理學(xué)類分子生物物理學(xué)

1、童夢無憂網(wǎng) 試管嬰兒論壇 本文由defang168貢獻 ppt文檔可能在WAP端瀏覽體驗不佳。建議您優(yōu)先選擇TXT，或下載源文件到本機查看。 Molecular Biophysics 分子生物物理學(xué) 分子水平 研究生物體系物理學(xué)性質(zhì)、行為 研究生物體系物理學(xué)性質(zhì)、 結(jié)構(gòu) 功能 Molecules in Biosystem Biopolymers: Nucleic acid (DNA, RNA) Protein Saccharide Lipid Other PROTEIN STRUCTURE 1965年中國在世界上首次用化學(xué)方法 1965年中國在世界上首次用化學(xué)方法 人工合成的蛋白質(zhì) 人工合成的

2、蛋白質(zhì)牛胰島素 SS A鏈 Gly.Tle.Val.Glu.Gln.Cys.Cys.Aln.Ser.Val.Cys.Ser.Leu.Tyr.Gln.Leu.Glu.Asn.Tyr.Cys.Asn OH 1 2 6 7 S 11 S 20 B鏈 S S Phe.Val.Asn.Gln.His.Leu.Cys.Gly.Ser.His.Leu.Val.Glu.Ala.Leu.Tyr.Leu.Val.Cys.Gly.Glu.Arg. 1 2 7 Gly.Phe.Phe.Tyr.Thr.Pro.Lys.Ala OH 30 牛胰島素的化學(xué)結(jié)構(gòu) 19 Hierarchy of Protein Structu

3、re by Linderstr?m-Lang Primary Structure Secondary Structure supersecondary Structure or motif domain Tertiary Structure Quaternary Structure Property of amino acid Chiral COOH NH2 H L alanine CH3 zwitterion Uncharged structure Minor component Dipolar ion, or zwitterion Major component Classificator

4、y of amino acid based sidechains (R groups) Non-polar neutral Polar acidic basic G,A,V,L,I; F,W, P,M, S,T, N,Q D,E; C,Y R,K, H Histidine Protein Primary Structure Side chain Carboxyl/C terminus Backbone Peptide bond Amine/N terminus Pauling & Corey =180° =180° C C =0° N,C =0°

5、 Minimal Distance (?) between nonbonding atom (? (G.N.Ramachandran) C C O N H 3.20 (3.0) O 2.80 (2.70) 2.70 (2.60) N 2.90 (2.80) 2.70 (2.60) 2.70 (2.60) H 2.40 (2.20) 2.40 (2.20) 2.40 (2.20) 2.00 (1.90) phi (), psi (), and omega (?) ?) Relation with Energy and distance interaction charger-charge cha

6、rger-dipole dipole-dipole charge-induced dipole dipole-induced dipole Transient dipoleinduced dipole Relation with Energy and distance r -1 r -2 r -3 r -4 r -6 r -6 Van der Waals force 10 kJ·mol-1，range:0.30.5 nm Lennard-Jones potential A B E = ? 6 + 12 r r Hydrogen bond H-bond definition, H-bo

7、nd location O.H-X .HHydrogen bonds can vary in strength from very weak (1-2 kJ mol?1) to extremely strong (40 kJ mol?1), so strong as to be indistinguishable from a covalent bond, 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) H O

8、X Protein Secondary Structure 1951, Pauling Z0 = -57° = -47° Helices repetitive secondary structure C Helices are the most abundant form of secondary structure containing approximately 32-38% of the residues in globular proteins (Kabsch and Sander, 1983) -helix 310 helix -helix N Parameter

9、s of secondary structure 3.613 310 Paral- -57 -49 -57 -119 Antiparal- -139 n is the number of residues per helical turn r is the helical rise per residue (nm) p is the helical pitch (nm). Parameters of secondary structure H-bond 3.613 310 -helix introduction 32-38% of all residues in globular protei

10、ns The average length of an alpha helix is 10 residues. 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 -helix has a pitch of 5.4 ?. -helices have 3.6 amino acid residues per turn, i.e. a helix 36 amino acids long

11、would form 10 turns. The separation of residues along the helix axis is 5.4/3.6 or 1.5 ?, i.e. the -helix has a rise per residue of 1.5 ? Why alpha-helix is abundant in native globular protein? the phi and psi angles of the alpha helix lie in the center of an allowed, minimum energy region of the Ra

12、machandran (phi, psi) map. the dipoles of hydrogen bonding 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

13、 carboxyl terminus NH group toward amide terminus H-bond, i-(i+4) Side chain: i-(i+3); i-(i+4) interactions between i and i+4 stabilize helix Distortions of -helices The majority of -helices in globular proteins are curved or distorted somewhat compared with the standard Pauling-Corey model. Why? 1.

