Protein NMR II. Lecture 5

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1 Protein NMR II Lecture 5

2 Standard and NMR chemical shifts in proteins Residue N A A B O Ala ys Asp Glu Phe Gly is Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr

4 N 3 O 3 OSY Magnetization is transferred by scalar coupling (bonds). Protons that are more than three chemical bonds apart ( 3 J) give no cross peaks because the higher coupling constants ( 4 J, 5 J, etc) are close to 0. Therefore, only signals of protons which are two or three bonds apart are visible in a OSY spectrum. TOSY Magnetization is dispersed over a complete spinsystem by successive scalar coupling. The TOSY experiment correlates all protons of a spin system.

5 N 3 O 3

6 N O N N O O O O N 2 O Asp Gly Asn i-1 i i+1

7 3D SQ-NOESY and SQ-TOSY Resolved N frequencies 15 N planes Aliphatic frequencies 1 1 N 15 N

8 1 15 N 1 Amide

9 3D SQ-TOSY Only protons of groups attached to amide group (N) will give rise to cross-peaks. δ1 δ2 N O γ β2 β1 3 3 α N

10 NOESY TOSY Leu Ala Asn Gly Leu Ala Asn Gly (N) (N)

11 (9.15,125.5) 2D 1-15 N SQ

12 NOA NA NOAB NAB 13

13 i N A B i i+1 Gln Val Asn

14 SQ-NOESY SQ-TOSY 1

15 N O N N O O 3 3 +N 3 Lys Gly Leu i-1 i i+1

18 2D 1-15 N SQ

19 4D 15 N, 13 -edited NOESY (NNOE) Indirect dimensions ( 1 N, 15 N) Direct dimensions ( 1, 13 ) O N 15 N N

20 4D 15 N, 13 -edited NOESY (NNOE) 117.hb/cb 116.hg/cg 116.hd2/cd2 116.ha/ca 117.ha/ca 117.hg2/cg2 116.hd1/cd1

21 4D 13, 13 -edited NOESY (NOE) O N

22 4D 13, 13 -edited NOESY (NOE) 117.hb/cb 117.ha/ca 117.hg2/cg2

23 Brief introduction to molecular modeling Now we have all (almost all ) the information pertaining structure that we could extract from our sample: NOE tables with all the different intensities, angle ranges, and orientations. We will try to see how these parameters are employed to obtain the picture of the molecule in solution. As opposed to X-ray, in which we actually see the electron density from atoms in the molecule and can be considered as a direct method, with NMR we only get indirect information on atoms. Therefore, we will have to rely on some form of theoretical model to represent the structure of the protein. Usually this means a computer-generated molecular model. Since we are dealing with proteins (thousands of atoms), we use a molecular mechanics (MM) approach. The center of MM is the force field, or equations that describe the energy of the system as a function of <xyz> coordinates. In general, it is a sum of different energy terms.

24 Using NMR data Strong NOE Å Medium NOE Å Weak NOE Å E total = E vdw + E bs + E ab + E torsion + E elctrostatics + ab initio - atomic/molecular orbitals Each term depends on the geometry of the system. E bs, the bond stretching energy of the system.

25 Simulated annealing: We heat the system to an obscene temperature (1000 K), and then we allow it to cool slowly. This will hopefully let the system fall into preferred conformations: ot conformers T Time (usually ps) ool conformers

26 What you need Software: yana (ombined assignment and dynamics algorithm for NMR applications) YANA is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. The combination of automated NOESY cross peak assignment, structure calculation with a fast torsion angle dynamics algorithm Files: A cyana script to perform the calculation steps test.upl test.seq

27 Script to calculate structures set expand=1 set swap=0 set tf_type=2 set weight_vdw=1.0 set weight_upl=1.0 set weight_lol=1.0 set weight_aco=5.0 set cut_upl=0.1 set cut_lol=0.1 set cut_vdw=0.1 set cut_aco=1.0 read seq../test.seq read upl../test-nohb.upl read lol../test-nohb.lol set seed= calc_all structures=200 command=anneal steps=40000 overview best structures=20 range= ang if (master) wrtpdb test- struct=20

28 # N(i)-N(i+2) 10 GLY 12 GLU E GLY 13 LEU E GLU 14 ASP E LEU 15 LYS E ASP 16 TRP E LYS 17 GLU E+00 # N(i)-N(i+3) 13 LEU 16 TRP E ASP 17 GLU E+00 # a(i)-n(i+1) 9 SER A 10 GLY E GLY A3 11 GLY E+00 # a(i)-n(i+2) 10 GLY A2 12 GLU E GLY A2 13 LEU E GLU A 14 ASP E LEU A 15 LYS E ASP A 16 TRP E LYS A 17 GLU E TRP A 18 LYS E GLU A 19 ILE E+00

29 #Sequential NOEs 19 ILE A 20 ARG E ARG A 21 LEU E LEU 22 ARG E ARG A 23 PRO D E ARG A 23 PRO D E GLY 25 GLY E GLY A2 26 LYS E GLY A3 26 LYS E LYS 27 LYS E LYS A 28 GLN E GLN A 29 TYR E TYR A 30 LYS E+00 # a(i)-a(j) 17 GLU A 29 TYR A E GLU A 30 LYS A E ARG A 28 GLN A E+00 # a(i)-n(j) 17 GLU A 29 TYR E LYS A 29 TYR E ARG A 29 TYR E LEU 28 GLN A E ARG 25 GLY A E PRO A 25 GLY E+00 # N(i)-N(j) 19 ILE 29 TYR E ARG 97 TR E LEU 27 LYS E ARG 25 GLY E+00

CFSSP: Chou and Fasman Secondary Structure Prediction server

Wide Spectrum, Vol. 1, No. 9, (2013) pp 15-19 CFSSP: Chou and Fasman Secondary Structure Prediction server T. Ashok Kumar Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil