ProteinIPPT课件.pptx
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1、Proteins IProteins 1830 Mulder what remained after removal of sugars, fats, salts, etc.1838 Berzelius “Proteins” from the Greek “of 1st rank or importance”Central Dogma: DNA RNA protein (information flow)DNA, RNA information is in the sequence - linearProtein function is in the 3D structureWhat are
2、proteins?Proteins are linear polymers (chains) of amino acids (more than 50 aa)“Protein”One or more polypeptide chains One polypeptide chain - a monomeric protein More than one - multimeric protein Homomultimer - one kind of chain Heteromultimer - two or more different chains Hemoglobin, for example
3、, is a heterotetramer It has two alpha chains and two beta chainsProteins - Large and SmallInsulin - A chain of 21 residues, B chain of 30 residues -total mol. wt. of 5,733Glutamine synthetase - 12 subunits of 468 residues each - total mol. wt. of 600,000Connectin proteins - alpha - MW 2.8 million!b
4、eta connectin - MW of 2.1 million, with a length of 1000 nm -it can stretch to 3000 nm!Main Protein ClassesFibrous - extended shape, insoluble (e.g. keratin, collagen, elastin)Globular - compact shape, water soluble (e.g. myoglobin, trypsin)Membranous - often multidomain one lipid soluble (e.g. phot
5、oreaction centre, ATP synthase)Biological Functions of ProteinsProteins are the agents of biological functionEnzymes - RibonucleaseSignal transduction Insulin and its receptorControl of Gene expression-Transcription factorsImmunity-AntibodyTransport and Storage - HemoglobinStructural proteins Hair,
6、CollagenContractile proteins - Actin, MyosinExotic proteins - Antifreeze proteins in fishProteins are: Polypeptides + possibly cofactors, coenzymes, prosthetic groups, other modifications Polypeptides are covalently linked -amino acids Cofactors are non-amino acid components e.g. metal ions like Zn2
7、+ in carboxypeptidase Coenzymes are organic cofactors e.g. nucleotides in lactate dehydrogenase Prosthetic groups are tightly attached cofactors e.g. heme in myoglobinHierarchy of protein structurePrimary Structure (1) : Unique sequence of amino acids: sequence is determined by genetic materialSecon
8、dary Structure (2) : regular repeating structures of the polypeptide chain (i.e. -helices, b b-sheets) ;coiling /folding as a result of hydrogen bondingTertiary Structure (3) : 3-D shape due to bonding of R- groupsQuaternary Structure (4) : association of 2 or more polypeptides; Ex HGB ; not all hav
9、e this level Hierarchy of protein structurePrimarySecondaryTertiaryQuaternaryPrimary- sequenceSecondary- e.g -helix or b-sheetTertiary- 3D shapeQuaternary- subunit organization ( one polypeptide chain)Four levels of protein structurePrimary: amino acid sequenceDue to covalent bondThe Sequence of Ami
10、no Acids in a Proteinis a unique characteristic of every proteinis encoded by the nucleotide sequence of DNAis thus a form of genetic informationis read from the amino terminus to the carboxyl terminus1o structure =linear amino acid sequenceFor the Insulin A chain, the 1o structure is:Gly-Ile-Val-Gl
11、u-Gln-Cys-Cys-Thr-Ser-Ile-Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-Asn Insulin was the first polypeptide to be sequenced (by Frederick Sanger in 1953). The sequencing of insulin demonstrated for the first time that proteins are composed of specific, defined amino acid sequences.The amino acid sequenc
12、e of a protein is specified by the gene encoding that proteinDNA: ggc att gtg gaa caa tgc tgt acc agcmRNA: ggc auu gug gaa caa ugc ugu acc agcProtein: Gly-Ile-Val-Glu-Gln-Cys-Cys-Thr-SerThe Peptide Bondhas partial (40%) double bond characteris about 0.133 nm long - shorter than a typical single bond
