Lecture 6:Protein Architecture II: Secondary Structure or From peptides to proteins Margaret Daugherty Fall 2004 Outline Four levels of structure are used to describe proteins; Alpha helices and beta sheets form the majority of secondary structure found in proteins; turns are also important in structure formation Certain folds or modules are frequently used; Proteins are always in motion. Levels of Protein Structure Primary (1 ) Structure Linear sequence of AAs linked by peptide bonds 1 M R L A F C V L L C A G S L G L C L A F P K E T V R W C T V 31 S S Q E A S K C S S F R H N M K K I L P V E G P H V S C V K 61 R T S Y L E C I R A I L A N E A D A V T I D G G L V F E A G 91 L A P Y N L K P V V A E F Y G S K D D P Q T H Y Y A V A V V Primary, 1 o ; Secondary 2o; (Supersecondary); Tertiary, 3 o ; Quaternary, 4 o.
Secondary Structure Elements These are local structures that are stabilized by hydrogen bonds; Local means arising from interactions of amino acids near one another in the polypeptide sequence How to tell a left- vs. right-handed a-helix Point your thumb up in the direction of the α-helix (N-->C). α - helix other helices β - sheets β - turns left-handed α-helix right-handed α-helix Look where the base of the helix spirals are. If they match the knuckles on your right hand it is a righthanded helix. ----------or----------- If the helix spirals up in a counterclockwise direction, it is a right-handed helix. The α - helix: the facts Helical structures Hydrogen bonding scheme THE NUMBERS! *Residues per turn: 3.6 *Rise per resiude: 1.5 Å n n+1 n+2 n+3 n+4 rise per residue Pitch *Rise per turn (pitch): 3.6 x 1.5Å = 5.4Å *φ = -60 o ; ψ = -45 o All NH and C=O groups are joined with H bonds except the first NH group and last C=O groups at end of helix. α-helix:hydrogen bonds between C=O of residue n and NH of residue n+4;
The α Helix has a Dipole Note that there is a different polarity of the NH and C=O groups; A dipole is created in the helix with a partial positive charge at the N-termini, and partial negative charge at the C-termini; Corresponds to a 0.5 to 0.7 unit charge at the end of each helix. Helix Capping: Taking care of unmatched chemical groups at helix ends Unpaired C=O groups at C-terminal end Unpaired N-H groups at N-terminal end Unfavorable hydrophobic interactions: ends of helices are often near surface of proteins. If the side chains are hydrophobic, there is the potential for interaction with H 2 0. Proteins fold to provide appropriate hydrophobic groups to avoid unfavorable interactions. Stereo view of an a-helix HELIX MAKERS AND BREAKERS What happens with long stretches of polyglu and polyasp? What is their charge at ph 7.0? What would a bunch of negative charges close together do? What about ph 1-2?
Arrangement of AA in Helices Secondary Structure:The β Sheet α-helices usually partially buried one side faces hydrophobic core the other faces the solvent Pseudo-repeat (n+3) for sidedness; Helical wheel projects helix onto a plane perpendicular to the plane of the axis. Second type of structure stabilized by local cooperative formation of hydrogen bonds Component: stretched out polypeptide chain (β strand). The β strands are located next to each other Also a Pauling and Corey proposal Hydrogen bonds can form between C=O groups of one strand and NH groups of an adjacent strand. Two different orientations Parallel: all strands run same direction Antiparallel: strands in alternating orientation Antiparallel β Sheet Hydrogen Bonding Parallel β sheet hydrogen bonding β-sheet is most extended; stabilized by interstrand hydrogen bonds Residues alternate hydrophobe/hydrophilic --> amphiphilic nature to sheet Can be composed of as little as 2 strands Ideal hydrogen bonds; alternating spacing Rise per residue: 3.47 Å Nonideal, but evenly spaced hydrogen bonds that bridge at an angle. Stabilized by interstrand hydrogen bonds Rise per residue: 3.25Å Large structures: consist of > 5 strands Usually hydrophobes found on both sides
Antiparallel β-sheet Thioredoxin A mixed parallel/antiparallel β sheet protein Parallel β-sheet Side view of parallel β-sheet Note the twist! Chris Francklyn @1999 AMINO ACID DISTRIBUTION IN A β-sheet Stereo view! β-turns: a protein must stay compact Two short 2-stranded antiparallel β-sheets Hydrophobic interactions stabilize core of protein Polar and charged amino acids on surface Note: Steric complementarity between sheets! Three types of turns (I, II, 3 10 ) Proline is often found in second position Question to think about: If hydrophilic groups can hydrogen bond with each other, why are they rarely found on the inside of a protein? Glycine is often found in turns Turns often have polar or charged groups
β-bulges: mismatched β-strands Characteristic Compositions Does the AA sidechain (R) really matter in the formation of any of the secondary structures? Return of the Ramachandran Plot α L Plot of residues in a small protein (BPTI) Region in gray - sterically inaccessible; Allowed regions - white. β A, β p, α R and 3 denote regions permissible to different secondary structure elements Amino acids cluster to the preferred regions for the secondary structural elements Supersecondary Structure: How small units of secondary structure come together Motif= small secondary structure elements; not stable folding units, however are often important parts of the functional sites of proteins Domain= independently folding structural element; can be a protein in and of itself, oftentime are repeated in proteins
Motifs simple geometric arrangements of one or more secondary structure elements; not capable of independent folding/stability. Helix-turn-helix Calcium binding motif COMMON MOTIFS FOUND IN PROTEINS Troponin-C Chris Francklyn @1999 Domains (or modules p. 186-188) Examples of Domains "Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981 Features of domains: built from structural motifs; independent folding elements; functional units; separable by proteases. Typically, globular proteins are organized into one or more domains.
COMMON DOMAIN FOLDS complement coat protein immunoglobulin fold fibronectin type I module EXAMPLES OF PROTEINS THAT ARE MODULAR IN DESIGN growth factor module kringle module γcg - contain many γ-carboxyglu residues G - epidermal growth factor K - kringle C - complement F1, F2, F3 - fibronectin domains N - found in growth factors E - E-F Ca++ binding domain homology LB - lectin binding domain Review 1). Primary structure refers to linear sequence of amino acids. 2). Secondary structure refers to local structures that are stabilized by hydrogen bonds. 3). α-helices have a non-integral number (3.6) of residues per turn and a rise per residue of 1.5 A (these numbers are key). 4). α-helices are variable in length and have a dipole. 5). Some amino acids are preferentially found in helices; others are not. 6). β-sheets are extended structures stabilized by hydrogen bonds. 7). β-sheets can be antiparallel or parallel; can you list the similarities and differences? 8). β-turns are the most common type of turns in structures. Why would prolines and glycines often be found in turns? Why would charged residues be likely to be found in turns? (Think location!) 9). Secondary structure elements can arrange themselves into motifs or domains (modules). Motifs are not stable, independent folding units- they are found only in the context of the whole protein. Domains are independent folding units that can exist in isolation. Important numbers to know Structure rise pitch H-bonding pattern α-helix 1.5 Å 5.4Å C=O to NH that is 4 residues up β-sheet parallel 3.25 Å non-ideal H-bonds, large sheets antiparallel 3.47 Å ideal H-bonds, small sheets