modeling of protein turns and derivation of nmr parameters related to turn structure
DESCRIPTION
Modeling of protein turns and derivation of NMR parameters related to turn structure. Megan Chawner BRITE REU Program Advisor: Dr. Dimitrios Morikis Department of Bioengineering University of California, Riverside. Outline. Background My Project Results Conclusions Acknowledgements. - PowerPoint PPT PresentationTRANSCRIPT
Modeling of protein turns and derivation of NMR parameters related to turn structure
Megan ChawnerBRITE REU Program
Advisor: Dr. Dimitrios MorikisDepartment of Bioengineering
University of California, Riverside
Outline
• Background• My Project• Results• Conclusions• Acknowledgements
Protein Structure: All proteins are made up of twenty amino acid building blocks into a sequence = primary structure
Protein structure: sequence folds into -sheet, -helix, random coil loops and various types of turns stabilized by atomic interactions (e.g., H-bonds) = secondary structure
Anti-parallel-sheet
-helix
Primary structure: GPLLNKFLTT
Primary structure: EKQKPDGVFQE
Strand 1
Strand 2Inter-strandH-bonds
C=O(i)…H-N(i+4) H-bonds1 helix turn = 3.6 a.a.
Protein Structure: three-dimensional protein folds are stabilized by long range interactions = tertiary structure
Turns introduce reversibility in the direction of other elements of secondary structure, such as -helices or -sheets• 3 amino acids = -turn • 4 amino acids = -turn
-turn
-turn
i-1 i i+1
ii i
-sheetRamachandran plot() plotdefines secondary structure
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
Backbone torsion angles:
Turns
-helix
Amino Acid i Amino Acid i+1Amino Acid i Amino Acid i+1
N C C
OR
H
N C C
O
H
R
i ii+1 i+1
H Hi
N C C
OR
H
N C C
O
H
R
i ii+1 i+1
H Hi
Amino Acid i Amino Acid i+1Amino Acid i Amino Acid i+1
N C C
OR
H
N C C
O
H
R
i ii+1 i+1
H Hi
N C C
OR
H
N C C
O
H
R
i ii+1 i+1
H Hi
Protein Structure Determination: uses Nuclear magnetic resonance (NMR) spectroscopy to get NMR observables, which are converted to NMR-derived structural parameters • Nuclear Overhauser effects (NOEs) inter-proton distances• 3J(HN-H)-coupling constants -torsion angles
Karplus Equation (Karplus, 1959, J Chem Phys)
NOE equation (Wuthrich, 1986) ri,j inter-proton distancec rotational correlation time
)(fr
1)HH(NOE c6
j,i
ji
CcosBcosA)HH(J 2N3
o60
A=6.98, B=-1.38, C=1.72 (Wang and Bax, 1996, JACS)
NOE < 5 Å through-space interactions inter-proton distances3J(HN-H) = 3-chemical bond coupling through-bond interactions -torsions
Amino Acid i Amino Acid i+1
N C C
OR
H
N C C
O
H
R
i i
3J(HN-H)
i+1 i+1
H Hi
HN(i)-H(i)
HN(i)-HN(i+1)HN(i)-H(i+1)
3J(HN-H) = 3-bond -torsionNOE < 5 Å distance in space
H(i)-H(i+1)
H(i)-HN(i+1)
Relations of experimental observables and structural parameters
dN (i,i+1)
dNN (i,i+1)
dN (i,i)dN (i,i) d (i,i+1)
o60
3J(
HN-H
)
(Hz)
(o)
Cis=0o
=60o
=90o
=150o
Newman Projections
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=O
C=O H
H
C
N
C=O
C=O H
H
C
=-90o
=-30o
N
C=O
C=OC
N
C=O
C=OH
H
C
N
C=O
C=OC
N
C=O
C=OH
H
C
Trans=180o
=-120o
Solution of Karplus equation using MatLab
-helix
-sheet
N C
H
H
Cis
N C
H
HTrans
N C
H H
Cis
N C
H
HTrans
C
N C
C
Cis
C
N C
C
Trans
C
N C
C
Cis
C
N C
C
C
N C
C
Cis
C
N C
C
Trans
C
N C
C
C
N C
C
Trans
Chawner & Morikis, in preparation
My ProjectGoals: To use NMR-derived parameters (inter-proton distances and -torsion angles) to create databases of expected NMR observables (NOEs and 3J(HN-H)-coupling constants) for ideal - and - turns with statistical deviations.
