1、Molecular Biophysics分子生物物理學(xué).分子程度構(gòu)造 功能研討生物體系物理學(xué)性質(zhì)、行為.Biopolymers: Nucleic acid (DNA, RNA) ProteinMolecules in BiosystemSaccharide LipidOther.PROTEIN STRUCTURE. 1965年中國在世界上初次用化學(xué)方法人工合成的蛋白質(zhì)牛胰島素.Secondary StructurePrimary StructureTertiary Structure supersecondary Structure or motifdomainQuaternary Struc

2、tureHierarchy of Protein Structure by Linderstrm-Lang.Chiral L alanineCOOHCH3NH2HProperty of amino acid.zwitterionUncharged structureMinor componentDipolar ion, or zwitterion Major component.Classificatory of amino acid based sidechains (R groups)Non-polarG,A,V,L,I; F,W, P,M,PolarneutralS,T, N,Qacid

3、icD,E; C,Y basicR,K, H.?Histidine.Protein Primary Structure.Peptide bondBackboneSide chain Amine/N terminusCarboxyl/C terminus. Pauling & Corey0.132nmC-N, 0.149nmC=N,0.127nm. =180 =180=0 =0?CCN,C. CONHC3.20(3.0)2.80(2.70)2.90(2.80)2.40(2.20)O2.70(2.60)2.70(2.60)2.40(2.20)N2.70(2.60)2.40(2.20)H2.00(1

4、.90)Minimal Distance () between nonbonding atom(G.N.Ramachandran).phi (F), psi (Y), and omega (W). interactionRelation with Energy and distancecharger-charger -1charger-dipoler -2dipole-dipoler -3charge-induced dipoler -4dipole-induced dipoler -6Transient dipole-induced dipoler -6Relation with Energ

5、y and distance. Van der Waals force Lennard-Jones potential 10 kJmol-1，range:0.30.5 nm .H-bond definition, H-bond location O.H-XHydrogen bond OHXHydrogen bonds can vary in strength from very weak (1-2 kJ mol1) to extremely strong (40 kJ mol1), so strong as to be indistinguishable from a covalent bon

6、d, as in the ion HF2. Typical values include:OH.:N (7 kcal/mol) OH.:O (5 kcal/mol) NH.:N (3 kcal/mol) NH.:O (2 kcal/mol) .Protein Secondary Structure. 1951, PaulingPZ0= -57= -47p= 0.54nmz0= 0.15nm.Helicesrepetitive secondary structureNCHelices are the most abundant form of secondary structure contai

7、ning approximately 32-38% of the residues in globular proteins (Kabsch and Sander, 1983) a-helix310 helixp-helix. nrP3.613-57-473.60.1540.55310-49-263.00.2000.60-57-74.40.1150.51Paral-119+1132.00.3200.64Antiparal- -139+1352.00.3400.68Parameters of secondary structuren is the number of residues per h

8、elical turnr is the helical rise per residue (nm)p is the helical pitch (nm). . H-bondAtoms in H-bond loopradius3.613i, i+4132.3310i, i+3101.9i, i+5162.8Parameters of secondary structure.a-helix introduction32-38% of all residues in globular proteins The average length of an alpha helix is 10 residu

9、es. Found(-64 +/- 7, -41 +/- 7) / ideal(-57.8, -47.0)The structure repeats itself every 5.4 along the helix axis, i.e. we say that the a-helix has a pitch of 5.4 . .a-helices have 3.6 amino acid residues per turn, i.e. a helix 36 amino acids long would form 10 turns. The separation of residues along

10、 the helix axis is 5.4/3.6 or 1.5 , i.e. the a-helix has a rise per residue of 1.5 .the phi and psi angles of the alpha helix lie in the center of an allowed, minimum energy region of the Ramachandran (phi, psi) map. Why alpha-helix is abundant in native globular protein?.the dipoles of hydrogen bon

11、ding backbone atoms are in near perfect alignment. .the radius (2.3 angstrom)of the helix allows for favorable van der Waals interactions across the helical axis side chains are well staggered minimizing steric interference.CO group toward carboxyl terminusNH group toward amide terminusH-bond, i-(i+

12、4)Side chain: i-(i+3); i-(i+4)interactions between i and i+4 stabilize helix.Distortions of a-helices The majority of a-helices in globular proteins are curved or distorted somewhat compared with the standard Pauling-Corey model. Why?The packing of buried helices against other secondary structure el

13、ements in the core of the proteinProline residues induce distortions of around 20 degrees in the direction of the helix axis3. Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O groups tend to point towards solvent to maximise their H-bonding capaci

