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Institute for Plasma Physics Rijnhuizen
PROTON TRANSFER IN NEUTRAL PEPTIDES
EXAMINED BY CONFORMATIONAL SPECIFIC IR/UV SPECTROSCOPY
Sander Jaeqx67th International Symposium on Molecular
Spectroscopy 19-06-2012
Motivation
Active site: Part of the protein that binds to the substrate and where the chemical reactions takes place
Structure of the active site is important for the function of a protein
Buried deep in peptide difficult to study
Protein
(large peptide)
Motivation
Active site mimics to study intrinsic properties of chemical reaction mediated by active site in the gas phase
Amino acids in the active site often exhibit proton transfer
Therefore, the mimic also needs to exhibit this proton transfer, however this is not trivial in the gas phase
Glu
Proton
Transfer
Glu
Arg
Arg
Motivation
Can proton transfer occur in the gas phase ???
Outline
Experimental set-up / computational methods
Proton transfer in Z-Arg-OH
Proton transfer in Z-Glu-Alan-Arg-NHMe (n=0,1,3)
Conclusions
Experimental
Gas-phase measurements Intrinsic properties
Laser desorption Create gas phase molecules
Supersonic expansion in a molecular beam (Ar) Cool the translational and
vibrational temperature of the molecules
desorption laser1064 nm
molecular beam (Ar)
sample
skimmer
IR-UV spectroscopy
Fix laser on electronic transition in REMPI Constant ion signal
belonging to a single conformation
IR pulse precedes the UV If resonant with
vibrational level depletion of ground state
dip in ion signal
Conformation specific IR absorption spectrum
Ion sig
nalIR wavelength
Techniques - IR spectroscopy
IR spectroscopy gives an direct view on the hydrogen bond network present:
Amide I C=O stretch Amide II NH bend
Experimental IR absorption spectra compared with theoretical spectra
Computational approach: Conformational search
Simulated annealing Max T: 1300 K
Simulation time: 10 – 20 ns
# structures: 500 – 1000
~50 structures optimized on B3LYP/6-31G** level
~25 structures optimized and frequency calculation on B3LYP/6-311+G** level
Proton transfer in Z-Arg-OH ?
Arginine most basic amino acid
Proton tranfer possible from C-terminus to guanidine side chain of arginine forming a zwitterion
Neutral Zwitterion
Proton
Transfer
Z-cap
Proton transfer in Z-Arg-OH ?
Gas phase structure arginine still under debate; Canonical form ( Carboxylic acid C=O stretch + 2 x NH bend )
Tautomeric form ( Carboxylic acid C=O stretch + 1 x NH bend )
Zwitterionic form ( 2 x NH bend )
Canonical Tautomeric Zwitterionic
Proton transfer in Z-Arg-OH ?
Z-Arg-OH has two dominant gas-phase conformations:
Conformation A : 2x NH bend + Carboxylic acid C=O stretch Canonical structure
Conformation B : 1 x NH bend + Carboxylic acid C=O stretch Tautomeric structure
There is no proton transfer in Z-Arg-OH
Z-Arg-OH: no proton transfer
Tautomeric form
Canonical form
Conformation A
Conformation B
Proton transfer in Z-Glu-Alan-Arg-NHMe (n = 0,1,3)
Proton transfer from carboxylic acid group (Glu) to guanidine group (Arg)
Z-cap Glu Ala Arg
NHMeGlu
Proton
Transfer
Glu
Arg
Arg
Z-Glu-Arg-NHMe: Side chain interactions
B
C D
GluGlu
Glu
Arg
ArgArg
Backbone
A
Glu
Arg
Z-Glu-Arg-NHMe: Side chain interactions
MATCH!!
No Match
No Match
No Match
Structural assignement Z-Glu-Arg-NHMe
Z-Glu-Alan-Arg-NHMe
Assigned structures for
Z-Glu-Ala-Arg-NHMe Z-Glu-Ala3-Arg-NHMe
Type of interactions
Two types of interactions: Conventional hydrogen bonding
◦ Electrostatic interactions
Dispersion interaction
◦ Induced dipole – induced dipole interactions
Major disadvantage DFT: Dispersion interactions are not included
New dispersion corrected functionals are being
developed: DFT-D
B3LYP deficiencies
DFT-D better than DFT for Structure optimization and energy calculations Includes more interactions
DFT (B3LYP) does better frequency calculations in Amide I and Amide II region However, it has difficulties in fingerprint region when dispersion
interactions are present
Dispersion No dispersion
Conclusions
Z-Glu-Alan-Arg-NHMe (n=0,1 and 3) all show proton transfer
All exhibit an electrostatic interaction + dispersion interaction
Two tautomers observed in gas-phase
Proton transfer does not occur in Z-Arg-OH
MOLDYN GroupJos OomensAnouk RijsJoost BakkerVivike Lapoutre
FELIX GroupLex van der MeerBritta RedlichGiel Berden
Josipa GrzeticDenis KiawiJuehan Gao
Cor TitoRene van BuurenWybe RoodhuyzenJoop StakenborgMichel Riet
Dispersion corrected DFT (DFT-D)
Structure optimization and energy calculations with DFT-D are of better quality compared with DFT Includes more interactions
DFT DFT-D
Z-Arg-OH Conformation A: With dispersion interaction
Dispersion corrected DFT (DFT-D)
Structure optimization and energy calculations with DFT-D are of better quality compared with DFT Includes more interactions
DFT DFT-D
Z-Arg-OH Conformation B: Without dispersion interaction
Intermolecular interactions
Two types of interactions: Conventional hydrogen bonding
◦ Electrostatic interactions
Dispersion interaction
◦ Induced dipole – induced dipole interactions
Major disadvantage DFT: Dispersion interactions are not included
New dispersion corrected functionals are being developed: DFT-D