Cis- peptides are energetically extremely unfavourable (~1000 fold) because of steric clashes between the neighbouring Cα atoms The trans configuration is adopted for almost all peptide bonds

Proline’s Cyclic Structure is Particularly Limiting some specific bonds are often cis The only exception is peptide bond before proline, where cis- peptide is just 4 times less favourable than trans- peptide, because there are some steric clashes in both cis- and trans- forms Tyr-Pro (25%), Ser-Pro (11%), X-Pro (6.5%) Proline’s Cyclic Structure is Particularly Limiting (phi) is limited

Proline adopts cis and trans forms Proline cis-trans isomerization is an important factor in protein folding – prolylpeptydyl isomerases catalyze isomerization step According to statistics, 0.03% of non-proline peptides and 5.2% of X-Pro peptides are in cis- conformation, resulting in a total of 0.3 % cis-peptides. It’s in cis configuration (6% of the time), frequently in b-turns

The key to protein folding lies in the torsion angles of the backbone The peptide backbone conformations can be described by Phi (φ) and Psi (ψ), pure single bonds. The two adjacent rigid peptide units may rotate about these bonds, taking on various orientations. This freedom of rotation about two bonds of each amino acid allows proteins to fold in many different ways.

The peptide bond constrains the polypeptide The length and angles are fairly invariant in the known protein structures The planarity of the peptide bond restricts omega to 180 degrees in very nearly all of the main chain peptide bonds. In rare cases omega = 0 degrees for a cis peptide bond which, usually involves proline. • φ and ψ are flexible, therefore rotation occurs here • However, φ and ψ of a given amino acid residue are limited due to steric hindrance like clashes of backbone atoms and Cb atom • Only 10% of the {φ, ψ} combinations are generally observed for proteins • First noticed by G.N. Ramachandran

Main Chain Conformations Factors that influence the conformational equilibria of peptide chains are: • Conformations are defined by dihedral angles Φ & Ψ. • Hydrogen bonding of amide carbonyl groups to N-H donors. • Steric crowding of neighboring groups. • Repulsion and attraction of charged groups. • The hydrophilic and hydrophobic character of substituent groups. Interference to rotation caused by spatial arrangement of atoms within molecule Atoms cannot overlap Atom size defined by van der Waals radii Electron clouds repel each other

Steric Collisions in addition to peptide bond φ = 0 ψ = 0 combination is forbidden Collision comes from peptide backbone and from R group.

Secondary Structure Elements Alpha-helix Secondary Structure Elements

Secondary structure elements in proteins A secondary structure element is a contiguous region of a protein sequence characterized by a repeating pattern of main-chain hydrogen bonds and backbone phi/psi angles alpha-helix (local interactions) beta-strand (non-local interactions)

Elements of protein structure 1˚ 2˚ Primary structure - the covalent Structure of the protein: sequence, Plus disulfides and modifications. Secondary structure - Local conformation of some part of a polypeptide. Primary structure determines secondary structure -

Secondary Structure Can a polypeptide chain fold into a regularly repeating structure? In 1951, Linus Pauling and Robert Corey proposed two periodic structures called the α helix (alpha helix) and the β pleated sheet (beta pleated sheet). Subsequently, other structures such as the β turn and omega (Ω) loop were identified. Protein 2ndary structure takes one of three forms: α helix β sheet Turn, coil or loop 2ndary structure are tightly packed in the protein core in a hydrophobic environment Although not periodic, these common turn or loop structures are well defined and contribute with α helices and β sheets to form the final protein structure.

The reasons of secondary structure formation Since sidechains of hydrophobic residues are located in the hydrophobic core, the mainchain atoms of the same residues in most cases are also within the hydrophobic core. Since the presence of polar groups in hydrophobic environment is very unfavourable, the main chain N- and O- atoms have to be neutralised by formation of hydrogen bonds. The two most efficient ways of hydrogen bond formation is to build an alpha helix or a beta sheet Reflects the tendency of backbone to hydrogen bond with itself in a semi-ordered fashion when compacted

the main-chain can hydrogen bond to itself there are also side-chain acceptors and donors the carbonyl oxygen: main-chain hydrogen bond acceptor the amide nitrogen: main-chain hydrogen bond donor

Main-chain H-bonds make proteins special “It would seem extraordinary that no other polymer structures exist in which internal hydrogen bonding can give rise to periodically ordered conformations, but no others have been found thus far. We are therefore forced to recognize the uniqueness of this capacity in polypeptide chains, one which enables them to meet the exacting and sophisticated demands of structure and function” --Doty P, Gratzer WB in Polyamino acids, polypeptides and proteins, pp. 111-118, 1962, University of Wisconsin Press 2° structure full of H-bonds Why so much 2° structure? Saturate with H-bonds neutralize dipoles in buried regions. Provide rigidity, stability: let mutations change chemical properties only not conformation.