13、 but longer than a double bondDue to the double bond character, the six atoms of the peptide bond group are always planar! is usually found in the trans conformation, but X-Pro is an exceptionN partially positive; O partially negativeThe Coplanar Nature of the Peptide BondSix atoms of the peptide gr
14、oup lie in a plane!Restriction by Amide PlaneAtoms in the peptide bond lie in a plane. Resonance stabilization energy of this planar structure is approximately 88 kJ/mol;Rotation can only occur around the two bonds connected to the C atom;Rotation around the Ca and carbonyl bond is called y (psi);Ro
15、tation around the Ca and nitrogen bond is called f (phi). Rotation of Amide PlanesIf (f,y) are known for all residues, the structure for the entire backbone is known.Some (f,y) are more likely than others in a folded proteinPositive (f,y) values correspond to clockwise rotation around bonds when vie
16、wed from the C. Zerois defined when the C=O or N-H bond bisects the R-C-H angle.(f,y)=(0,180), two carbonyl oxygens are too close;(f,y)=(180,0), two amide groups are overlapping;(f,y)=(0,0), carbonyl oxygen overlaps with amide group;Ramachandran PlotThe plot uses f as horizontal Axis y as vertical a
17、xis. The (f, y) angle for each residue can be entered on the plot. For folded proteins, their (f, y) angles cluster in few regions of the plot. The upper left corner are beta-sheet values and middle left are -helices values. Lines signifies the number of amino acids per turn of helix (+ means right-
18、handed, - left-handed)Classes of Secondary StructureAll these are local structures that are stabilized by hydrogen bonds Alpha helix Other helices Beta sheet (composed of beta strands) Tight turns (aka beta turns or beta bends) Beta bulge The Alpha Helix The alpha helix is a helical structure. All a
19、lpha helices in proteins are right-handed; H-bond patterns of the alpha helix: Alpha helix: Carbonyl oxygen of the ith residue forms H-bond with amide proton of the (i+4)th residue. So there are n-4 H-bonds in a helix of n amino acids; 310 helix: carbonyl oxygen of the ith residue forms H-bond with
20、amide proton of the (i+3)th residue. 3 residues (or 10 atoms) per turn; Proline is not found in -helix except at the beginning of an -helix; Helix propensity of an amino acid is a measure of the likelyhood for the amino acid to be in a helix; Glu, Met, Ala, Leu have high propensities; Examples of -h
21、elical proteins include -keratin (structural proteins) and collagen (fibrous protein); Linus Pauling (Nobel Prize in Chemistry, 1954) figured out the structure of -keratin helix. The carboxyl group of residue n is hydrogen bonded to the backbone amide of the amino acid at position n+4.NCCOR1HHNCCOR2
22、HHNCCOR3HHNCCOR4HHNCCOR5HHThe Alpha HelixKnow these numbers Residues per turn: 3.6 Rise per residue: 1.5 Angstroms Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms The backbone loop that is closed by any H-bond in an alpha helix contains 13 atoms phi = -60 degrees, psi = -45 degrees The non-integra
23、l number of residues per turn was a surprise to crystallographersThe Alpha HelixResidues per turn: 3.6Rise per residue: 1.5 Rise per turn: 5.4 (f,y)=(-60,-45)C=O N-H side chainTotal dipole moment Insulin chain A contains two -helices Schematic view of the cross-section of an -helix. Side chains are
24、shown as green circles. -helices are often amphipathicEINGFDLLRSGHydrophobic FaceHydrophilic Face A helical wheel representation of an amphipathic a-helix from alcohol dehydrogenase is shown. In a helical wheel, a cross-sectional view of the a -helix is drawn as a spiral with amino acids occurring e
25、very 100o along the spiral (360o divided by 3.6 amino acids per turn gives 100o per amino acid).The Beta-Pleated SheetComposed of beta strands Also first postulated by Pauling and Corey, 1951 Strands may be parallel or antiparallel Rise per residue: 3.47 Angstroms for antiparallel strands 3.25 Angst
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