14、 The packing of buried helices against other secondary structure elements in the core of the protein 2. Proline residues induce distortions of around 20 degrees in the direction of the helix axis 3. Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O

15、 groups tend to point towards solvent to maximise their Hbonding capacity, i.e. tend to form H-bonds to solvent as well as NH groups. 310 helix introduction Only 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,

16、-4.0) / found (-71.0 and -18.0) COHN hydrogen bond: i-i+3 Standard 310 helix Proline helix Left handed helix 3.0 residues per turn pitch = 9.4 ? No hydrogen bonding in the backbone but helix still forms. Poly-glycine also forms this type of helix Collagen: high in Gly-Pro residues has this type of h

17、elical structure -helices introduction The pi helix is an extremely rare secondary structural element in proteins. the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+5. 1. the phi and psi angles of the pure pi helix ( -57.1, -69.7) lie at the very edge of an allowed, minimu

18、m energy region of the Ramachandran (phi, psi) map. 2. the pi helix requires that the angle tau (N-CC') be larger (114.9) than the standard tetrahedral angle of 109.5 degrees. 3. the large radius of the pi helix means the polypeptide backbone is no longer in van der Waals contact across the heli

19、cal axis forming an axial hole too small for solvent water to fill. 4. side chains are more staggered than the ideal 3.10 helix but not as well as the alpha helix. H-bond: 1-5 Helical wheel tools alpha-helix, surface of protein, barrier amphiphilic protein design projects by Degrado, USA Helix dipol

20、e helix macrodipole The partial charges on the amide hydrogen and carbonyl oxygen are shown in units of the elementary charge contributing to an overall dipole moment of 3.46 Debye units. Sheet 20-28% (Kabsch & Sander, 1983; Creighton, 1993) a repeating secondary structure Parameters of secondar

21、y structure 3.613 310 Paral- -57 -49 -57 -119 Antiparal- -139 n is the number of residues per helical turn r is the helical rise per residue (nm) p is the helical pitch (nm). -139 and +135 Parallel sheet Antiparallel sheet Twists about 30 degrees per residue in right-handed sense Left-handed: crosso

22、ver angel Right-handed: progressive H-bond twist Parallel sheets are less twisted than anti-parallel and are always buried. Bulges One residue backbone, two H-bonds Strand connections Beta-hairpin Crossover connection: right-handed left-handed Turn 1. 2. 3. that serve to reverse the direction of the

23、 polypeptide chain Surface of the protein Antibody recognition, phosphorylation, glycosylation, hydroxylation Gamma-turn 1. H-bond: ii+2 2. (70, -60) and (-70, 60) for i+1 residue Type I and I turn 1. H-bond: ii+3 2. (-60, -30) and (-90, 0) for i+1, i+2 residues 2.3.3. Type II and II turn The backbo

24、ne dihedral angles of residue are (-60, 120) and (80, 0) of residues i+1 and i+2, respectively of the type 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

25、angles of residue are (-60, -30) and (-60, -30) of residues i+1 and i+2, respectively of the classical type III turn. 2.3.4. Other structures 1. Loop random coil 2. Paperclips cap of -helix Identification of secondary structure Identification without 3D structure CD 可信度： 可信度： -helix, 97%; sheet 75%;

26、 50% turn, 89% other From Manavalan & Johnson, 1987 FTIR amide band I 1600-1700 NMR coupling constant: 3JHAHN right-handed -helix, phi = -57, 3JHAHN = 3.9 Hz right handed 3.10 helix, phi = -60, 3JHAHN = 4.2 Hz antiparallel -sheet, phi = -139, 3JHAHN = 8.9 Hz parallel -sheet, phi = -119, 3JHAHN =

27、 9.7 Hz left-handed -helix, phi = 57, 3JHAHN = 6.9 Hz Prediction of secondary structure (a). Homology. If sequence >25-30%, structure similarity (b). Statistical. Chou & Fasman (1978). (c). Stereochemical Schiffer and Edmundson (1967) Motif & domain 超二級結(jié)構(gòu)motif 超二級結(jié)構(gòu)motif 相鄰的二級結(jié)構(gòu)單元組合在一起， 相

28、鄰的二級結(jié)構(gòu)單元組合在一起， 彼此相互作用，排列形成規(guī)則的、 彼此相互作用，排列形成規(guī)則的、 在空間結(jié)構(gòu)上能夠辨認的二級結(jié)構(gòu) 組合體， 組合體，并充當(dāng)三級結(jié)構(gòu)的構(gòu)件 building)， （block building)，成為超二級 結(jié)構(gòu)， 結(jié)構(gòu)，介于二級結(jié)構(gòu)與結(jié)構(gòu)域之間 的結(jié)構(gòu)層次。 的結(jié)構(gòu)層次。 常見的幾種超二級結(jié)構(gòu)形式 a.-loop-; b.-; c.-loop-; d. Rossmann折疊； a. loop- b. c. loopRossmann折疊 折疊； E,f,g. 回形拓撲結(jié)構(gòu) 細胞色素C 細胞色素 -loop- loop- 細胞核抗原的-結(jié)構(gòu) 結(jié)構(gòu) 細胞核抗原的 - 纖溶酶原的-loop-結(jié)構(gòu) 結(jié)構(gòu) 纖溶酶原的 結(jié)構(gòu)