The Alpha Helix Figure 3.29. Structure of the α Helix. (A) A ribbon depiction with the α-carbon atoms and side chains (green) shown. (B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups. (C) An end view shows the coiled backbone as the inside of the helix and the side chains (green) projecting outward. (D) A space-filling view of part C shows the tightly packed interior core of the helix.

The Alpha Helix Most common (about 25% of the amino acids in proteins are in this structure) Repetitive secondary structure 3.6 residues per turn; pitch (rise per turn) = 5.4 Å C′=O of i forms H bonds with NH of residue i+4 Intra-strand H bonding C′=O groups are parallel to the axis; side chains point away from the axis All NH and C′O are H-bonded, except first NH and last C′O H-bonds are in-line, optimum distance Hence, polar ends; present at surfaces Right –handed favored due to steric constrains Stability is greatly enhanced by internal van der Waals contacts R-groups project outward, and provide the main constraints on helical structure Interactions do not involve side chains Interaction with other helices, charged chains, ions and molecules

The Alpha Helix Is a Coiled Structure Stabilized by Intra-chain Hydrogen Bonds The α helix is stabilized by hydrogen bonds between the NH and CO groups of the main chain…. situated four residues ahead in the sequence. Dipoles of H-bonding atoms NH and CO are well aligned along the axis of helix. Except for amino acids near the ends of an α helix, all the main-chain CO and NH groups are hydrogen bonded. Each residue rises 1.5 Å along the helix axis…a rotation of 100 degrees…3.6 amino acid residues per turn of helix. pitch of 5.4 Å. Amino acids spaced three and four apart in the sequence are spatially quite close to one another in an α helix. Radius allows favorable van der Waals contacts across helical axis. Side chains are well staggered minimizing steric interference. The internal cavity is dominated by H-bonds and (all atoms at allowed intra-atomic contacts).

α-Helix has: 3.6 residues per turn Rise/residue = 1.5 Å Rise/turn = 5.4Å Hydrogenbonds are made between residues n and n+4

Hydrogen-Bonding Scheme For an α helix In the α helix, the CO group of residue n forms a hydrogen bond with the NH group of residue n+ 4.

Dipole moment A helix has an overall macro dipole moment , -ive at carboxy end and +ive at amino end. Helix dipole results from orientation of CO - NH hydrogen bonds of the peptide bond pointing along the helix axis. The dipole is neutralized by H-bonds between NH and CO groups in the center of helix but ends. The overall dipole can lead to destabilization of the helix through entropic effects. As a result, α helices are often capped at the N-terminal end by a negatively charged amino acid, such as glutamic acid, in order to neutralize this helix dipole. Less common (and less effective) is C-terminal capping with a positively charged amino acid, such as lysine.

The dipole moment of a helix The N-terminal positive charge is commonly used to bind negatively charged ligands such as phosphate groups, because the backbone amides can serve as hydrogen bond donors.

Other Types of Helical Structures 3.10 helix pi-helix

Secondary Structure – Triple Helix Three polypeptide chains woven together Glycine, proline, hydroxy proline and hydroxylysine H bonding between –OH groups gives a strong structure Typical of collagen, connective tissue, skin, tendons, and cartilage

Polar α -helices can be: R-groups extend radially from the α-helix core, shown in helical wheel diagram. α -helices can be: Polar Amphipathic Hydrophobic

Amino-acid propensities Different amino-acid sequences have different propensities for forming α-helical structure. Methionine, alanine, leucine, glutamate, and lysine ("MALEK“ ) all have especially high helix-forming propensities. Proline, glycine, tyrosine and serine have poor helix-forming propensities. Proline tends to break or kink helices because it cannot donate an amide hydrogen bond (having no amide hydrogen), and because its side-chain interferes sterically. Proline’s ring structure also restricts its backbone φ dihedral angle to the vicinity of -70°, which is less common in α-helices. However, proline is often seen as the first residue of a helix, presumably due to its structural rigidity. At the other extreme, glycine also tends to disrupt helices .. its high conformational flexibility makes it entropically expensive to adopt the relatively constrained α-helical structure.

