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

Abstract

S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification (PTM) that can affect the function of proteins. As such, PTMs extend and diversify protein function and thus characterizing consequences of PTM at a molecular level is of great interest. Although PTMs can be detected through various direct/indirect methods, they lack the capability to investigate the modifications with molecular detail. In the present work local and global structural dynamics, their correlation, the hydration structure, and the infrared spectroscopy for WT and S-nitrosylated Kirsten rat sarcoma virus (K-RAS) and hemoglobin (Hb) are characterized from molecular dynamics simulations. It is found that attaching NO to Cys118 in K-RAS rigidifies the protein in the Switch-I region which has functional implications, whereas for Hb, nitrosylation at Cys93 at the β 1 chain increases the flexibility of secondary structural motives for Hb in its T 0 and R 4 conformational substates. Solvent water access decreased by 40% after nitrosylation in K-RAS, similar to Hb for which, however, local hydration of the R 4 SNO state is yet lower than for T 0 SNO. Finally, S-nitrosylation leads to detectable peaks for the NO stretch frequency, but the congested IR spectral region will make experimental detection of these bands difficult. Overall, S-nitrosylation in these two proteins is found to influence hydration, protein flexibility, and conformational dynamics which are all eventually involved in protein regulation and function at a molecular level.

Understanding Hydrogen: Lessons to Be Learned from Physical Interactions between the Inert Gases and the Globin Superfamily

“…As H 2 is not able to directly facilitate post-translational modifications (PTMs) of proteins such as S-nitrosylation, there must be a different interaction involved. Rather than PTMs affecting directly polypeptide topology, very recent work on the hydration of proteins such as hemoglobin suggests that the interaction with water may affect the allosteric nature of the polypeptides, and hence their function [102]. It is possible that inert gases such as Xe (or H 2 ) may have an influence on such hydration by occupying polypeptide cavities.…”

Regulation of Ras Signaling by S-Nitrosylation

“…More recently, by means of sophisticated computational simulations, it was found that S-nitrosylation of K-Ras affects the dynamics of this protein, specifically at the structural level [ 56 ]. These authors demonstrated that S-nitrosylation of K-Ras on Cys118 residue alters the flexibility of the protein leading to a hardening of the Switch I region.…”

“…These authors demonstrated that S-nitrosylation of K-Ras on Cys118 residue alters the flexibility of the protein leading to a hardening of the Switch I region. This is the region in the structure of the protein where interactions with GAPs and effector molecules occur, meaning that changes in this area have functional implications [ 56 ].…”