14、ty, i.e. tend to form H-bonds to solvent as well as N-H groups.310 helix introductionOnly 3.4% of the residues are involved in 310 helices, and nearly all those in helical segments containing i-i+3 hydrogen bonds. Ideal (-74.0, -4.0) / found (-71.0 and -18.0)CO-HN hydrogen bond: i-i+3.Standard 310 h

15、elix.Proline helixLeft handed helix3.0 residues per turnpitch = 9.4 No hydrogen bonding in the backbone but helix still forms.Poly-glycine also forms this type of helixCollagen: high in Gly-Pro residues has this type of helical structure.p-helices introductionThe pi helix is an extremely rare second

16、ary structural element in proteins. the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+5.i- - i + 5H-bonds2.8angstrom.the phi and psi angles of the pure pi helix ( -57.1, -69.7) lie at the very edge of an allowed, minimum energy region of the Ramachandran (phi, psi) map. th

17、e pi helix requires that the angle tau (N-Ca-C) be larger (114.9) than the standard tetrahedral angle of 109.5 degrees. the large radius of the pi helix means the polypeptide backbone is no longer in van der Waals contact across the helical axis forming an axial hole too small for solvent water to f

18、ill. side chains are more staggered than the ideal 3.10 helix but not as well as the alpha helix.H-bond: 1-5.alpha-helix, surface of protein, barrieramphiphilicprotein design projects by Degrado, USAHelical wheel tools.Helix dipoleThe partial charges on the amide hydrogen and carbonyl oxygen are sho

19、wn in units of the elementary charge contributing to an overall dipole moment of 3.46 Debye units.helix macrodipole . Sheet20-28% (Kabsch & Sander, 1983; Creighton, 1993)a repeating secondary structure. nrP3.613-57-473.60.1540.55310-49-263.00.2000.60-57-74.40.1150.51Paral-119+1132.00.3200.64Antipara

20、l- -139+1352.00.3400.68Parameters of secondary structuren is the number of residues per helical turnr is the helical rise per residue (nm)p is the helical pitch (nm). .- and + .Parallel sheetAntiparallel sheet.Twistsabout 30 degrees per residue in right-handed senseLeft-handed: crossover angelRight-

21、handed: progressive H-bond twist.Parallel sheets are less twisted than anti-parallel and are always buried.BulgesBeta-hairpinCrossover connection: right-handed left-handedOne residue backbone, two H-bondsStrand connections.Turnthat serve to reverse the direction of the polypeptide chain Surface of t

22、he proteinAntibody recognition, phosphorylation, glycosylation, hydroxylation .Gamma-turnH-bond: i-i+2(70, -60) and (-70, 60) for i+1 residue.Type I and I turnH-bond: i-i+3(-60, -30) and (-90, 0) for i+1, i+2 residues.The backbone dihedral angles of residue are (-60, 120) and (80, 0) of residues i+1

23、 and i+2, respectively of the type II turn. 2.3.3. Type II and II turn.the hydrogen bond between CO of residue i and NH of residue i+3. This is a single turn of right-handed (III) and left-handed (III) 3.10 helix, respectively. The backbone dihedral angles of residue are (-60, -30) and (-60, -30) of

24、 residues i+1 and i+2, respectively of the classical type III turn. .2.3.4. Other structures1. Loop random coil2. Paperclips cap of a-helix.Identification of secondary structure.Identification without 3D structureCD可信度：a-helix, 97%; sheet 75%; 50% turn, 89% otherFrom Manavalan & Johnson, 1987.FTIRam

25、ide band I 1600-1700.NMR coupling constant: 3JHAHN right-handed a-helix, phi = -57, 3JHAHN = 3.9 Hz right handed 3.10 helix, phi = -60, 3JHAHN = 4.2 Hz antiparallel b-sheet, phi = -, 3JHAHN = 8.9 Hz parallel b-sheet, phi = -119, 3JHAHN = 9.7 Hz left-handed a-helix, phi = 57, 3JHAHN = 6.9 Hz.Predicti

26、on of secondary structure(a). Homology. If sequence 25-30%, structure similarity(b). Statistical. Chou & Fasman (1978). (c). Stereochemical Schiffer and Edmundson (1967) .Motif & domain.超二級(jí)構(gòu)造motif相鄰的二級(jí)構(gòu)造單元組合在一同，彼此相互作用，陳列構(gòu)成規(guī)那么的、在空間構(gòu)造上可以識(shí)別的二級(jí)構(gòu)造組合體，并充任三級(jí)構(gòu)造的構(gòu)件block building)，成為超二級(jí)構(gòu)造，介于二級(jí)構(gòu)造與構(gòu)造域之間的構(gòu)造層次。.常見的幾種超二級(jí)構(gòu)造方式a