In proteomic research, to improve protein solubility of membrane proteins and nuclear proteins, buffers containing high concentration of detergent, such as 4% SDS, were widely used. However, high concentration of detergent might severely interfere with the downstream proteomic analysis, including protein quantitation and trypsin digestion. To improve the proteomic compatibility of buffers with high concentration of detergent, we used short gel method to pretreat buffers containing detergent. Protein samples were first separated by a short (2-2.5 mm) SDS-PAGE electrophoresis, and proteins were quantitated by comparing with bovine serum albumin standards via optical density analysis. The gel was then cut and peptides were recovered using in-gel digestion. The quantitative linearity range of this method was 1 to 8 μg. The quantitation was accurate and reproducible. After short gel analysis, recovered peptides generated high mass spectrometry signals. In conclusion, short gel method eliminated the interference of high concentration detergent in the proteomics analysis, and it was suitable for protein samples' pretreatment, and was worth to apply in proteomic research.
Detergents ; chemistry ; Electrophoresis, Polyacrylamide Gel ; methods ; Mass Spectrometry ; Membrane Proteins ; chemistry ; Nuclear Proteins ; chemistry ; Proteins ; chemistry ; Proteomics ; methods ; Trypsin

While the field of ATP synthase research has a long history filled with landmark discoveries, recent structural works provide us with important insights into the mechanisms that links the proton movement with the rotation of the Fo motor. Here, we propose a mechanism of unidirectional rotation of the Fo complex, which is in agreement with these new structural insights as well as our more general ΔΨ-driving hypothesis of membrane proteins: A proton path in the rotor-stator interface is formed dynamically in concert with the rotation of the Fo rotor. The trajectory of the proton viewed in the reference system of the rotor (R-path) must lag behind that of the stator (S-path). The proton moves from a higher energy site to a lower site following both trajectories simultaneously. The two trajectories meet each other at the transient proton-binding site, resulting in a relative rotation between the rotor and stator. The kinetic energy of protons gained from ΔΨ is transferred to the c-ring as the protons are captured sequentially by the binding sites along the proton path, thus driving the unidirectional rotation of the c-ring. Our ΔΨ-driving hypothesis on Fo motor is an attempt to unveil the robust mechanism of energy conversion in the highly conserved, ubiquitously expressed rotary ATP synthases.
Membrane Potentials ; physiology ; Membrane Proteins ; chemistry ; metabolism ; Mitochondrial Proton-Translocating ATPases ; chemistry ; metabolism ; Protein Conformation

Animals ; Cell Membrane ; chemistry ; metabolism ; Humans ; Membrane Proteins ; chemistry ; metabolism ; Protein Structure, Secondary

Bacterial Outer Membrane Proteins ; chemistry ; genetics ; physiology ; Bacteriophages ; chemistry ; Humans ; Receptors, Virus ; chemistry ; Vibrio cholerae ; virology

Kindlin-2 belongs to a subfamily of FERM domain containing proteins, which plays key roles in activating integrin transmembrane receptors and mediating cell adhesion. Compared to conventional FERM domains, kindlin-2 FERM contains an inserted pleckstrin homology (PH) domain that specifically binds to phosphatidylinositol (3,4,5) trisphosphate (PIP3) and regulates the kindlin-2 function. We have determined the crystal structure of kindlin-2 PH domain at 1.9 Å resolution, which reveals a conserved PH domain fold with a highly charged and open binding pocket for PIP3 head group. Structural comparison with a previously reported solution structure of kindlin-2 PH domain bound to PIP3 head group reveals that upon PIP3 insertion, there is a significant conformational change of both the highly positively charged loop at the entry of the PIP3 binding pocket and the entire β barrel of the PH domain. We propose that such "induced-fit" type change is crucial for the tight binding of PIP3 to anchor kindlin-2 onto the membrane surface, thereby promoting its binding to integrins. Our results provide important structural insight into kindlin-2-mediated membrane anchoring and integrin activation.
Animals ; Crystallography, X-Ray ; Cytoskeletal Proteins ; chemistry ; metabolism ; Humans ; Integrins ; metabolism ; Membrane Proteins ; chemistry ; metabolism ; Mice ; Models, Molecular ; Muscle Proteins ; chemistry ; metabolism ; Neoplasm Proteins ; chemistry ; metabolism ; Protein Conformation

Mitophagy is an essential intracellular process that eliminates dysfunctional mitochondria and maintains cellular homeostasis. Mitophagy is regulated by the post-translational modification of mitophagy receptors. Fun14 domain-containing protein 1 (FUNDC1) was reported to be a new receptor for hypoxia-induced mitophagy in mammalian cells and interact with microtubule-associated protein light chain 3 beta (LC3B) through its LC3 interaction region (LIR). Moreover, the phosphorylation modification of FUNDC1 affects its binding affinity for LC3B and regulates selective mitophagy. However, the structural basis of this regulation mechanism remains unclear. Here, we present the crystal structure of LC3B in complex with a FUNDC1 LIR peptide phosphorylated at Ser17 (pS), demonstrating the key residues of LC3B for the specific recognition of the phosphorylated or dephosphorylated FUNDC1. Intriguingly, the side chain of LC3B Lys49 shifts remarkably and forms a hydrogen bond and electrostatic interaction with the phosphate group of FUNDC1 pS. Alternatively, phosphorylated Tyr18 (pY) and Ser13 (pS) in FUNDC1 significantly obstruct their interaction with the hydrophobic pocket and Arg10 of LC3B, respectively. Structural observations are further validated by mutation and isothermal titration calorimetry (ITC) assays. Therefore, our structural and biochemical results reveal a working model for the specific recognition of FUNDC1 by LC3B and imply that the reversible phosphorylation modification of mitophagy receptors may be a switch for selective mitophagy.
Crystallography, X-Ray ; Membrane Proteins ; chemistry ; metabolism ; Microtubule-Associated Proteins ; chemistry ; metabolism ; Mitochondrial Degradation ; Mitochondrial Proteins ; chemistry ; metabolism ; Peptides ; chemistry ; metabolism ; Phosphorylation ; Protein Structure, Quaternary