Bottom line: we are back-calculating NMR observables. Remember, during structure determination, NMR-derived parameters are obtained from NMR spectroscopic observables, NOEs and 3J(HN-H)-coupling constants.
Use: Rapid protein turn structure identification by examination of raw NMR observables, without a complete structure calculation.
Color code:
Blue: N
Light blue: H
Gray: C
Red: O
Color code:
Blue: N
Light blue: H
Gray: C
Red: O
VIIIVIII
I I’
II’II
1
32
4
H-bond
C-C
I I’
II’II
1
32
4
H-bond
C-C
-turns
Computational modeling of ideal -and -turns according to torsion angles using DeepView
Classic -turn criteria
Distance: C(1)-C(4) < 7 ÅC=O(1)…H-N(4) H-bondedDistance: O(1)-N(4) < 3.3 Å Distance: O(1)-HN(4) < 2.4 ÅAngle: O(1)-H(4)-N(4) almost linear ± 35o
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
Torsion angles (o)
Type 2 2 3 3
I -60 -30 -90 0
II -60 120 80 0
I' 60 30 90 0
II' 60 -120 -80 0
VIII -60 -30 -120 120
Chawner & Morikis, in preparation
Torsion angles (o)
Type 2 2
Direct 70 -60
70 -70
85 -60
85 -70
Inverse -70 60
-70 70
-85 60
-85 70
direct inverse
-turns
Computational modeling of ideal -and -turns according to torsion angles
Classic -turn criteria
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
-180
-120
-60
0
60
120
180
-180 -120 -60 0 60 120 180
-
-II
-I’
-II’
-VIII
-direct
-inverse
Chawner & Morikis, in preparation
Nuclear Overhauser effects (NOEs) inter-proton distances
Characteristic -turn distancesH(2)-HN(4): (i, i+2)H(2)-HN(3): (i, i+1)H(3)-HN(4): (i, i+1)HN(2)-HN(3): (i, i+1)HN(3)-HN(4): (i, i+1)
1
2
3
H
HN
N
C
C
OHN
HN
H
H
(1,2)(2,3)
(1,2) (2,3)
(1,3)
J
1
2
3
H
HN
N
C
C
OHN
HN
H
H
(1,2)(2,3)
(1,2) (2,3)
(1,3)
J
Characteristic -turn distancesH(1)-HN(3): (i, i+2)H(1)-HN(2): (i, i+1)H(2)-HN(3): (i, i+1)HN(1)-HN(2): (i, i+1)HN(2)-HN(3): (i, i+1)
J2
J3
H
HN
NC
OC
1
3
2
HN
H
HN
HN
H
H
(2,3)(3,4)
(2,3)
(3,4)(2,4)
4
J2
J3
H
HN
NC
OC
1
3
2
HN
H
HN
HN
H
H
(2,3)(3,4)
(2,3)
(3,4)(2,4)
4
-turn -turn
Torsion angles (o) D < 7 Å H-bond distance (Å) H-bond angle (°)
Type 2 2 3 3 C(1)-C(4) O(1)-N(4) O(1)-HN(4) O(1)-H(4)-N(4)
I -60 -30 -90 0 4.7 2.6 1.6 153.2
II -60 120 80 0 4.7 2.6 1.7 152.2
I' 60 30 90 0 4.7 3.0 2.1 151.1
II' 60 -120 -80 0 4.7 2.9 2.0 153.4
VIII -60 -30 -120 120 6.2 4.3 4.5 69.5
Torsion angles (o) D < 7 Å H-bond distance (Å) H-bond angle (°)
Type 2 2 C(1)-C(3) O(1)-N(3) O(1)-HN(3) O(1)-H(3)-N(3)
Direct 70 -60 5.4 2.7 1.8 142.2
70 -70 5.5 2.7 1.9 135.5