Table. Relative frequencies of amino acid residues in secondary structures a helix b sheet Turn Ala 1.29 0.9 0.78 Cys 1.11 0.74 0.8 Leu 1.3 1.02 0.59 Met 1.47 0.97 0.39 Glu 1.44 0.75 1 Gln 1.27 His 1.22 1.08 0.69 Lys 1.23 0.77 0.96 Val 0.91 1.49 0.47 Ile 1.45 0.51 Phe 1.07 1.32 0.58 Tyr 0.72 1.25 1.05 Trp 0.99 1.14 Thr 0.82 1.21 1.03 Gly 0.56 0.92 1.64 Ser 0.95 1.33 Asp 1.04 1.41 Asn 0.76 1.28 Pro 0.52 0.64 1.91 Arg 0.88 After T. E. Creighton, Proteins: Structures and Molecular Properties, 2d ed. (W. H. Freeman and Company, 1992), p. 256.

Five different kinds of constraints affect the stability of an α-helix: Electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups (2) Bulkiness of adjacent R groups (3) Interactions between R groups spaced three (or four) residues apart (4) Occurrence of Pro and Gly residues (5) Interaction between amino acid residues at the ends of the helical segment and the electric dipole inherent to the α- helix. The tendency of a given segment of a polypeptide chain to fold up as an α-helix therefore depends on the identity and sequence of amino acid residues within that segment.

Where are -helices? Globular protein. Hydrophobic helices cross lipid membranes. Amphiphilic are common: Surfaces of globular proteins. Membrane surface proteins, e.g. mellittin Hydrophobic Hydrophilic Globular protein.

Beta Pleated Sheet Secondary Structure

β sheet The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins. A single stretch of β-structure is termed a β-strand. The sheets are made of individual beta strands - The first β sheet structure was proposed by William Astbury in the 1930s. - A refined version was proposed by Linus Pauling and Robert Corey in 1951.

The β-strand A beta strand (also β-strand) is a stretch of amino acids; Typically 5–10 amino acids long. Peptide backbones are almost fully extended. Highly extended form of polypeptide chain. Adjacent side chains point in opposite directions. A beta strand usually is associated with other beta strands…. sheet

Beta Sheet Conformation consists of; Several β-strands associate laterally to form β-sheets. Sheets are stabilized by backbone hydrogen bonds. Sheets can be made of nearby (in sequence) or faraway strands. Main chain H-bonding between CO and NH on adjacent strands is a major contribution to stability R groups extend above and below the sheet…. along each strand, they alternate in pointing “up” and “down” Beta-sheets are very common in globular proteins mostly less than six strands. With a width of approximately 25 Ǻ No preference for parallel or antiparallel beta-sheets Beta strands often interact to form beta sheets: - Parallel - Antiparallel: optimum H-bonding - Mixed

Dihedral angles for secondary structures

β−sheets vs. α-helices Unlike α-helices: Are formed with different parts of the sequence H-bonding is inter-strand (opposed to intra-strand) Side chains from adjacent residues on opposite sides of the sheet and do not interact with one another. Peptide groups of adjacent residues point in opposite directions. The axial distance between adjacent residues is 3.5 Ǻ (0.35nm). Two residues per repeat unit which gives the beta-strand a 7 Ǻ pitch. In alpha-helix the axial distance between adjacent residues is only 1.5 Ǻ. Polypeptides are far more extended than those in the alpha-helix. Sheets are common in the core of protein structures Like α-helices: Repeating secondary structure (2 residues per turn) Can be amphipathic

β-sheet dihedral angles β-sheet consists in the repetition of dihedral angles φ= - 45 to -180 º and ψ= 110 to 180º parallel: phi = -119° psi = +113° antiparallel: phi = -139° psi = +135° This repeated pattern forms a zigzag structure with; a rise per turn of 0.65-0.7 nm a rise per residue of 0.32-0.35 nm , and 2 residues per turn

Hydrogen bonding patterns β strands too can be said to be directional as peptide chains have a directionality conferred by their N-terminus and C-terminus Direction represented an arrow pointing toward the C-terminus in protein topology diagrams Adjacent β strands can form hydrogen bonds in; antiparallel parallel, or mixed arrangements Hydrogen bonding need not be perfect… can exhibit localized disruptions known as beta bulges. Hydrogen bonds lie roughly in the plane of the sheet, with the peptide carbonyl groups pointing in alternating directions with successive residues. β strands are arranged adjacent to other strands and form an extensive hydrogen bond network with each other. N-H groups in the backbone of one strand establish hydrogen bonds with the C=O groups in the backbone of the adjacent strands.

b–structures: Comparison of H- bonding patterns

Antiparallel sheets: How is sheet made? In an antiparallel arrangement, the successive β strands alternate directions … N-terminus of one strand adjacent to the C-terminus of next This arrangement produces strongest inter-strand stability ….. planar inter-strand hydrogen bonds between CO and NH Peptide backbone dihedral angles; φ = –140° ψ = 135° Close pair hydrogen bonds: Two atoms adjacent in two H-bonded β strands form two mutual backbone H-bonds to each other's flanking peptide groups.