OBJECTIVETo investigate the distribution, changes and a possible role for retinal dopamine transporter (DAT) in experimental myopia in chickens.

METHODSTwo-day-old chickens were divided into four groups. Chicken eyes were fitted with lenses of -10D,-20D and translucent goggles unilaterally. Normal eyes were used as controls. After 3 wk, all chickens were given an intramuscular injection of (125)I-beta-CIT 2beta-carbomethoxy-3beta-(4-iodophenyl)tropane and sacrificed two hours post injection. Retinal pigment epithelium (RPE) and the neural retina were obtained together or RPE was dissected out from the neural retina. Radioactive DAT from each specimen was assayed by gamma-counter.

RESULTSRetinal DAT was detected in RPE specimens rather than in the neural retina in all eyes. Radioactive DAT in myopic eyes was higher, compared with control eyes.

CONCLUSIONSRetinal DAT is mainly located in the RPE and may be involved in the formation of lens induced myopia (LIM) and form deprivation myopia (FDM). These methods may provide a new approach for further studying the role of the dopamine system in experimental myopia.

Animals ; Chickens ; Dopamine Plasma Membrane Transport Proteins ; Eye ; growth & development ; Membrane Glycoproteins ; Membrane Transport Proteins ; analysis ; physiology ; Myopia ; metabolism ; Nerve Tissue Proteins ; Retina ; chemistry

With the advance of drug development and research techniques, the drug metabolic processes and mechanism can be more deeply achieved. As the drug metabolism and pharmacokinetics process are mediated by drug metabolizing enzymes and transporters, study of drug metabolizing enzymes and transporters has become an important part for drug development. The traditional immunoassays with low sensitivity and poor specificity can not reflect the accurate expression level of drug metabolizing enzymes and transporters. We now give a brief review on the quantitative study of drug metabolizing enzymes and transporters by mass spectrometry-based proteomic approach.
Enzymes ; chemistry ; Humans ; Inactivation, Metabolic ; Mass Spectrometry ; Membrane Transport Proteins ; chemistry ; Pharmacokinetics ; Proteomics

Biomolecular condensates formed by phase separation are widespread and play critical roles in many physiological and pathological processes. cGAS-STING signaling functions to detect aberrant DNA signals to initiate anti-infection defense and antitumor immunity. At the same time, cGAS-STING signaling must be carefully regulated to maintain immune homeostasis. Interestingly, exciting recent studies have reported that biomolecular phase separation exists and plays important roles in different steps of cGAS-STING signaling, including cGAS condensates, STING condensates, and IRF3 condensates. In addition, several intracellular and extracellular factors have been proposed to modulate the condensates in cGAS-STING signaling. These studies reveal novel activation and regulation mechanisms of cGAS-STING signaling and provide new opportunities for drug discovery. Here, we summarize recent advances in the phase separation of cGAS-STING signaling and the development of potential drugs targeting these innate immune condensates.
Humans ; Nucleotidyltransferases/chemistry* ; Signal Transduction/physiology* ; Membrane Proteins/chemistry* ; Phase Separation

BACKGROUNDQacA, a main exporter mediating the multidrug-resistance of Staphylococcus aureus to a variety of antiseptics and disinfectants, possesses a topology of 14 alpha-helical transmembrane segments (TMS). Our study aimed to determine the importance and topology of amino acid residues in and flanking the cytoplasmic end of TMS5.

METHODSSite-directed mutagenesis was used to mutate 5 residues, including L146, A147, V148, W149 and S150, into cysteine. A minimum inhibitory concentration (MIC) and transport assay with or without N-ethylmaleimide (NEM) were performed to analyse the function of these mutants.

RESULTSAll of the mutants showed comparable protein expression levels. MIC analysis suggested that mutant W149C showed low resistance levels to the drugs, but the mutations at L146, A147, V148, and S150C had little or no effect on the resistance level. And the results of the fluorimetric transport assay were in agreement with those of MIC analysis, that is to say, W149C did not allow transport to the substrates to be tested, while the other mutants retained significant transport ability. The reaction of the different mutant proteins with Fluorescein-NEM revealed that the mutant L146C was highly reactive with NEM; the W149C and S150C mutants were moderately reactive; A147C was barely reactive and V148C showed no reactivity.

CONCLUSIONSThe study identified that residues W149 and S150 situated at the interface of the aqueous: lipid junction as functionally important residues, probably involved in the substrate binding and translocation of QacA.

Bacterial Proteins ; chemistry ; physiology ; Drug Resistance, Bacterial ; Ethylmaleimide ; pharmacology ; Indoles ; metabolism ; Membrane Transport Proteins ; chemistry ; physiology ; Structure-Activity Relationship