Identification of Proteins on Archived 2D Gels.

Separation technology of proteins from a complex mixture by two-dimensional gel (2D gel) was invented more than 40 years ago. With a good laboratory practice, the 2D gels are likely to be dried and stored at ambient temperature as archived record. Up until the beginning of this century, it had been difficult to identify the protein spots isolated on 2D gels.

Two-Dimensional Gel Electrophoresis by Glass Tube-Based IEF and SDS-PAGE.

The genome information combined with data derived from modern mass spectrometry enables us to determine the identity of a protein once it is isolated from a complex mixture. Two-dimensional gel electrophoresis established more than four decades ago serves as a powerful protocol to isolate many proteins at once for such protein analysis. In the first two decades, the original procedure to use a glass tube-based IEF had been commonly used.

Determination of Protein Molecular Weights on SDS-PAGE.

An apparent molecular weight (MW) of a protein can be determined from the migration distance of a protein complexed with a strong cationic detergent sodium dodecyl sulfate (SDS) separated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This method was established around 1969 and has been utilized substantially even today because of its simplicity. During the following half a century, although it has been reported that many proteins show some deviation in MW when determined on SDS-PAGE especially when their peptide chains are posttranslationally modified, this versatile method is still being used very often in current biochemical works.

Exploration of cone cyclic nucleotide-gated channel-interacting proteins using affinity purification and mass spectrometry.

Photopic (cone) vision essential for color sensation, central vision, and visual acuity is mediated by the activation of photoreceptor cyclic nucleotide-gated (CNG) channels. Naturally occurring mutations in the cone channel subunits CNGA3 and CNGB3 are associated with achromatopsia and cone dystrophies. This work investigated the functional modulation of cone CNG channel by exploring the channel-interacting proteins.

Effects of immunization with natural and recombinant lysine decarboxylase on canine gingivitis development.

Periodontal disease, gingival inflammation (gingivitis) and periodontal attachment loss (periodontitis), causes tooth loss and susceptibility to chronic inflammation. Professionally scaling and cleaning the teeth regularly controls the disease, but is expensive in companion animals. Eikenella corrodens is common in canine oral cavities where it is a source of lysine decarboxylase (LDC).

Protein identification on archived 2-D gels.

Because of the availability of genome information combined with proteomics techniques, it is possible to determine the identity of a protein which had been isolated many years ago on a two-dimensional gel electrophoresis and stored in a dry state as a data archive. The protocol described in this chapter will assist researchers who want to know the identity of a protein separated decades ago when no techniques were available to determine the identity of the protein.

Two-dimensional gel electrophoresis: glass tube-based IEF followed by SDS-PAGE.

The genome information combined with data derived from modern mass spectrometry enables us to determine the identity of a protein once it is isolated from a complex mixture. Two-dimensional gel electrophoresis established more than three decades ago serves as a powerful protocol to isolate many proteins at once for such protein analysis. In the first two decades, the original procedure to use a glass tube-based isoelectric focusing (IEF) had been commonly used.

Biochemical characterization of cone cyclic nucleotide-gated (CNG) channel using the infrared fluorescence detection system.

Cone vision mediated by photoreceptor cyclic nucleotide-gated (CNG) channel is essential for central and color vision and visual acuity. Cone CNG channel is composed of two structurally related subunit types, CNGA3 and CNGB3. Naturally occurring mutations in cone CNG channel are associated with a variety of cone diseases including achromatopsia, progressive cone dystrophy, and some maculopathies.

Mechanism for the regulation of mammalian cGMP phosphodiesterase6. 2: isolation and characterization of the transducin-activated form.

Rod photoreceptor cGMP phosphodiesterase (PDE6) consists of a catalytic subunit complex (Palphabeta) and two inhibitory subunits (Pgamma). In the accompanying article, using bovine photoreceptor outer segment homogenates, we show that Pgamma as a complex with the GTP-bound transducin alpha subunit (GTP-Talpha) dissociates from Palphabetagammagamma on membranes, and the Palphabetagammagamma becomes Pgamma-depleted. Here, we identify and characterize the Pgamma-depleted PDE.

