Regulation of nitric oxide/reactive oxygen species redox signaling by nNOS splicing variants

Emerging approaches to investigating functional protein dynamics in modular redox enzymes: Nitric oxide synthase as a model system

Approximately 80% of eukaryotic and 65% of prokaryotic proteins are composed of multiple folding units (i.e., domains) connected by flexible linkers. These dynamic protein architectures enable diverse, essential functions such as electron transfer, respiration, and biosynthesis. This review critically assesses recent advancements in methods for studying protein dynamics, with a particular focus on modular, multidomain nitric oxide synthase (NOS) enzymes. Moving beyond traditional static "snapshots" of protein structures, current research emphasizes the dynamic nature of proteins, viewing them as flexible architectures modulated by conformational changes and interactions. In this context, the review discusses key developments in the integration of quantitative crosslinking mass spectrometry (qXL MS) with AlphaFold 2 predictions, which provides a powerful approach to disentangling NOS structural dynamics and understanding their modulation by external regulatory cues. Additionally, advances in site-specific infrared (IR) spectroscopy offer exciting potential in providing rich details about the conformational dynamics of NOSs in docked states. Moreover, optimization of genetic code expansion machinery enables the generation of genuine phosphorylated NOS enzymes, paving the way for detailed biophysical and functional analyses of phosphorylation's role in shaping NOS activity and structural flexibility; notably, this approach also empowers site-specific IR probe labeling with cyano groups. By embracing and leveraging AI-driven tools like AlphaFold 2 for structural and conformational modeling, alongside solution-based biophysical methods such as qXL MS and site-specific IR spectroscopy, researchers will gain integrative insights into functional protein dynamics. Collectively, these breakthroughs highlight the transformative potential of modern approaches in driving fundamental biological chemistry research.

Computational modeling of neuronal nitric oxide synthase biochemical pathway: A mechanistic analysis of tetrahydrobiopterin and oxidative stress

Neuronal cell dysfunction plays an important role in neurodegenerative diseases. Oxidative stress can disrupt the redox balance within neuronal cells and may cause neuronal nitric oxide synthase (nNOS) to uncouple, contributing to the neurodegenerative processes. Experimental studies and clinical trials using nNOS cofactor tetrahydrobiopterin (BH4) and antioxidants in neuronal cell dysfunction have shown inconsistent results. A better mechanistic understanding of complex interactions of nNOS activity and oxidative stress in neuronal cell dysfunction is needed. In this study, we developed a computational model of neuronal cell using nNOS biochemical pathways to explore several key mechanisms that are known to influence neuronal cell redox homeostasis. We studied the effects of oxidative stress and BH4 synthesis on nNOS nitric oxide production and biopterin ratio (BH4/total biopterin). Results showed that nNOS remained coupled and maintained nitric oxide production for oxidative stress levels less than 230 nM/s. The results showed that neuronal oxidative stress above 230 nM/s increased the degree of nNOS uncoupling and introduced instability in the nitric oxide production. The nitric oxide production did not change irrespective of initial biopterin ratio of 0.05-0.99 for a given oxidative stress. Oxidative stress resulted in significant reduction in BH4 levels even when nitric oxide production was not affected. Enhancing BH4 synthesis or supplementation improved nNOS coupling, however the degree of improvement was determined by the levels of oxidative stress and BH4 synthesis. The results of our mechanistic analysis indicate that there is a potential for significant improvement in neuronal dysfunction by simultaneously increasing BH4 levels and reducing cellular oxidative stress.

Differential superoxide production in phosphorylated neuronal nitric oxide synthase mu and alpha variants

Neuronal nitric oxide synthase (nNOS) is regulated by phosphorylation in vivo, yet the underlying biochemical mechanisms remain unclear, primarily due to difficulty in obtaining milligram quantities of phosphorylated nNOS protein; detailed spectroscopic and rapid kinetics investigations require purified protein samples at a concentration in the range of hundreds microM. Moreover, the functional diversity of the nNOS isoform is linked to its splice variants. Also of note is that determination of protein phosphorylation stoichiometry remains as a challenge. To address these issues, this study first expanded a recent genetic code expansion approach to produce phosphorylated rat nNOSμ and nNOSα holoproteins through site-specific incorporation of phosphoserine (pSer) at residues 1446 and 1412, respectively; this site is at the C-terminal tail region, a NOS-unique regulatory element. A quantitative mass spectrometric approach was then developed in-house to analyze unphosphorylated peptides in phosphatase-treated and -untreated phospho-nNOS proteins. The observed pSer-incorporation efficiency consistently exceeded 80%, showing high pSer-incorporation efficiency. Notably, EPR spin trapping results demonstrate that under l-arginine-depleted conditions, pSer1412 nNOSα presented a significant reduction in superoxide generation, whereas pSer1446 nNOSμ exhibited the opposite effect, compared to their unphosphorylated counterparts. This suggests that phosphorylation at the C-terminal tail has a regulatory effect on nNOS uncoupling that may differ between variant forms. Furthermore, the methodologies for incorporating pSer into large, complex protein and quantifying the percentage of phosphorylation in recombinant purified protein should be applicable to other protein systems.