A molecular mechanism for the cleavage of a disulfide bond as the primary function of agonist binding to G-protein-coupled receptors based on theoretical calculations supported by experiments

Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity

This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.

Empirical Potential Energy Function Toward ab Initio Folding G Protein-Coupled Receptors

Approximately 40-50 percent of all drugs targets are G protein-coupled receptors (GPCRs). Three-dimensional structure of GPCRs is important to probe their biophysical and biochemical functions and their pharmaceutical applications. Lacking reliable and high quality free function is one of the ugent problems of computational predicting the three-dimensional structure in this community. We proposed a GPCR-specified energy function composed of four novel empirical potential energy terms: a two-dimensional contact energy force field, knowledge-based helix pair connection distance energy term, knowledge-based helix pair angle restraint energy term and a disulfide bond energy term. To validate the energy function, we employed an ab initio GPCR three-dimensional structure predictor to test if the energy function improved the accuracy of prediction. We evaluated 28 solved GPCRs and found that 21(75 percent) targets were correctly folded (TM-score>0.5). Also, the average TM-score using the energy function was 0.54, which was improved 134 percent than the TM-score 0.23 for MODELLER energy function and 170 percent than the TM-score 0.20 for Rosetta membrane energy function. The results confirmed that our empirical potential energy function toward ab initio folding is competitive to state-of-the-art solutions for structural prediction of GPCRs.

Nature of the E⋯E′ interactions (E, E′ = O, S, Se, and Te) at naphthalene 1,8-positions with fine details of the structures: experimental and theoretical investigations

The nature of E⋯E′ in 1-RE–8-R′E′C₁₀H₆ (E/E′ = O, S, Se and Te) is clarified with the QTAIM approach and NBO analysis, after structural determinations.

Redox Signaling by Reactive Electrophiles and Oxidants

The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.

Molecular Pharmacology of δ-Opioid Receptors

Opioids are among the most effective analgesics available and are the first choice in the treatment of acute severe pain. However, partial efficacy, a tendency to produce tolerance, and a host of ill-tolerated side effects make clinically available opioids less effective in the management of chronic pain syndromes. Given that most therapeutic opioids produce their actions via µ-opioid receptors (MOPrs), other targets are constantly being explored, among which δ-opioid receptors (DOPrs) are being increasingly considered as promising alternatives. This review addresses DOPrs from the perspective of cellular and molecular determinants of their pharmacological diversity. Thus, DOPr ligands are examined in terms of structural and functional variety, DOPrs' capacity to engage a multiplicity of canonical and noncanonical G protein-dependent responses is surveyed, and evidence supporting ligand-specific signaling and regulation is analyzed. Pharmacological DOPr subtypes are examined in light of the ability of DOPr to organize into multimeric arrays and to adopt multiple active conformations as well as differences in ligand kinetics. Current knowledge on DOPr targeting to the membrane is examined as a means of understanding how these receptors are especially active in chronic pain management. Insight into cellular and molecular mechanisms of pharmacological diversity should guide the rational design of more effective, longer-lasting, and better-tolerated opioid analgesics for chronic pain management.

The immunomodulation mediated by a delta-opioid receptor for [Met(5)]-enkephalin in oyster Crassostrea gigas

Opioid receptors (OR) are a group of G protein-coupled receptors with opioids as ligands, which play an important role in triggering the second messengers to modulate immune response in vertebrate immunocytes. In the present study, the full length cDNA of a homologue of δ-opioid receptor (DOR) for [Met(5)]-enkaphalin was cloned from oyster Crassostrea gigas (designated as CgDOR), which was 1104 bp encoding a peptide of 367 amino acids containing a conserved 7tm_1 domain. After the stimulation of [Met(5)]-enkephalin, the concentration of second messengers Ca(2+) and cAMP in the HEK293T cells decreased significantly (p <0.05) with the expression of CgDOR. However, this trend was reverted with the addition of DOR antagonist BNTX. The CgDOR transcripts were ubiquitously detected in the tested tissues including haemocytes, gonad, mantle, kidney, gill, adductor muscle and hepatopancreas, with the highest expression level in the hepatopancreas. After LPS stimulation, the expression level of CgDOR mRNA began to increase (4.05-fold, p <0.05) at 6 h, and reached the highest level (5.00-fold, p <0.05) at 12 h. Haemocyte phagocytic and antibacterial activities increased significantly after [Met(5)]-enkephalin stimulation, whereas the increase was repressed with the addition of DOR antagonist BNTX. These results collectively suggested that CgDOR for [Met(5)]-enkephalin could modulate the haemocyte phagocytic and antibacterial functions through the second messengers Ca(2+) and cAMP, which might be requisite for pathogen elimination and homeostasis maintenance in oyster.

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions

In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A₂ (PLA₂), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.