Mechanism for the regulation of mammalian cGMP phosphodiesterase6. 1: identification of its inhibitory subunit complexes and their roles.

Cyclic GMP phosphodiesterase (PDE) in bovine rod photoreceptor outer segments (OS) comprises a catalytic subunit complex (Palphabeta) and two inhibitory subunits (Pgamma) and is regulated by the alpha subunit of transducin (Talpha). Here, we show an overall mechanism for PDE regulation by identifying Pgamma complexes in OS homogenates prepared with an isotonic buffer. Before Talpha activation, three Pgamma complexes exist in the soluble fraction.

Retinophilin is a light-regulated phosphoprotein required to suppress photoreceptor dark noise in Drosophila.

Photoreceptor cells achieve high sensitivity, reliably detecting single photons, while limiting the spontaneous activation events responsible for dark noise. We used proteomic, genetic, and electrophysiological approaches to characterize Retinophilin (RTP) (CG10233) in Drosophila photoreceptors and establish its involvement in dark-noise suppression. RTP possesses membrane occupation and recognition nexus (MORN) motifs, a structure shared with mammalian junctophilins and other membrane-associated proteins found within excitable cells.

Proteome Profiling of Vitreoretinal Diseases by Cluster Analysis.

Vitreous samples collected in retinopathic surgeries have diverse properties, making proteomics analysis difficult. We report a cluster analysis to evade this difficulty. Vitreous and subretinal fluid samples were collected from 60 patients during surgical operation of non-proliferative diabetic retinopathy, proliferative diabetic retinopathy, proliferative vitreoretinopathy, and rhegmatogenous retinal detachment.

Extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) pathways involved in spinal cord stimulation (SCS)-induced vasodilation.

Background And Aims: SCS is used to improve peripheral circulation in selected patients with ischemia of the extremities. However the mechanisms are not fully understood. The present study investigated whether blockade of ERK and AKT activation modulated SCS-induced vasodilation.

Circadian proteomics of the mouse retina.

The circadian clock in the retina regulates a variety of physiological phenomena such as disc shedding and melatonin release. Although these events are critical for retinal functions, it is almost unknown how the circadian clock controls the physiological rhythmicity. To gain insight into the processes, we performed a proteomic analysis using 2-DE to find proteins whose levels show circadian changes.

Novel eye-specific calmodulin methylation characterized by protein mapping in Drosophila melanogaster.

Post-translational methylation of the epsilon-amino group of lysine residues regulates a number of protein functions. Calmodulin, a key modulator of intracellular calcium signaling, is methylated on lysine 115 in many species. Although the amino acid sequence of calmodulin is highly conserved in eukaryotes, it has been shown that lysine 115 is not methylated in Drosophila calmodulin and no other methylation site has been reported.

Roles of peripheral terminals of transient receptor potential vanilloid-1 containing sensory fibers in spinal cord stimulation-induced peripheral vasodilation.

Background: Spinal cord stimulation (SCS) is used to relieve ischemic pain and improve peripheral blood flow in selected patients with peripheral arterial diseases. Our previous studies show that antidromic activation of transient receptor potential vanilloid-1 (TRPV1) containing sensory fibers importantly contributes to SCS-induced vasodilation.

Objectives: To determine whether peripheral terminals of TRPV1 containing sensory fibers produces vasodilation that depends upon the release of calcitonin gene-related peptide (CGRP) and nitric oxide (NO) during SCS.

Proteomics study of neuropathic and nonneuropathic dorsal root ganglia: altered protein regulation following segmental spinal nerve ligation injury.

Peripheral nerve injury is often followed by the development of severe neuropathic pain. Nerve degeneration accompanied by inflammatory mediators is thought to play a role in generation of neuropathic pain. Neuronal cell death follows axonal degeneration, devastating a vast number of molecules in injured neurons and the neighboring cells.

Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A new methodology for quantitative analysis of proteins is described, applying stable-isotope labeling by small organic molecules combined with one- or two-dimensional electrophoresis and MALDI-TOF-MS, also allowing concurrent protein identification by peptide mass fingerprinting. Our method eliminates fundamental problems in other existing isotope-tagging methods requiring liquid chromatography and MS/MS, such as isotope effects, fragmentation, and solubility. It is also anticipated to be more practical and accessible than those LC-dependent methods.

Sensory fibers containing vanilloid receptor-1 (VR-1) mediate spinal cord stimulation-induced vasodilation.

Background And Aims: Spinal cord stimulation (SCS) is used to improve peripheral blood flow in selected populations of patients with ischemia of the extremities. Previous studies show that antidromic activation of sensory fibers is an important mechanism that contributes to SCS-induced vasodilation. However, the characteristics of sensory fibers involved in vasodilation are not fully known.

Proteomic trajectory mapping of biological transformation: Application to developmental mouse retina.

In this report we introduce a new concept "proteomic trajectory mapping" for the investigation of a complex phenomenon underlying biological transformation and transition. We define proteomic trajectory to be the kinetic trace of protein expression and present a successful proteomic trajectory mapping of complex molecular events underlying postnatal development of mouse retina. Cluster analysis of the trajectory data using a two-state model identified four proteomic trajectory types: two distinct trajectory types accounting for the decline or the rise of protein molecules actively expressed in the juvenile stage (J-type) or in the adult stage (A-type), a class of transient trajectories that mediate the transformation from the juvenile to the adult stage (T-type), and the steady trajectories throughout the entire process of transformation (C-type).

Highly sensitive multistage mass spectrometry enables small-scale analysis of protein glycosylation from two-dimensional polyacrylamide gels.

Structural characterization of glycoproteins remains among the most challenging areas of glycomics due to the requirement of large quantities of samples and laborious biochemical steps involved in the analytical procedure. Here we report the structural characterization of glycoproteins separated on a 2-D gel by using a MALDI-QIT-TOF MS where QIT is quadrupole IT. The combination of MALDI-ion source and QIT appears to generate a unique tendency to cause fragmentation of glycopeptides without collision-induced dissociation.

Mechanisms of sustained cutaneous vasodilation induced by spinal cord stimulation.

This study was performed to investigate whether spinal cord stimulation (SCS) at intensities below motor threshold prolongs cutaneous vasodilation and whether sustained vasodilation by SCS is mediated through sympathetic inhibition and/or antidromic activation of sensory fibers. SCS was applied to the dorsal surface of the L2-L3 spinal cord of anesthesized rats with stimulus parameters used clinically (i.e.

Presence of beta-arrestin-1 immunoreactivity in the cutaneous nerve fibers of rat glabrous skin.

beta-Arrestin-1 (betaArr1) plays a major role in the desensitization and internalization of G protein-coupled receptors. We previously localized betaArr1 in the sensory neurons of rat lumbar 4 and 5 dorsal root ganglia (DRG) and reported the predominant presence of betaArr1 in the small-diameter DRG neurons that are often implicated with nociception. Because of betaArr1's crucial role in regulating the initiation of cellular signaling, in the current study we evaluated the distribution of betaArr1 in the peripheral sensory terminals where various receptors are present.

Identification of a major protein upon phosphate starvation of Pseudomonas aeruginosa PAO1.

To understand the physiology of non-differentiating bacteria exposed to nutrient deprivation and stress, various approaches have been employed in combination with detailed analysis of protein synthesis pattern. In this study, separation of proteins from clarified cell extracts of Pseudomonas aeruginosa PAO1 grown under phosphorus limiting conditions was achieved by high resolution two-dimensional gel electrophoresis (2-DE). Limitation of phosphate in the growth medium revealed significant differences in the 2-DE pattern of proteins between phosphate starved cells and an unstarved control.