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