85 -60 5.5 3.1 2.2 137.4
85 -70 5.6 3.1 2.3 134.6
Inverse -70 60 5.4 2.4 1.5 143.6
-70 70 5.5 2.5 1.7 131.3
-85 60 5.5 2.8 1.9 141.9
-85 70 5.6 2.8 2.0 136.0
Marginal H-bonds presentbecause of larger deviations from linearity
Test of compliance of molecular models with ideal turn criteria
Notpresent
H-bond present
Chawner & Morikis, in preparation
Inter-proton distance (Å)
TypeHN(2)-HN(3)
HN(3)-HN(4)
H(2)-HN(3)
H(3)-HN(4)
H(2)-HN(4)
H(2)-H(3)
H(3)-H(4)
HN(2)-H(3)
HN(3)-H(4)
I 2.6 2.4 3.5 3.3 3.7 4.7 4.8 5.3 4.7
II 4.5 2.5 2.1 3.3 3.3 4.4 4.8 6.4 5.2
I' 2.6 2.4 3.0 3.3 4.2 4.8 4.8 5.0 5.0
II' 4.5 2.5 3.3 3.3 4.2 4.5 4.8 5.7 4.9
VIII 2.6 4.3 3.5 2.1 5.8 4.6 4.4 5.3 4.9
Torsion angles (°)
Inter-proton distance (Å)
Type 2 2HN(1)-HN(2)
HN(2)-HN(3)
H(1)-HN(2)
H(2)-HN(3)
H(1)- HN(3)
H(1)- H(2)
H(2)- H(3)
HN(1)- H(2)
HN(2)- H(3)
Direct 70 -60 2.0 3.7 3.6 3.6 4.0 5.3 4.8 3.9 5.7
70 -70 2.0 3.8 3.6 3.6 4.2 5.3 4.7 3.9 5.7
85 -60 2.0 3.6 3.6 3.6 4.2 5.3 4.8 3.8 5.5
85 -70 2.0 3.8 3.6 3.6 4.4 5.3 4.7 3.8 5.6
Inverse -70 60 2.0 3.7 3.6 2.6 3.8 4.8 4.6 4.5 5.1
-70 70 2.0 3.8 3.6 2.5 4.1 4.8 4.6 4.5 5.1
-85 60 2.0 3.6 3.6 2.6 3.9 4.7 4.6 4.4 4.9
-85 70 2.0 3.8 3.6 2.5 4.2 4.7 4.6 4.4 4.9
Ideal -turns
Ideal-turns
Molecular models: measured distances corresponding to characteristic NOEs
We classified the inter-proton distances as corresponding to strong, medium, weak and very weak NOE intensities:
1.8-2.6 Å = strong 2.7-3.5 Å = medium 3.6-4.4 Å = weak 4.5-5.0 Å = very weak
Relative NOE intensities
TypeHN(2)-HN(3)
HN(3)-HN(4)
H(2)-HN(3)
H(3)-HN(4)
H(2)-HN(4)
H(2)-H(3)
H(3)-H(4)
HN(2)-H(3)
HN(3)-H(4)
I S S M M W VW VW N/O VW
II VW S S M M W VW N/O N/O
I' S S M M W VW VW VW VW
II' VW S M M W VW VW N/O VW
VIII S W M S N/O VW W N/O VW
-turns
Relative classification of NOE intensities
Chawner & Morikis, in preparation
1.8 Å: sum of van der Waals radii with some overlap
Torsion angles (°)
Relative NOE intensities
Type 2 2HN(1)-HN(2)
HN(2)-HN(3)
H(1)-HN(2)
H(2)-HN(3)
H(1)- HN(3)
H(1)- H(2)
H(2)- H(3)
HN(1)- H(2)
HN(2)- H(3)
Direct 70 -60 S W W W W N/O VW W N/O
70 -70 S W W W W N/O VW W N/O
85 -60 S W W W W N/O VW W N/O
85 -70 S W W W W N/O VW W N/O
Inverse -70 60 S W W S W VW VW VW N/O
-70 70 S W W S W VW VW VW N/O
-85 60 S W W S W VW VW W VW
-85 70 S W W S W VW VW W VW
-turns
We classified the inter-proton distances: 1.8-2.6 Å = strong 2.7-3.5 Å = medium 3.6-4.4 Å = weak 4.5-5.0 Å = very weak
