分子生物物理学MolecularBiophysics
合集下载
相关主题
- 1、下载文档前请自行甄别文档内容的完整性，平台不提供额外的编辑、内容补充、找答案等附加服务。
- 2、"仅部分预览"的文档,不可在线预览部分如存在完整性等问题,可反馈申请退款(可完整预览的文档不适用该条件!)。
- 3、如文档侵犯您的权益，请联系客服反馈,我们会尽快为您处理(人工客服工作时间：9:00-18:30)。
Molecular Biophysics 分子生物物理学
分子水平
研究生物体系物理学性质、行为
结构
功能
Molecules in Biosystem
Biopolymers:
Nucleic acid (DNA, RNA) Protein
Saccharide Lipid Other
PROTEIN STRUCTURE
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:0.3～0.5 nm
Lennard-Jones potential
E A B r 6 r12
Classificatory 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
C-N, 0.149nm C=N,0.127nm
?
=180 =180
C C N,C
=0 =0
Minimal Distance (Å) between nonbonding atom
n
r
P
3.613
-57 -47 3.6 0.154 0.55
310
-49 -26 3.0 0.200 0.60
p
-57 -7 4.4 0.115 0.51
Paral- -119 +113 2.0 0.320 0.64
Antiparal- -139 +135 2.0 0.340 0.68
[n] is the number of residues per helical turn [r] is the helical rise per residue (nm) [p] is the helical pitch (nm).
strong as to be indistinguishable from
O
a covalent bond, as in the ion HF2−. Typical values include:
O—H...:N (7 kcal/mol)
O—H...:O (5 kcal/mol)
N—H...:N (3 kcal/mol)
C
of secondary structure containing
approximately 32-38% of the
residues in globular proteins
(Kabsch and Sander, 1983)
a-helix 310 helix p-helix
N
Parameters of secondary structure
1965年中国在世界上首次用化学方法 人工合成的蛋白质－牛胰岛素
A链
S—S
Gly.Tle.Val.Glu.Gln.Cys.Cys.Aln.Ser.Val.Cys.Ser.Leu.Tyr.Gln.Leu.Glu.Asn.Tyr.Cys.Asn OH
12
67
11
20
S
S
B链
S
S
ຫໍສະໝຸດ Baidu
Phe.Val.Asn.Gln.His.Leu.Cys.Gly.Ser.His.Leu.Val.Glu.Ala.Leu.Tyr.Leu.Val.Cys.Gly.Glu.Arg.
Tertiary Structure Quaternary Structure
Property of amino acid
Chiral
COOH
NH2 H
CH3
L alanine
zwitterion
Uncharged structure Minor component
Dipolar ion, or zwitterion Major component
N—H...:O (2 kcal/mol)
H
X
Protein Secondary Structure
1951, Pauling
p= 0.54nm P z0= 0.15nm
Z0
= -57 = -47
Helices
repetitive secondary structure
Helices are the most abundant form
(G.N.Ramachandran)
C
O
N
H
C
3.20 2.80 2.90 2.40
(3.0) (2.70) (2.80) (2.20)
O
2.70 2.70 2.40
(2.60) (2.60) (2.20)
N
2.70 2.40
(2.60) (2.20)
H
2.00
(1.90)
phi (), psi (Y), and omega (W)
12
7
19
Gly.Phe.Phe.Tyr.Thr.Pro.Lys.Ala OH
30
牛胰岛素的化学结构
Hierarchy of Protein Structure by Linderstrøm-Lang
Primary Structure Secondary Structure
supersecondary Structure or motif domain
Hydrogen bond
H-bond definition, H-bond location O….H-X
Hydrogen bonds can vary in strength
from very weak (1-2 kJ mol−1) to
extremely strong (40 kJ mol−1), so
Relation with Energy and distance
interaction
charger-charge charger-dipole dipole-dipole charge-induced dipole dipole-induced dipole Transient dipoleinduced dipole
分子水平
研究生物体系物理学性质、行为
结构
功能
Molecules in Biosystem
Biopolymers:
Nucleic acid (DNA, RNA) Protein
Saccharide Lipid Other
PROTEIN STRUCTURE
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:0.3～0.5 nm
Lennard-Jones potential
E A B r 6 r12
Classificatory 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
C-N, 0.149nm C=N,0.127nm
?
=180 =180
C C N,C
=0 =0
Minimal Distance (Å) between nonbonding atom
n
r
P
3.613
-57 -47 3.6 0.154 0.55
310
-49 -26 3.0 0.200 0.60
p
-57 -7 4.4 0.115 0.51
Paral- -119 +113 2.0 0.320 0.64
Antiparal- -139 +135 2.0 0.340 0.68
[n] is the number of residues per helical turn [r] is the helical rise per residue (nm) [p] is the helical pitch (nm).
strong as to be indistinguishable from
O
a covalent bond, as in the ion HF2−. Typical values include:
O—H...:N (7 kcal/mol)
O—H...:O (5 kcal/mol)
N—H...:N (3 kcal/mol)
C
of secondary structure containing
approximately 32-38% of the
residues in globular proteins
(Kabsch and Sander, 1983)
a-helix 310 helix p-helix
N
Parameters of secondary structure
1965年中国在世界上首次用化学方法 人工合成的蛋白质－牛胰岛素
A链
S—S
Gly.Tle.Val.Glu.Gln.Cys.Cys.Aln.Ser.Val.Cys.Ser.Leu.Tyr.Gln.Leu.Glu.Asn.Tyr.Cys.Asn OH
12
67
11
20
S
S
B链
S
S
ຫໍສະໝຸດ Baidu
Phe.Val.Asn.Gln.His.Leu.Cys.Gly.Ser.His.Leu.Val.Glu.Ala.Leu.Tyr.Leu.Val.Cys.Gly.Glu.Arg.
Tertiary Structure Quaternary Structure
Property of amino acid
Chiral
COOH
NH2 H
CH3
L alanine
zwitterion
Uncharged structure Minor component
Dipolar ion, or zwitterion Major component
N—H...:O (2 kcal/mol)
H
X
Protein Secondary Structure
1951, Pauling
p= 0.54nm P z0= 0.15nm
Z0
= -57 = -47
Helices
repetitive secondary structure
Helices are the most abundant form
(G.N.Ramachandran)
C
O
N
H
C
3.20 2.80 2.90 2.40
(3.0) (2.70) (2.80) (2.20)
O
2.70 2.70 2.40
(2.60) (2.60) (2.20)
N
2.70 2.40
(2.60) (2.20)
H
2.00
(1.90)
phi (), psi (Y), and omega (W)
12
7
19
Gly.Phe.Phe.Tyr.Thr.Pro.Lys.Ala OH
30
牛胰岛素的化学结构
Hierarchy of Protein Structure by Linderstrøm-Lang
Primary Structure Secondary Structure
supersecondary Structure or motif domain
Hydrogen bond
H-bond definition, H-bond location O….H-X
Hydrogen bonds can vary in strength
from very weak (1-2 kJ mol−1) to
extremely strong (40 kJ mol−1), so
Relation with Energy and distance
interaction
charger-charge charger-dipole dipole-dipole charge-induced dipole dipole-induced dipole Transient dipoleinduced dipole