Two-dimensional Infrared Spectra Of Four Biomolecules Under Electric Field:Theoretical Study

With the development of ultra-fast light sources,two-dimensional infrared spectra(2D IR)experimental spectroscopy has gradually developed into a practical spectroscopy technology.Based on its rich peak shape information,unique cross-peak mechanism and sensitive anharmonicity,it is an advantageous way to analyze the structure and properties of the biological molecules for using 2D IR spectroscopy.Moreover,2D IR spectroscopy has ultra-high time resolution and can sensitively detect the information of small changes in the structure of bio-molecules,which shows great application in the detection and analysis of coupling mechanism and vibration energy transfer of intermolecules and intramolecules.In the paper,we systematically study the energy transfer,vibration coupling and rotational isomerization of biomolecules,including dopamine,hemoglobin,phosphocholine and potassium channel protein,under different electric field by using 2D IR spectroscopy.1.Using theoretical calculation DFT/B3LYP/6-311G(d,p),the vibration frequencies and geometry optimization of DAH+were studied under different electric fields,and 2D IR spectra were drawn based on anharmonic frequency.For C-H stretching vibration,which is closing with benzene ring,when the electric fields are range from-1.543 to 1.028 V/nm,the symmetric and asymmetric vibrations are coupled.However,the two vibrations modes are no long coupled when electric field is 1.543 V/nm;For C-H stretching vibrations,which is closing with amidogen,the symmetric and asymmetric vibration are uncoupled when electric field are-1.028 V/nm,-0.5142 V/nm,0 and 1.542 V/nm.What's more,electric fields play an important role in rotational isomerization of DAH+,which indicates that electric field would affect the ability of DAH+bind to proteins.2.Hemoglobin proteins carry oxygen into the body and carbon monoxide out of the body.The carboxyhemoglobin subsystem includes iron-porphyrin-imidazole-CO and two distal histidines.Using theoretical method(B3LYP-D3(BJ))with the basis set 6-31G(d,p)for C,H,O and N atoms and Lanl2dz for Fe atom to calculate the potential energy and vibration frequency of the subsystem.Although the size of subsystem is reduced,the anharmonicity and anharmonic frequency of the CO-stretch mode are consistent with the experimental values.The revealing noncovalent interactions method is used to study the hydrogen bond between the CO molecule and H? atom of the His63.The study indicates that the Fe-CO mode and the CO-stretch mode are uncoupled when the subsystem without electric field perturbation,which are coupled when the electric field is-0.5142 V/nm.What's more,there is no vibrational energy transfer between the active site and the His92 when the electric field is 1.028 V/nm because their distance increases.The study indicates that the electric field would affect the efficiency of hemoglobin in synergistically binding oxygen or carbon monoxide in the body.3.The ONIOM model,QM/MM method(DFT/B3LYP/6-31G(d,p)/Dreiding),is used to study the two-dimensional infrared spectra of the system composed of phosphocholine molecules,which is the basis unit of phospholipid membrane,and peptides under different electric fields which is in range of-1.543 V/nm to 1.028 V/nm.Theoretical calculations show that the vibration frequency of the P-O bond is consistent with the experimental values.Through the changes of the two-dimensional infrared spectra of phosphorylcholine molecules under different electric fields,it is found that the electric fields would affect the number and strength of the hydrogen bonds between the phosphorylcholine molecules and the peptides,which affects the vibration coupling of the phosphate group P-O bonds stretching vibration.It is found that the electric fields of specific intensity and direction would affect the ability of phosphorylcholine molecules undergo rotational isomerization,which means the electric field would affect the spatial structure of the phospholipid molecular layer.4.Potassium channel protein regulate the transport of potassium ions between cell membranes,and play an important role in conducting nerve signals.We conduct molecular dynamic simulations to investigate how different electric fields affect potassium channel protein structure and function using two-dimensional infrared spectra(2D IR).The 2D IR spectra indicate two features,whose relative intensities and frequencies are on the basis of the state of the ion occupancy at the S2 binding site in the selectivity filter of potassium channel protein.By analysis of structures and areas of the S2 binding site predicted by MD simulations,we determine the two features as corresponding to states with S2 binding site unoccupied or occupied by K+.We learn that S2 is>99%occupied when electric field is-0.1 V/nm,and S2 is>80%occupied when electric field is-0.05 V/nm and 0.05 V/nm,and S2 is>75%occupied when there is no electric field perturbation,and S2 is>85%occupied when electric field is 0.1 V/nm.Ourresults demonstrate that the electric field have an important role in structures and function of potassium channel protein.Above all,we conduct theoretical computational methods,from Ab initio to molecular dynamic simulation,to study biomolecules using 2D IR spectra under different electric field.Our results indicate that electric fields of specific frequency and intensity could excite certain vibrational modes of a macromolecule,which alters its mode coupling,energy transfer and conformation,and our results enrich the application of 2D IR spectra.