Formation, reactivity, and detection of protein sulfenic acids

It has become clear in recent decades that the post-translational modification of protein cysteine residues is a crucial regulatory event in biology. Evidence supports the reversible oxidation of cysteine thiol groups as a mechanism of redox-based signal transduction, while the accumulation of proteins with irreversible thiol oxidations is a hallmark of stress-induced cellular damage. The initial formation of cysteine-sulfenic acid (SOH) derivatives, along with the reactive properties of this functional group, serves as a crossroads whereby the local redox environment may dictate the progression of either regulatory or pathological outcomes. Protein-SOH are established as transient intermediates in the formation of more stable cysteine oxidation products both under basal conditions and in response to several redox-active extrinsic compounds. This review details both direct and multistep chemical routes proposed to generate protein-SOH, the spectrum of secondary reactions that may follow their initial formation and the arsenal of experimental tools available for their detection. Pioneering studies that have provided a framework for our current understanding of protein-SOH as well as state-of-the-art proteomic strategies designed for global assessments of this post-translational modification are highlighted.

Polar coordinate representation of Hb(rc) versus (h2/8m)nabla2rhob(rc) at BCP in AIM analysis: classification and evaluation of weak to strong interactions

Polar coordinate (R, theta) representation is proposed for the plot of Hb(rc) versus (h2/8m)nabla2rhob(rc) in AIM analysis to classify, evaluate, and understand weak to strong interactions in a unified way and in more detail; Hb(rc) and nabla2rhob(rc) are total electron energy densities and the Laplacian of rhob(rc) at bond critical points (BCPs: rc), respectively, where rhob(rc) are electron densities at rc. Both the x- and y-axes of the plot are expressed in the common unit of energy since Hb(rc) = Gb(rc) + Vb(rc) and (h2/8m)nabla2rhob(rc) = Hb(rc) - Vb(rc)/2 (= Gb(rc) + Vb(rc)/2), where Gb(rc) and Vb(rc) are kinetic energy densities and potential energy densities, respectively. Data employed for the plot are calculated at BCPs for full-optimized structures and optimized structures with the fixed distances (r) of r = r(o) + wa(o), where r(o) are the full-optimized distances, a(o) is the Bohr radius, and w = +/-0.1 and +/-0.2. The plot draws a helical stream starting from near origin (Hb(rc) = (h2/8m)nabla2rhob(rc) = 0) for very weak interactions and turns to the right as interactions become stronger. The helical stream is well described by the polar coordinate representation with (R, theta); R is given in the energy unit, and theta in degrees is measured from the y-axis. The ratio of Vb(rc)/Gb(rc) (= k) controls theta, of which an acceptable range in the plot is 45.0 < theta < 206.6 degrees. Each plot for an interaction gives a curve, which supplies important information. It is expressed by theta(p) and kappa(p); theta(p) corresponds to the tangent line measured from the y-direction, and kappa(p) is the curvature of the plot at w = 0. The polar coordinate (R, theta) representation with (theta(p), kappa(p)) helps us to classify, evaluate, and understand the nature of weak to strong interactions in a unified way.

Disulfide bond cleavage induced by a platinum(II) methionine complex

The cleavage of a disulfide bond and the redox equilibrium of thiol/disulfide are strongly related to the levels of glutathione (GSH)/oxidized glutathione (GSSG) or mixed disulfides in vivo. In this work, the cleavage of a disulfide bond in GSSG induced by a platinum(II) complex [Pt(Met)Cl2] (where Met = methionine) was studied and the cleavage fragments or their platinated adducts were identified by means of electrospray mass spectrometry, high-performance liquid chromatography, and ultraviolet techniques. The second-order rate constant for the reaction between [Pt(Met)Cl2] and GSSG was determined to be 0.4 M(-1) s(-1) at 310 K and pH 7.4, which is 100- and 12-fold faster than those of cisplatin and its monoaqua species, respectively. Different complexes were formed in the reaction of [Pt(Met)Cl2] with GSSG, mainly mono- and dinuclear platinum complexes with the cleavage fragments of GSSG. This study demonstrated that [Pt(Met)Cl2] can promote the cleavage of disulfide bonds. The mechanistic insight obtained from this study may provide a deeper understanding on the potential involvement of platinum complexes in the intracellular GSH/GSSG systems.

Possible roles of S···O and S···N interactions in the functions and evolution of phospholipase A2

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A₂ (PLA₂) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA₂ domain group (PLA₂-DG), while an additional three S···O interactions were found for the snake PLA₂ domain group (sPLA₂-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA₂-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA₂ were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA₂ family.

Orthogonal Multipolar Interactions in Structural Chemistry and Biology

The past few decades of molecular recognition studies have greatly enhanced our knowledge on apolar, ion-dipole, and hydrogen-bonding interactions. However, much less attention has been given to the role that multipolar interactions, in particular those with orthogonal dipolar alignment, play in organizing a crystal lattice or stabilizing complexes involving biological receptors. By using results from database mining, this review attempts to give an overview of types and structural features of these previously rather overlooked interactions. A number of illustrative examples of these interactions found in X-ray crystal structures of small molecules and protein-ligand complexes demonstrate their propensity and thus potential importance for both, chemical and biological molecular recognition processes.

