分子生物物理学[1]
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helix
PPT文档演模板
分子生物物理学[1]
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?
分子生物物理学
PPT文档演模板
2020/11/10
分子生物物理学[1]
分子水平
研究生物体系物理学性质、行为
PPT文档演模板
结构
功能
分子生物物理学[1]
Molecules in Biosystem
Biopolymers:
Nucleic acid (DNA, RNA) Protein
Saccharide Lipid Other
1. 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
along the helix axis, i.e. we say that the
a-helix has a pitch of 5.4 Å.
PPT文档演模板
分子生物物理学[1]
a-helices have 3.6 amino acid residues per turn, i.e. a helix 36 amino acids long would form 10 turns.
PPT文档演模板
分子生物物理学[1]
Parameters of secondary structure
H-bond Atoms in Hbond loop
radius
3.613
i, i+4
13
2.3
310
i, i+3
10
1.9
p
i, i+5
16
2.8
PPT文档演模板
分子生物物理学[1]
a-helix introduction
C
O
N
H
C O N H
PPT文档演模板
3.20 (3.0)
2.80 (2.70) 2.70 (2.60)
2.90 (2.80) 2.70 (2.60) 2.70 (2.60)
2.40 (2.20) 2.40 (2.20) 2.40 (2.20) 2.00 (1.90)
分子生物物理学[1]
phi (), psi (Y), and omega (W)
the dipoles of hydrogen bonding backbone atoms are in near perfect alignment.
PPT文档演模板
分子生物物理学[1]
the radius (2.3 angstrom)of the helix allows for favorable van der Waals interactions across the helical axis
Pauling & Corey
PPT文档演模板
C-N, 0.149nm C=N,0.127nm
分子生物物理学[1]
?
=180 =180
C C N,C
=0 =0
PPT文档演模板
分子生物物理学[1]
Minimal Distance (Å) between nonbonding atom
(G.N.Ramachandran)
p= 0.54nm P z0= 0.15nm
Z0
= -57 = -47
PPT文档演模板
分子生物物理学[1]
C
N
PPT文档演模板
Helices
repetitive secondary structure
Helices are the most abundant form of secondary structure containing approximately 32-38% of the residues in globular proteins (Kabsch and Sander, 1983)
a-helix 310 helix p-helix
分子生物物理学[1]
Parameters of secondary structure
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
Histidine
PPT文档演模板
?
分子生物物理学[1]
Protein Primary Structure
PPT文档演模板
分子生物物理学[1]
Side chain
Carboxyl/C terminus
PPT文档演模板
Backbone
Peptide bond
Amine/N 分子生物物理学t[e1]rminus
Transient dipoleinduced dipole
Relation with Energy and distance
r -1 r -2 r -3 r -4 r -6 r -6
分子生物物理学[1]
Van der Waals force
10 kJ·mol-1，range:0.3～0.5 nm
PPT文档演模板
分子生物物理学[1]
PROTEIN STRUCTURE
PPT文档演模板
分子生物物理学[1]
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
PPT文档演模板
分子生物物理学[1]
Hierarchy of Protein Structure by Lial/mol)
N—H...:N (3 kcal/mol)
N—H...:O (2 kcal/mol)
H
X
PPT文档演模板
分子生物物理学[1]
Protein Secondary Structure
PPT文档演模板
分子生物物理学[1]
PPT文档演模板
分子生物物理学[1]
1951, Pauling
32-38% of all residues in globular proteins
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 Å
Ideal (-74.0, -4.0) / found (-71.0 and -18.0)
CO---HN hydrogen bond: i-i+3
PPT文档演模板
分子生物物理学[1]
Standard 310 helix
PPT文档演模板
分子生物物理学[1]
Proline helix
Left handed helix 3.0 residues per turn pitch = 9.4 Å 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 helical structure
maximise their H-
bonding capacity, i.e.
tend to form H-bonds
to solvent as well as N-
H groups.
PPT文档演模板
分子生物物理学[1]
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.
Chiral
COOH
NH2 H
CH3
L alanine
PPT文档演模板
分子生物物理学[1]
zwitterion
Uncharged structure Minor component
PPT文档演模板
Dipolar ion, or zwitterion Major component
分子生物物理学[1]
Primary Structure Secondary Structure
supersecondary Structure or motif domain
Tertiary Structure Quaternary Structure
PPT文档演模板
分子生物物理学[1]
Property of amino acid
The separation of residues along the helix axis is 5.4/3.6 or 1.5 Å, i.e. the a-helix has a rise per residue of 1.5 Å
PPT文档演模板
分子生物物理学[1]
Why alpha-helix is abundant in native globular protein?
side chains are well staggered minimizing steric interference
PPT文档演模板
分子生物物理学[1]
• CO group toward 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
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).
the helix axis
3. 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
extremely strong (40 kJ mol−1), so
strong as to be indistinguishable from
O
a covalent bond, as in the ion HF2−. Typical values include:
O—H...:N (7 kcal/mol)
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.
PPT文档演模板
分子生物物理学[1]
Lennard-Jones potential
PPT文档演模板
分子生物物理学[1]
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
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
PPT文档演模板
分子生物物理学[1]
PPT文档演模板
分子生物物理学[1]
Relation with Energy and distance
interaction
charger-charge
charger-dipole
dipole-dipole
charge-induced dipole
dipole-induced dipole
PPT文档演模板
PPT文档演模板
分子生物物理学[1]
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?
