Molecular dynamics study of early events during photooxidation of eye lens protein γB-crystallin

A computational study of the R120G mutation in human αB-crystallin: implications for structural stability and functionality

The eye is a vital organ in the visual system, which is composed of transparent vascular tissue. αB-crystallin, a significant protein found in the lens, plays a crucial role in our understanding of lens diseases. Mutations in the αB-crystallin protein can cause lens diseases, such as cataracts and myopathy. However, the molecular mechanism underlying the R120G mutation is not fully understood. In this study, we utilized molecular dynamics simulations to illustrate, in atomic detail, how the R120G mutation leads to the aggregation of αB-crystallin and scattering of light in the lens. Our findings show that the R120G mutation alters the dynamic and structural properties of the αB-crystallin protein. Specifically, this mutation causes the angle of the hairpin at the C-terminal to increase from 80° to 150°, while reducing the distance between the hydrophobic patches around residues 10 and 44-55 from 1.5 nm to 1 nm. In addition, our results showed that the mutation could disrupt the IPI motif - β4/β8 interaction. The disruption of this interaction could affect the αB-crystallin oligomerization and the chaperone activity of αB-crystallin protein. The exposed hydrophobic area at the IPI motif - β4/β8 could become the primary site for interprotein interactions, which are responsible for large-scale aggregation. We have demonstrated that, in wild-type αB-crystallin protein, salt bridges R120 and D109, R107 and D80 are formed. However, in the case of the R120G mutation, the salt bridges R120 and R109 are disrupted, and a new salt bridge with a different pattern is formed. In our study, it has been found that all of the changes associated with the R120G mutation are located at the interface of chains A and B, which could impact the multimerization of the αB-crystallin. Previous research on the K92-E99 residue has shown that a salt bridge in the dimer I can reduce the chaperone activity of the protein. Furthermore, the salt bridges R120 and D109, as well as R107 and D80 in dimer II, induce changes in the hydrophobic envelope of β-sheets in the α-crystallin domain (ACD). These changes could have an impact on the multimerization of the αB-crystallin, leading to disruption of the oligomer structure and aggregation. Moreover, the changes in the αB-crystallin resulting from the R120G mutation can lead to faulty interactions with other proteins, which can cause the aggregation of αB-crystallin with other proteins, such as desmin. These findings may provide new insights into the development of treatments for lens diseases.Communicated by Ramaswamy H. Sarma.

Singlet-Oxygen-Induced Phospholipase A2 Inhibition: A Major Role for Interfacial Tryptophan Dioxidation

Several studies have revealed that various diseases such as cancer have been associated with elevated phospholipase A2 (PLA2 ) activity. Therefore, the regulation of PLA2 catalytic activity is undoubtedly vital. In this study, effective inactivation of PLA2 due to reactive species produced from cold physical plasma as a source to model oxidative stress is reported. We found singlet oxygen to be the most relevant active agent in PLA2 inhibition. A more detailed analysis of the plasma-treated PLA2 identified tryptophan 128 as a hot spot, rich in double oxidation. The significant dioxidation of this interfacial tryptophan resulted in an N-formylkynurenine product via the oxidative opening of the tryptophan indole ring. Molecular dynamics simulation indicated that the efficient interactions between the tryptophan residue and phospholipids are eliminated following tryptophan dioxidation. As interfacial tryptophan residues are predominantly involved in the attaching of membrane enzymes to the bilayers, tryptophan dioxidation and indole ring opening leads to the loss of essential interactions for enzyme binding and, consequently, enzyme inactivation.

Amyloid fiber formation in human γD-Crystallin induced by UV-B photodamage

γD-Crystallin is an abundant structural protein of the lens that is found in native and modified forms in cataractous aggregates. We establish that UV-B irradiation of γD-Crystallin leads to structurally specific modifications and precipitation via two mechanisms: amorphous aggregates and amyloid fibers. UV-B radiation causes cleavage of the backbone, in large measure near the interdomain interface, where side chain oxidations are also concentrated. 2D IR spectroscopy and expressed protein ligation localize fiber formation exclusively to the C-terminal domain of γD-Crystallin. The native β-sandwich domains are not retained upon precipitation by either mechanism. The similarities between the amyloid forming pathways when induced by either UV-B radiation or low pH suggest that the propensity for the C-terminal β-sandwich domain to form amyloid β-sheets determines the misfolding pathway independent of the mechanism of denaturation.

Molecular dynamics simulations of the photoactive protein nitrile hydratase

Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, alpha and beta. Hydrogen bonds between betaArg-56 and alphaCys-114 sulfenic acid (alphaCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength lambda < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon.

Characterisation of photo-oxidation products within photoyellowed wool proteins: tryptophan and tyrosine derived chromophores

Understanding the photodegradation of complex protein systems represents a significant goal in protein science. The photo-oxidation and resultant photoyellowing of wool in sunlight is a severe impediment to its marketability. However, although some photomodifications have been found in irradiated model amino acid systems, direct identification of the chromophoric photoproducts responsible for photoyellowing in irradiated wool itself has proved elusive. We here describe the direct characterisation and location of yellow chromophores and related photomodifications within the proteins of photoyellowed wool fabric, utilising a quasi-proteomic approach. In total, eight distinct photoproducts were characterised. Of these, five were derived from tryptophan; namely hydroxytryptophan, N-formylkynurenine, kynurenine, residues consistent with the dehydration of kynurenine, and hydroxykynurenine, while three were derived from tyrosine; namely dihydroxyphenylalanine, dityrosine, and a cross-linked residue consistent with a hydroxylated dityrosine residue. Fourteen modified peptide sequences were identified and the positions of modification for thirteen of these were located within the primary structure of known wool proteins. The nature of the photoproducts characterised offer valuable insight into the reaction pathways followed in the UV-induced photoyellowing of wool proteins.

Determination of Photo-oxidation Products Within Photoyellowed Bleached Wool Proteins

Photo-oxidative processes occurring in wool can lead to significant photoyellowing of the fiber. In particular, wool that has been chemically bleached photoyellows more rapidly and to a greater degree than untreated wool. Direct identification of the chromophores responsible for such yellow discoloration in irradiated wool has proven to be elusive for many years. This article describes the characterization and location of yellow photo-oxidation products within the proteins of photoyellowed bleached wool fabric, using advanced protein chemistry techniques. The discolored fabric was enzymatically digested and chromatographed by high-pressure liquid chromatography, with monitoring at 400 nm, to select out fractions containing yellow chromophoric species. Thorough tandem mass spectrometric analysis was then used to sequence peptides and, in turn, to characterize modifications to key amino acid residues that had resulted in yellow chromophore formation. In total, 11 separate yellow chromophoric species were identified, ten derived from tryptophan residues and one from tyrosine. The tryptophan-derived modifications characterized included hydroxytryptophan, N-formylkynurenine, hydroxyformylkynurenine, kynurenine, hydroxykynurenine, carbolines, tryptophandiones and nitrotryptophan. The tyrosine-derived modification of tyrosine to dopa was also identified. The range of photomodifications we observed provides insight into the photo-oxidation pathways occurring within irradiated fibrous proteins leading to the formation of yellow chromophores.