Modeling and simulation of the human delta opioid receptor

A model for the human delta opioid receptor has been generated via sequence alignment, structure building using the crystal structure of bovine rhodopsin as a template, and refinement by molecular dynamics simulation. The model building suggested that, in addition to the previously postulated interaction between D128 and Y308, an internal salt bridge also exists between residues D128 and R192, both of which are conserved in all the opioid receptors. The model and salt bridge were then shown to be stable during a 20-nsec simulation in a lipid bilayer. It is therefore proposed that both of these interactions play a role in stabilizing the inactive state of the receptor. The model is also used in an effort to rationalize many of the mutational studies performed on delta opioid receptors, and to suggest a plausible explanation for the differences between known delta opioid agonists and antagonists.

Disulfide bonds as switches for protein function

The prevailing view is that disulfide bonds have been added during evolution to enhance the stability of proteins that function in a fluctuating cellular environment. However, recent evidence indicates that disulfide bonds can be more than inert structural motifs. The function of some secreted soluble proteins and cell-surface receptors is controlled by cleavage of one or more of their disulfide bonds; this cleavage is mediated by catalysts or facilitators that are specific for their substrate.

Biological regulation through protein disulfide bond cleavage

It is thought that disulfide bonds in secreted proteins are inert because of the oxidizing nature of the extracellular milieu. We have suggested that this is not necessarily the case and that certain secreted proteins contain one or more disulfide bonds that can be cleaved and that this cleavage is central to the protein's function. This review discusses disulfide bond cleavage in the secreted soluble protein, plasmin. Cleavage of plasmin disulfide bond(s) triggers peptide bond cleavage and formation of the tumour angiogenesis inhibitor, angiostatin. Tumour cells secrete phosphoglycerate kinase which facilitates cleavage of the plasmin disulfide bond(s). Phosphoglycerate kinase is not a conventional disulfide bond reductase. We propose that phosphoglycerate kinase facilitates cleavage of a particular plasmin disulfide bond by hydroxide ion, which results in formation of a sulfenic acid and a free thiol. The free thiol is then available to exchange with another nearby disulfide bond resulting in formation of a new disulfide and a new free thiol. The reduced plasmin is then susceptible to discreet proteolysis which results in release of angiostatin.

Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S...O interactions in small organic compounds, although the linearity of the C-S...O or S-S...O atomic alignment was commonly observed. To elucidate the observed discrepancy, a comprehensive search for nonbonded S.O interactions in the Cambridge Structural Database (CSD) and MP2 calculations on the model complexes between dimethyl disulfide (CH(3)SSCH(3)) and various carbonyl compounds were performed. It was found that the O atom showed a strong intrinsic tendency to approach the S atom from the backside of the S-C or S-S bond (in the sigma(S) direction). On the other hand, the S atom had both possibilities of approach to the carbonyl O atom within the same plane (in the n(O) direction) and out of the plane (in the pi(O) direction). In the case of S...O(amide) interactions, the pi(O) direction was significantly preferred as observed in proteins. Thus, structural features of S...O interactions depend on the type of carbonyl groups involved. The results suggested that S.O interactions may control protein structures to some extent and that the unique directional properties of S...O interactions could be applied to molecular design.

Role of disulfides and sulfhydryl groups in agonist and antagonist binding in serotonin1A receptors from bovine hippocampus

I. The serotonin1A (5-HT1A) receptors are members of a superfamily of seven-transmembrane-domain receptors that couple to G-proteins. They appear to be involved in various behavioral and cognitive functions. Mutagenesis and modeling studies point out that the ligand-binding sites in serotonin receptors are located in the transmembrane domain. However, these binding sites are not very well characterized. Since disulfide bonds and sulfhydryl groups have been shown to play vital roles in the assembly, organization, and function of various G-protein-coupled receptors, we report here the effect of disulfide and sulfhydryl group modifications on the agonist and antagonist binding activity of 5-HT1A receptors from bovine hippocampus. 2. DTT or NEM treatment caused a concentration-dependent reduction in specific binding of the agonist and antagonist in 5-HT1A receptors from bovine hippocampal native and solubilized membranes. This is supported by a concomitant reduction in binding affinity. 3. Pretreatment of the receptor with unlabeled ligands prior to chemical modifications indicate that the majority of disulfides or sulfhydryl groups that undergo modification giving rise to inhibition in binding activity could be at the vicinity of the ligand-binding sites. 4. In addition, ligand-binding studies in presence of GTP-gamma-S, a nonhydrolyzable analogue of GTP, indicate that sulfhydryl groups (and disulfide bonds to a lesser extent) are vital for efficient coupling between the 5-HT1A receptor and the G-protein. 5. Our results point out that disulfide bonds and sulfhydryl groups could play an important role in ligand binding in 5-HT1A receptors.