Spectroscopy, Dynamics, and Hydration of S-Nitrosylated Myoglobin

Abstract

S-Nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the −SNO group, it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO agrees with experimental findings on other proteins as is the observation of buried −SNO. For MbSNO the observed relocation of the EF loop in the simulations by ∼3 Å is consistent with the available X-ray structure, and the conformations adopted by the −SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the −SNO group compared with −SH, MbSNO recruits more water molecules in the first two hydration shells due to stronger electrostatic interactions. Similarly, when comparing the hydration between the A- and H-helices, they differ by up to 30% between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.

Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer

“…Vibrational spectroscopy is a powerful means to relate the structure and dynamics of molecules in the gas phase 1 and in solution. 2,3 Combined with state-of-the art atomistic simulation techniques, molecular-level information related to the structural dynamics of spectroscopic reporters (-CO, -NO, -SCN, -N 3 ), [4][5][6][7][8] or the thermodynamics in protein-ligand complexes 9,10 can be obtained. One of the pertinent questions is (a) whether or not classical molecular dynamics (MD) simulations can be used for accurate vibrational dynamics and (b) what level of theory and accuracy in representing the energies from electronic structure calculations is required for a meaningful contribution of simulations to assigning and interpreting experimentally determined spectra.…”

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer

“…Using MTP electrostatics on other spectroscopic probes is possible in general and has, in fact, already been used for NO attached to the sulfur of cysteine ("nitrosylation") to probe the structural dynamics and spectroscopy in myoglobin. 77 The present work demonstrates that the structural dynamics of a small, hydrated peptide can be correctly described from MD simulations based on an MTP force field in explicit solvent together with FNM analysis. Such studies provide the necessary basis to link structural dynamics, spectroscopy, and aggregation in larger proteins from experiments and simulations.…”

“…This agrees qualitatively with a Bayesian refined analysis of recent IR experiments which find occupations of (P II , β, and α R ) and (85 ± 6, 14 ± 5, and 1 ± 2) % but differ somewhat from earlier results which report (80, 0, and 20) %. Using MTP electrostatics on other spectroscopic probes is possible in general and has, in fact, already been used for NO attached to the sulfur of cysteine (“nitrosylation”) to probe the structural dynamics and spectroscopy in myoglobin …”

Local Hydration Control and Functional Implications Through S-Nitrosylation of Proteins: Kirsten Rat Sarcoma Virus (K-RAS) and Hemoglobin (Hb)

“…Such findings have also contributed to establishing the three-gas respiratory cycle involving O 2 , CO 2 , and NO, driving physiological blood flow and tissue oxygenation by red blood cells, with S-nitrosylation at Cys93β as one of the important cornerstones due to strict conservation of this residue in all mammals and birds. At a molecular level, local hydration of the protein also can be modified by S-nitrosylation, as was found for myoglobin . Oxidation of Met to the sulfoxide MetSO renders the side chain of Met both, polar and hydrophilic .…”