Relative classification of NOE intensities
2 (°) J2 (Hz) 3 (°) J3 (Hz)
Type I -60 4.2 -90 8.2
Type I’ 60 7.3 90 5.8
Type II -60 4.2 80 6.6
Type II’ 60 7.3 -80 6.9
Type VIII -60 4.2 -120 10.1
Type 2 (°) J2 (Hz)
Direct 70 7.1
Direct 85 6.2
Inverse -70 5.5
Inverse -85 7.5
Solution of Karplus equation:calculations of characteristic 3J(HN-H)-coupling constants
-turns
-turns
Chawner & Morikis, in preparation
2 (°) J2 (Hz) 3 (°) J3 (Hz)
Type I -60 Weaker -90 Stronger
Type I’ 60 Stronger 90 Weaker
Type II -60 Weaker 80 Stronger
Type II’ 60 Stronger -80 Weaker
Type VIII -60 Weaker -120 Stronger
Type 2 (°) J2 (Hz)
Direct 70 S
Direct 85 W
Inverse -70 W
Inverse -85 S
We classified the turn’s 3J(HN-H)-coupling constants as stronger or weaker relative to itself, so that the different types can be differentiated comparatively
-turns
-turns
Caution: small variations in -torsion angles result to very large variations in j-coupling constants. In general, the use of j-coupling constants is not as helpful as NOE intensity patterns and connectivities.
-helix
-sheet
Chawner & Morikis, in preparation
Conclusions
• NOE intensity patterns and connectivities can be used to distinguish turn type without a complete structure determination. We have created small NOE intensity databases that discriminate Type I, I’, II, II’, and VIII -turns, and direct and inverse -turns.
Caution: Classification of strong, medium, weak, and very weak NOEs is relative.
• Small variations of the characteristic -torsion angles introduce very large variations in the 3J(HN-H)-coupling constant values, sometimes spanning the whole range of possible solutions for the Karplus equation and the whole allowed region of the Ramachandran plot.
Why? the small variations in -torsion angles are owed to the dynamic character of turns in proteins and peptides and to conformational averaging.
• Overall, NOEs are more useful than J-coupling constants.
Acknowledgements
• Dr. Dimitrios Morikis• Li Zhang• Coordinators of BRITE Program• Fellow BRITE students
o60
3J(HN-H)
N C
H
3J(HN-H)
H
Cis
N C
H
HTrans
C
N C
C
Cis
C
N C
C
Trans
N C
H
3J(HN-H)
H
Cis
N C
H
HTrans
C
N C
C
Cis
C
N C
C
C
N C
C
Cis
C
N C
C
Trans
C
N C
C
C
N C
C
Trans
Cis=0o
=60o
=90o
=150o
Newman Projection
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=OC=O
HHC
N
C=O
C=O H
H
C
N
C=O
C=O H
H
C
=-90o
=-30oN
C=O
C=OC
N
C=O
C=OH
H
C
N
C=O
C=OC
N
C=O
C=OH
H
C
Trans=180o
=-120o