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1、Chapter 5-1 Protein function, modulation and evolution (Fibrous proteins)Biochemistry Lecture (Sept. 27, 2012)Fibrous proteins play protective, connective and supportive roles Highly elongated and filamentous; forming rod or wire -like regular repeating structures. Water-insoluble and structurally i
2、nert. Keratin, collagen, silk fibroin and elastin are typical examples. Used to construct as hair, horns, wool, nails, feathers, scales, or connective tissues, tendons, bone matrix and muscle fibers, or silk cloth and spider webs. A preponderance of amino acids with small, nonreactive side groups is
3、 characteristic for structural proteins, for which H-bonded close packing is more important than chemical specificity (unlike globular proteins). Amino acid sequences favor a particular kind of secondary structure which, in turn, confer particular mechanical properties on the proteins.“Structure dic
4、tates function” is nicely illustrated in fibrous proteinsFibrous proteins give strength and/or flexibility to the structure containing them.Rope-like protein filaments are often cross-linked with covalent bonds (through Cys or Lys residues).(b b-keratins)Exact molecular structure of fibrous proteins
5、 are difficult to determineBecause they do not form crystals and insoluble, thus can be examinedneither by X-ray crystallography, nor by NMR. Abundant in amino acids Of non-bulky side chains (e.g., Gly, Ala); Pro or its hydroxylated form is rich in collagen and elastin (preventing the formation of t
6、ypical a a-helices) Certain amino acids are lacking in certain fibrous proteins (e.g., Cys, Tryp, His,Met for elastin; Cys and tryp for collagen, Cys and Met for fibroin). Collagen is not a good nutrient (low percentage of essential amino acids)Amino acid compositions of four typical fibrous protein
7、s Each has aUnique Amino acidComposition!Fibrous proteins often contain repetitive sequences forming extended structures of strength and flexibilityCollagen (triple helix)a a-keratin (coiled coils)Silk fibroin (b b sheets)Elastin(a a form)Every other residue is a Gly (others are Ala & Ser)! a a-kera
8、tins contain coiled coils Main constituent of tough and insoluble non-mineral structures that grow from the skin like hair (wool), horns, claws, nails and hooves in mammals (a a-keratins), shells, scales and claws in reptiles, beaks and feathers in birds (b b-keratins); armor or exoskeleton of arthr
9、opod (in combination with chitin); Durable, insoluble, chemically unreactive, pliable.b b-keratina a-keratinsX-ray diffraction was used to study the structure of hair and wool (a a-keratin) (1930s, Astbury;1950s, Pauling and Crick)a-a-Keratin(unstretched hair)-keratin was proposed to form coiled coi
10、ls (Crick, 1952) This was soon after structure of a-helix suggested in 1951 by Linus Pauling. a-keratin gave reflexion at 5.15 A, but normal a-helix at 5.4 A. A coiled coil model explain the data better than a straight a-helix. Crick, FHC (1952) Is -Keratin a coiled coil?. Nature 170: 882883 a a-ker
11、atin forms coiled coils The central segment of each polypeptide chain has a 7-residue pseudorepeat, a-b-c-d-e-f-g (a heptad), with nonpolar residues predominating at positions a and d. The two keratin helices are inclined about 18 relative to one another, resulting in the coiled coil arrangement, al
12、lowing the contacting side chains to interdigitate (i.e., the knobs into holes packing).HydrophobicstripsCoiled coils are also commonly found in globular proteins (e.g., in leucine zipper)a a-keratin coiled coils assemble further to form larger supramolecular structures Terminal heads and tails impo
13、rtant; Level of S-S- bonds related to hardness and springness; Assemble mechanism still poorly understood.Hairs are curled (“permanent waving”) by reestablishing the disulfide bonds between the a a-keratin peptide chain 112233445566112233445656Collagen proteins found in connective tissues in mammals
14、 Found in tendon, ligament, skin, cornea, cartilage, bone, blood vessels, the gut, etc. provide tensile strength. Make up 1/3 of all protein of an animal body. Collagen proteins found to possess unique amino acid composition and repeating sequences A main extracellular protein of the connective tiss
15、ues of mammals (often produced by fibroblasts). Having about 300 repeated Gly-Pro-X or Gly-X-HyPro sequences (X being any other residue) with intra-chain H-boding not favored. Half of the collagen sequence contain amino acid residues other than Gly and Pro! Such high glycine and regular repetitions
16、are found in other fibrous proteins (e.g, silk fibroin, elastin) but never found in globular proteins. X-ray reflection studies hinted a regular molecular structure for collagen The molecular and packing structures of collagen have eluded scientists over decades of research. The reflection pattern o
