Examples of Protein Structures Protein types Proteins fall into three general classes based on their overall three dimensional structure and on their functional role fibrous membrane and globular Fibrous proteins Fibrous proteins tend to be long narrow molecules Fibrous proteins are used to construct macroscopic structures especially structures outside of cells Fibrous proteins tend to have a structural role although some have more active functions as well Examples The protein keratin is used to form hair nails and skin Keratin is a coiledcoil of helices 300 residues long corresponding to about 450 in length Keratin is formed from two helices wrapped around one another the backbone shown below is of a coiled coil protein from PDB ID 3Q0X this portion of the protein probably resembles the keratin coiled coil structure and two of those structures wrapped around each other Thus the keratin molecule contains a total of four intertwined helices The helices in keratin are slightly distorted in order to allow the coiled coil but otherwise are formed from torsion angles similar to those present in normal helices The approximate pair for the keratin helix is 64 42 compared to a normal helix of 57 47 The position of the keratin helices are maintained in their relative locations by hydrogen bonds and disulfide bonds formed between side chains of the helical chains Hair and nail keratin molecules have a higher disulfide bond content than the form of keratin found in skin and are tougher as a result High humidity allows facile rearrangement of hydrogen bonds and can therefore allow the keratin molecules in hair to change their relative positions somewhat Individuals with curly hair frequently find the degree of curling depends on the humidity they also usually find that hair shaped while wet tends to retain its structure upon drying A permanent results from reduction of the disulfide bonds between the chains followed by shaping the hair and by then oxidizing the free sulfhydryl groups to form new disulfide bonds that hold the hair in the new shape Smaller coiled coil structures are also found at the interaction interface between Copyright 2000 2011 Mark Brandt Ph D 42 some types of proteins that form less permanent complexes than keratin especially in some transcription factors such as leucine zipper proteins The multiple types of collagen together comprise the most common animal protein about 25 of the protein in animals is some form of collagen Collagen is a triple helix formed from three polypeptide chains The individual polypeptides form helices that are much more extended than an helix A collagen helix contains 3 3 residues turn compared to 3 6 residues turn but has a rise of 10 turn compared to 5 4 for an helix An helix has a rise per residue of 1 5 in contrast a collagen helix has a rise of 3 per residue and is therefore nearly as extended a structure as a sheet 3 5 residue The extended collagen helix is the result of its pair of 51 153 The angle is thus close to that of the helix but the angle is quite different and is close to the maximal extension angle 180 The collagen triple helix has three of these extended helices wrapped around one another 10 Gly Ser Gly Gly HydroxyPro Pro Pro Pro Pro The collagen triple helix is 14 in diameter Each chain in the collagen triple helix is 1000 residues long The collagen molecule is therefore about 3000 0 3 m long 1000 3 3 residue turn 10 In collagen the polypeptides have the typical sequence Gly X Y n The X residues are frequently proline while the Y residues are frequently hydroxyproline or hydroxylysine Glycine fits in the center of triple helix it is the only residue that is small enough to do so Proline readily adopts the angles required by the triple helix Note the proline rings in the strands shown above In collagen the helices are held in register by several factors One is hydrogen bonding formed using hydroxyproline residues The hydroxyl group is added to the proline residues following the synthesis of the collagen molecule in a vitamin Cdependent reaction Some of the symptoms of scurvy vitamin C deficiency are due to inhibition of proline hydroxylation in collagen Another factor that stabilizes the collagen structure is the result of covalent cross links formed between lysine hydroxylysine and histidine residues within the protein 11 10 The drawing of collagen was created in VMD from PDB ID 3ADM the structure was determined using trimers of a 27 residue artificial model peptide rather than a full length collagen molecule 11 Since collagen molecules are much shorter than the macroscopic structures such as tendons and ligaments that are produced largely from collagen it is apparent that the larger structures require interactions between collagen molecules Some of these interactions are also mediated by side chain hydrogen bonding and other links Copyright 2000 2011 Mark Brandt Ph D 43 Membrane proteins Membrane proteins comprise a unique class of proteins For membrane proteins a significant region of the protein must be stable in a hydrophobic environment This is typically achieved by having non polar side chains on specific surface regions of the protein Because of this exposed hydrophobic surface and because many membrane proteins are destabilized by removal from the membrane most membrane proteins are difficult to work with As a result structural information is available for only a relatively small number of these proteins although new techniques have allowed three dimensional structure determination for increasing numbers of membrane proteins in the last few years An example of a membrane protein is cytochrome c oxidase Cytochrome c oxidase is one of the more important membrane proteins it is the protein that donates electrons to oxygen in the electron transport chain Cytochrome c oxidase is therefore the primary oxygen utilization enzyme in aerobic organisms Its importance stimulated the series of studies that resulted in the solution of its threedimensional structure The region of the cytochrome c oxidase protein that interacts with the membrane is readily visible in the structural representation below 12 In the figure yellow residues are non polar light blue residues are polar blue residues have basic sidechains and red residues have acidic side chains Note the band of non polar residues across the center of the protein Note also that the region is predominantly helical This is because helices satisfy all of the hydrogen bonding