Abstract:Nonequilibrium molecular dynamics (MD) simulations together with physics-based force fields are used to follow energy flow between vibrationally excited N-methylacetamide (NMA) and water. The simulations are carried out with a previously validated force field for NMA, based on a multipolar representation of the electrostatics, and with a new fluctuating point charge model. For the water solvent, a flexible and a rigid model was employed to distinguish between the role of inter- and intramolecular degrees of fr… Show more
“…In these simulations the entire NMA molecule was treated with multipoles. 35,[52][53][54] For the bonded terms the parameters were those of the CHARMM22 force field except for the -CO stretch for which a Morse potential V (r) = D e (1 − exp(−β(r − r e ))) 2 was used. The parameters are D e = 120.47 kcal/mol, β = 2.174 Å −1 and r 0 = 1.294 Å which reproduce the experimental gas phase C=O stretch frequency of 1731 cm −1 .…”
The monomer↔dimer equilibrium for insulin is one of the essential steps in forming the receptor binding-competent monomeric form of the hormone. Despite this importance, the thermodynamic stability-in particular for modified insulins-is quite poorly understood in part due to experimental difficulties. This work explores 1-and 2-dimensional infrared spectroscopy in the range of the amide-I band for the hydrated monomeric and dimeric wild type hormone. It is found that for the monomer the frequency fluctuation correlation function (FFCF) and the 1d-infrared spectra are position sensitive. The spectra for the-CO probes at the dimerization interface (residues Phe24, Phe25, Tyr26) split and indicate an asymmetry despite the overall (formal) point symmetry of the dimer structure. Also, the decay times of the FFCF for the same-CO probe in the monomer and the dimer can differ by up to one order of magnitude, for example for residue PheB24 which is solvent exposed for the monomer but at the interface for the dimer. The spectroscopic shifts correlate approximately with the average * To whom correspondence should be addressed 1 number of hydration waters and the magnitude of the FFCF at time zero. However, this correlation is only qualitative due to the heterogeneous and highly dynamical environment. Based on density functional theory calculations the dominant contribution for solvent-exposed-CO is found to arise from the surrounding water (∼ 75 %) whereas the protein environment contributes considerably less. The results suggest that infrared spectroscopy is a positionally sensitive probe of insulin dimerization, in particular in conjunction with isotopic labeling of the probe.
“…In these simulations the entire NMA molecule was treated with multipoles. 35,[52][53][54] For the bonded terms the parameters were those of the CHARMM22 force field except for the -CO stretch for which a Morse potential V (r) = D e (1 − exp(−β(r − r e ))) 2 was used. The parameters are D e = 120.47 kcal/mol, β = 2.174 Å −1 and r 0 = 1.294 Å which reproduce the experimental gas phase C=O stretch frequency of 1731 cm −1 .…”
The monomer↔dimer equilibrium for insulin is one of the essential steps in forming the receptor binding-competent monomeric form of the hormone. Despite this importance, the thermodynamic stability-in particular for modified insulins-is quite poorly understood in part due to experimental difficulties. This work explores 1-and 2-dimensional infrared spectroscopy in the range of the amide-I band for the hydrated monomeric and dimeric wild type hormone. It is found that for the monomer the frequency fluctuation correlation function (FFCF) and the 1d-infrared spectra are position sensitive. The spectra for the-CO probes at the dimerization interface (residues Phe24, Phe25, Tyr26) split and indicate an asymmetry despite the overall (formal) point symmetry of the dimer structure. Also, the decay times of the FFCF for the same-CO probe in the monomer and the dimer can differ by up to one order of magnitude, for example for residue PheB24 which is solvent exposed for the monomer but at the interface for the dimer. The spectroscopic shifts correlate approximately with the average * To whom correspondence should be addressed 1 number of hydration waters and the magnitude of the FFCF at time zero. However, this correlation is only qualitative due to the heterogeneous and highly dynamical environment. Based on density functional theory calculations the dominant contribution for solvent-exposed-CO is found to arise from the surrounding water (∼ 75 %) whereas the protein environment contributes considerably less. The results suggest that infrared spectroscopy is a positionally sensitive probe of insulin dimerization, in particular in conjunction with isotopic labeling of the probe.
“…3b). Indeed, the notion of vibrational mixing in the peptide unit of N -methylacetamide and dipeptides has been theoretically predicted 57–59 and experimentally supported by the Raman band shape of amide I, which depends on H 2 O density 60–63 . In addition, such Förster-like resonant energy transfer mechanism has been observed in the case of the cyanide ion 64 , cyano 65 , and metal carbonyl complex 66 , in which the relaxation time in H 2 O is faster than that in D 2 O.Fig.…”
The influence of hydration water on the vibrational energy relaxation in a protein holds the key to understand ultrafast protein dynamics, but its detection is a major challenge. Here, we report measurements on the ultrafast vibrational dynamics of amide I vibrations of proteins at the lipid membrane/H
2
O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy. We find that the relaxation time of the amide I mode shows a very strong dependence on the H
2
O exposure, but not on the D
2
O exposure. This observation indicates that the exposure of amide I bond to H
2
O opens up a resonant relaxation channel and facilitates direct resonant vibrational energy transfer from the amide I mode to the H
2
O bending mode. The protein backbone motions can thus be energetically coupled with protein-bound water molecules. Our findings highlight the influence of H
2
O on the ultrafast structure dynamics of proteins.
“…All molecular dynamics (MD) simulations were carried out using the CHARMM 30 package together with CHARMM36 31 force field including the CMAP correction 32,33 and multipoles up to quadrupole on the [CONH]-part of the backbone. 21,34 The X-ray crystal structure of the insulin dimer was solvated in a cubic box (75 3 Å3 ) of TIP3P 35 water molecules, which leads to a total system size of 40054 atoms. For the monomer simulations, chains A and B were retained and also solvated in a water box (75 3 Å3 ), the same box size as the dimer.…”
Section: Molecular Dynamics Simulationsmentioning
confidence: 99%
“…For the monomer simulations, chains A and B were retained and also solvated in a water box (75 3 Å3 ), the same box size as the dimer. In these simulations the multipolar 13,21,34,36 force field is used for the entire amide groups and all CO bonds are treated with a Morse potential V (r) = D e (1 − exp(−β(r − r e ))) 2 . The parameters are D e = 141.666 kcal/mol, β = 2.112 Å−1 and r 0 = 1.231 Å.…”
The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric forms in the region of the amide-I vibration differs for residues B24-B26 and D24-D26, which are involved in dimerization of the hormone. Also, the spectroscopic signatures change for mutations at position B24 from phenylalanine -which is conserved in many organisms and known to play a central role in insulin aggregation -to alanine or glycine. Using three different methods to determine the frequency trajectoriessolving the nuclear Schrödinger equation on an effective 1-dimensional potential energy curve, instantaneous normal modes, and using parametrized frequency mapslead to the same overall conclusions. The spectroscopic response of monomeric WT and mutant insulin differs from that of their respective dimers and the spectroscopy of the two monomers in the dimer is also not identical. For the WT and F24A and F24G monomers spectroscopic shifts are found to be ∼ 20 cm −1 for residues (B24 to B26) located at the dimerization interface. Although the crystal structure of the dimer is that of a symmetric homodimer, dynamically the two monomers are not equivalent on the nanosecond time scale. Together with earlier work on the thermodynamic stability of the WT and the same mutants it is concluded that combining computational and experimental infrared spectroscopy provides a potentially powerful way to characterize the aggregation state and dimerization energy of modified insulins.
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