17、f collagen (tendon) indicate the impossibility of having irregular structures (1935).X-ray diffractionpattern of DNAfibers.X-ray diffraction patternof collagen fiber (tendon)Meridian arcEquatorial reflectionTriple helix structure models proposed for collagen structure (Pauling)Pauling, L. & Corey, R
18、. B. (1951) The Structure of Fibrous Proteins of the Collagen-Gelatin Group. PNAS, 37:272-281.BUT cis- cis-trans- peptide bonds incorrectly proposed!1901-1994Triple helix structure models proposed for collagen structure (Ramachandran) Ramachandran, G.N. and Kartha, G. 1954. Structure of collagen. Na
19、ture 174:269270. All in trans-configuration; Two of three NH groups in each turn of a chain form H-bonds with an O of each of the other two chains; The third NH from a Pro residue points outward from the cylinder. The collagen triple helix is thus called the “Madras helix” (the a-helix the “Californ
20、ia helix”; the DNA double helix the “British helix”)1922-2001 The triple helices can either be homo- or hetero-trimers Forming a long, rod-like structure, stiff but flexible, ,1.5 nm wide and over 300 nm long, topped at both ends by globular domains (procollagen). Genetic disease (e.g., Osteogenesis
21、 Imperfecta) caused by a single substitution of the Gly residue!Every third residue lies near the center of the triple helix and can only by Gly.Biosynthesis and assembly of collagen. Extensive posttranslational modifications before secretion. Head domains removed after secretion and before assembly
22、 into fibrils.The C-propeptideseems to mediatechain assembly.The sugars play key roles in tissue organizationVitamin C (Ascorbate) is needed for the prolyl hydroxylase to function, deficiency causes scurvy It seems to reduce ferric iron ( Fe3+ ) to ferrous (Fe2+), as well as to reduce O2. Scurvy:Red
23、ucedOxidizedVitamin CThe hierarchical supramolecular arrangement within collagen fibers is far more elusive None of the models so far advanced is universally accepted. Major issue: Correlate the striated pattern with a molecular staggering pattern.One model of molecular packing in collagen fibrilsTr
24、iple-helices arranged in hexagonal or quasihexagonal array in cross-section. Collagen triple helices are cross-linked via the Lys residues Catalyzed by enzymes.Fibroins Produced by insects and spiders; tough but flexible. b-pleated sheets of antiparallel strands. The side chain R groups in silk are
25、not very bulky The b sheets stack to form a microcrystalline array in which layers of contacting Gly side chains from neighboring sheets alternate with layers of contacting Ser and Ala side chainsCocoonVery flexible but relatively inextensible!X-ray diffraction and Electron microscopy were applied t
26、o study the structure of silk fibers Suggesting a sheet-like structure.X-ray photograph of powder silk (1954）Electron micrograph of silk (1967)Spider webSpiders silk fiber formation: spidroin protein adopts different secondary structure at different locations The a-helice structure prevents them fro
27、m assembly into b-sheet structures before they are secreted.Elastin endow connective tissues with resilience Permitting long-range deformability and passive recoil without energy input. Critical to the function of arteries, which undergo repeated cycles of extension and recoil, and to lungs, skin an
28、d all other dynamic connective tissues.aorta LysLysLysLysHydrophilic cross-linked domains (rich in Lys and Ala)Instrinsically disordered Hydrophobic domains (rich in Val, Pro, and Gly; dynamic conforamtion)An “oiled coil” model was proposed to explain elastins elastic behaviorGray, W. R., Sandberg,
29、L. B. & Foster, J A.(1973) Molecular Model for Elastin Structure and Function Nature 246, 461-466. Mainly based on striking sequence features. Each monomer is fibrillar, of alternating segments of cross-linked regions and “oiled coils”; form a network of 3D spring.Highlights of the structure of elas
30、tin (1) Occurrence of alternating regions rich in alanine and lysine (cross-link regions) and in glycine, valine and proline (hydrophobic regions). (2) Glycine, alanine, valine and proline comprise approximately 75% of the total residues. (3) The cross-links (desmosine, isodesmosine and others) main
31、tain peptides in register during extension and retraction. (4) The hydrophobic regions are responsible for elasticity. (5) Extensive differences in hydrophobic sequences occur between bovine and chick elastins, compatible with random coil structures.Quiz 3 Gram-negative bacteria characteristically a
32、re surrounded by outer membrane and cytoplasmic membrane (inner membrane). Among outer membrane proteins, the sheets are the most regular structure, the -helix is commonly used by inner membrane proteins. A hypothesis is that outer membrane proteins need more stable structure than inner membrane proteins. Please explain why - sheets are more stable than -helix? If you dont agree with this hypothesis, please give an appropriate explanation why outer membrane proteins utilize - sheets.
生物化學：Chapter 5-1 Protein function, modulation and evolution