分子生物物理学
PPT文档演模板
2020/11/10
分子生物物理学[1]
分子水平
研究生物体系物理学性质、行为
PPT文档演模板
结构
功能
分子生物物理学[1]
Molecules in Biosystem
Biopolymers:
Nucleic acid (DNA, RNA) Protein
Saccharide Lipid Other
1. 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
along the helix axis, i.e. we say that the
a-helix has a pitch of 5.4 Å.
PPT文档演模板
分子生物物理学[1]
a-helices have 3.6 amino acid residues per turn, i.e. a helix 36 amino acids long would form 10 turns.
PPT文档演模板
分子生物物理学[1]
Parameters of secondary structure
H-bond Atoms in Hbond loop
radius
3.613
i, i+4
13
2.3
310
i, i+3
10
1.9
p
i, i+5
16
2.8
PPT文档演模板
分子生物物理学[1]
a-helix introduction
C
O
N
H
C O N H
PPT文档演模板
3.20 (3.0)
2.80 (2.70) 2.70 (2.60)
2.90 (2.80) 2.70 (2.60) 2.70 (2.60)
2.40 (2.20) 2.40 (2.20) 2.40 (2.20) 2.00 (1.90)
分子生物物理学[1]
phi (), psi (Y), and omega (W)
the dipoles of hydrogen bonding backbone atoms are in near perfect alignment.
PPT文档演模板
分子生物物理学[1]
the radius (2.3 angstrom)of the helix allows for favorable van der Waals interactions across the helical axis
Pauling & Corey
PPT文档演模板
C-N, 0.149nm C=N,0.127nm
分子生物物理学[1]
?
=180 =180
C C N,C
=0 =0
PPT文档演模板
分子生物物理学[1]
Minimal Distance (Å) between nonbonding atom
(G.N.Ramachandran)
p= 0.54nm P z0= 0.15nm
Z0
= -57 = -47
PPT文档演模板
分子生物物理学[1]
C
N
PPT文档演模板
Helices
repetitive secondary structure
Helices are the most abundant form of secondary structure containing approximately 32-38% of the residues in globular proteins (Kabsch and Sander, 1983)
a-helix 310 helix p-helix
分子生物物理学[1]
Parameters of secondary structure
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
Histidine
PPT文档演模板
?
分子生物物理学[1]
Protein Primary Structure
PPT文档演模板
分子生物物理学[1]
Side chain
Carboxyl/C terminus
PPT文档演模板
Backbone
Peptide bond
Amine/N 分子生物物理学t[e1]rminus
Transient dipoleinduced dipole
Relation with Energy and distance
r -1 r -2 r -3 r -4 r -6 r -6
分子生物物理学[1]
Van der Waals force
10 kJ·mol-1，range:0.3～0.5 nm
PPT文档演模板
分子生物物理学[1]
PROTEIN STRUCTURE
PPT文档演模板
分子生物物理学[1]
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
PPT文档演模板
分子生物物理学[1]
Hierarchy of Protein Structure by Lial/mol)
N—H...:N (3 kcal/mol)
N—H...:O (2 kcal/mol)
H
X
PPT文档演模板
分子生物物理学[1]
Protein Secondary Structure
PPT文档演模板
分子生物物理学[1]
PPT文档演模板
分子生物物理学[1]
1951, Pauling
32-38% of all residues in globular proteins
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 Å
Ideal (-74.0, -4.0) / found (-71.0 and -18.0)
CO---HN hydrogen bond: i-i+3
PPT文档演模板
分子生物物理学[1]
Standard 310 helix
PPT文档演模板
分子生物物理学[1]
Proline helix
Left handed helix 3.0 residues per turn pitch = 9.4 Å 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 helical structure
maximise their H-
bonding capacity, i.e.
tend to form H-bonds
to solvent as well as N-
H groups.
PPT文档演模板
分子生物物理学[1]
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.
Chiral
COOH
NH2 H
CH3
L alanine
PPT文档演模板
分子生物物理学[1]
zwitterion
Uncharged structure Minor component
PPT文档演模板
Dipolar ion, or zwitterion Major component
分子生物物理学[1]
Primary Structure Secondary Structure
supersecondary Structure or motif domain
Tertiary Structure Quaternary Structure
PPT文档演模板
分子生物物理学[1]
Property of amino acid
The separation of residues along the helix axis is 5.4/3.6 or 1.5 Å, i.e. the a-helix has a rise per residue of 1.5 Å
PPT文档演模板
分子生物物理学[1]
Why alpha-helix is abundant in native globular protein?
side chains are well staggered minimizing steric interference
PPT文档演模板
分子生物物理学[1]
• CO group toward 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
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).
the helix axis
3. 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
extremely strong (40 kJ mol−1), so
strong as to be indistinguishable from
O
a covalent bond, as in the ion HF2−. Typical values include:
O—H...:N (7 kcal/mol)
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.
PPT文档演模板
分子生物物理学[1]
Lennard-Jones potential
PPT文档演模板
分子生物物理学[1]
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
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
PPT文档演模板
分子生物物理学[1]
PPT文档演模板
分子生物物理学[1]
Relation with Energy and distance
interaction
charger-charge
charger-dipole
dipole-dipole
charge-induced dipole
dipole-induced dipole
PPT文档演模板