Side Chain Effect on IR Spectra of Heterogeneous Peptide Sequences. Theoretical Investigation of a Series of Tripeptides (AXA) Ahmed Lakhani. George A. Papadantonakis, Timothy A. Keiderling Department of Chemistry University of Illinois at Chicago

show fundamental characteristics of protein folding define well secondary structure good for theoretical modeling Peptide model systems Conformation     -helix -57 – PPII

R. Huang et al, J. Am. Chem. Soc., 126 (8), , 2004 Heterogeneous Sequence Ac-(AAAAK) 4 AAAAY-NH 2 unlabeled 2LT 2L1S (Ac-AAAAkAAAAk AA AAKAAAAKAAAAY- NH2) Experiment (aqueous) Motivation: coupling of two 13 C=O (labeled amide) modes shown experimentally

1) Investigation of the side chain effect on diagonal force constant on the spectra of a series of tripeptides. A X A (X = Gly, Phe, Trp Ser, Ala, Val) 2) Simulation of vibrational spectra of a series of target peptide Ac-AAA X AAA X AAA-NMe to study the coupling constant (X, X= Lys,Val,Ala,Trp) Goals

Geometry of tripeptides constrained in  -helical, PPII-helical and helical conformation Parameters fully optimized at DFT BPW91/6-31G * level Amide I’ isotopic labeling (AXA ) – decouple from rest of the chain Methods

Isotopic labeling 13 C= 18 O on amide C=O shifts frequency down by cm -1 ) AXAAXAMode ( cm -1 ) AGA1658 AAA1651 AVA1641 AKA1672 AFA1649 AWA conformation

Isotopic labeling 13 C= 18 O on amide C=O shifts frequency down by cm -1 ) AXAAXAMode ( cm -1 )  - helix conformation AKA1646 AFA1663 AWA1647 AGA1667 AAA1662 AVA1655

Isotopic labeling 13 C= 18 O on amide C=O shifts frequency down by cm -1 ) AXAAXAMode ( cm -1 ) AKA1664 AFA1647 AWA1649 AGA1658 AAA1655 AVA1657 PPII conformation

Ac-AAA A A 5 A 6 A 7 A AAANMe Ac-AAA W A 5 A 6 A 7 W AAANMe Ac-AAA K A 5 A 6 A 7 K AAA-NMe Ac-AAA V A 5 A 6 A 7 V AAA-NMe Heterogeneous 12-mer 13 C= 18 O labeling scheme Ac-AAA V A 5 A 6 A 7 K AAA-NMe Ac-AAA W A 5 A 6 A 7 K AAA-NMe Ac-AAA K A 5 A 6 A 7 V AAA-NMe Ac-AAA K A 5 A 6 A 7 W AAA-NMe i (A 5 ) i, i+1 (A 5 A 6 ) i, i+2 (A 5 A 7 ) A: 13 C= 18 O labeled

7-mer: FF, APT calculated at DFT BPW91/6-31G * * level Scheme of transfer method Target Molecule Transfer tri-peptide Cartesian coordinates transfer (CCT)(method of transfer force field (FF) and atomic polar tensor (APT) from AXA to the target molecule) P. BOUŘ, J. SOPKOV Ά, BERN ΆROV Ά, MALOŇ, KEIDERLING, Journal of Computational Chemistry, 18, (1997)

Symmetric mode (in-phase) higher intensity Asymmetric mode (out-of-phase) lower intensity Peptide 13 C= 18 O Vibrational normal modes

Typical example of Degenerate splitting Large Splitting i, i+1 (A 5 A 6 ) Small Splitting i, i+2 (A 5 A 7 )

Splitting of Amide I’ labeled residue

Ac-AAAKAAAVAAA-NMeAc-AAAKAAAWAAA-NMe Simulated IR: 13 C= 18 O Normal Modes i, i+2 (A 5 A 7 )  -helix

Ac-AAAVAAAKAAA-NMeAc-AAAWAAAKAAA-NMe Simulated IR: 13 C= 18 O Normal Modes i, i+2 (A 5 A 7 )  -helix

1. 13 C= 18 O labeling of the AXA amide group resolves the contribution of the labeled residue from the rest of 12 C= 16 O groups C= 18 O labeling of the AXA amide group downshifts the frequency of the Amide I’ by cm -1 3.The AXA series showed distinct patterns of side chain impact Conclusions

Acknowledgements Prof. Keiderling Prof. Keiderling’s—Group Members –Ning Ge –Ling Wu –Anjan Roy –Weiying Zhu –Dr. Zhenija Wang –Dr. Takahiro Takekiyo –Dr. George Papadantonakis