Anti parallel Beta sheets: strand directions

Parallel sheets: How is sheet made? All of the N-termini of successive strands are oriented in the same direction. … N-terminus of one strand adjacent to the N-terminus of next This orientation is slightly less stable…. introduces non-planarity in the inter-strand hydrogen bonding pattern. The dihedral angles: φ = –119 ψ) = 113° Two adjacent atoms in two H-bonded β strands do not H-bond…. one residue forms H-bonds to the residues that flank the other Wide pair of H-bonds: Residue i may form H-bonds to residues j − 1 and j + 1; this is known as a. By contrast, residue j may H-bond to different residues altogether, or to none at all. Sheets smaller than five strands may be unstable.

Parallel Beta sheets: strand directions

A mixed b sheet: strand directions An individual strand may exhibit a mixed bonding pattern, with a parallel strand on one side and an antiparallel strand on the other. Mixed sheets are far less common indicating that this pattern is less stable than the antiparallel arrangement.

β -Sheets are said to be pleated The "pleated" appearance of β strands arises from……. tetrahedral chemical bonding at the Cα atoms of the peptide bond which alternates above and below the plane of the sheet. . Pleating causes the distance between adjacent Cα atoms 6Å ….7.6Å (2 × 3.8 Å) expected from two fully extended trans peptide virtual bonds. “Sideways" distance between adjacent Cα atoms in H-bonded β strands is roughly 5 Å.

Pleated antiparallel sheet Note: H-bonds R-groups orientation, distance. Pleated character Ave. strand length is about 6 aa’s 0.7 nm

Pleated parallel sheet Note: H-bonds not at optimal angle. R-group orientations, distances Pleated character Avg. Strand length ~ 6 aa. 0.65 nm

Twist facilitates 3D packing into globular structures Twist in sheets The Pauling-Corey model of the beta-sheet is planar β strands are rarely perfectly extended; rather, they exhibit a slight twist due to; - the chirality of their component amino acids - alternating fluctuations in the dihedral angles prevent the individual β strands in a larger sheet from moving wide apart - a relative rotation of each residue in the strands by 300 per amino acid in a right-handed sense. Twist facilitates 3D packing into globular structures

Sources of the twist: Right-handed looking along strands. optimal f, y Each residue rotates (< 40º) Directions of C==O form slowly turning helix To stay optimally H-bonded, neighboring strands must twist around Almost all b sheets in the known protein structures are twisted…..always right-handed

R-chain arrangements - Two residues per repeat unit The R-groups (side chains) of neighboring residues in a beta-strand point in opposite directions - Axial distance between residues is 3.5 A (alpha helix: 1.5A) - Two residues per repeat unit - beta-strand pitch 7 Ǻ Fully extended β strand…. successive side chains point straight up, then straight down, then straight up, etc. Adjacent β strands in a β sheet are aligned…. Cα atoms are adjacent and their side chains point in the same direction. Amphipathic sheets: adjacent side chains on one side of the sheet are hydrophobic, while other on the alternate side of the sheet are polar or charged (hydrophilic)

Side chain residues alternate above The β-sheet: R Chains Side chain residues alternate above and below β-Sheets Anti-parallel β-Sheet Parallel β-Sheet The side chains point outwards from the folds of the pleats, roughly perpendicularly to the plane of the sheet. successive residues point outwards on alternating faces of the sheet.

Amino-acids have different propensities to form β-sheet β-strand forming amino acids: Amino acids with large bulky side chains prefer to form β-sheet structures Tyr, Trp, Ile, Val, Thr, Cys, Phe Different amino-acids have different propensities to form β-sheet: V,T,I,F,W are sheet makers G,P,A,S,D,E are sheet breakers Large aromatic residues (Tyr, Phe and Trp) and β-branched amino acids (Thr, Val, Ile) favored in the middle of β sheets. Pro likely to be found in the edge strands in β sheets, presumably to avoid the "edge-to-edge" association between proteins that might lead to aggregation and amyloid formation.

β-Sheet energetics Interactions that affect β-sheet stability: 1- Backbone hydrogen bonds between CO and NH of adjacent strands 2- Sidechain-sidechain interactions -> weak intra-chain i,,i+2 interactions -> strong interactions between same positions of adjacent strands 3- β-sheets in proteins are not flat, but have a twist that facilitates their 3D packing into globular structures.

Whenever a bend is introduced… The β-strands that enter and leave the bend must be antiparallel…

Connections Between Parallel b-Strands