The application of mass spectrometry to Ginkgo biloba analysis and identification of phosphorylated proteins in response to elevated level of cCMP.

Mass spectrometry is widely used nowadays especially in the fields of pharmaceutical and proteomics research. Ginkgo biloba is one of the top selling phytophamiaceuticals in the US and Europe. The two major active components of Ginkgo leaf extract are the flavonoids and terpene lactones. Identification, determination, as well as the physiological effects of these two sets of compounds have been of increasing interest over the last 20 years. In this thesis, systematic qualitative and quantitative studies of the flavonoids and terpene lactones in Ginkgo biloba by liquid chromatography / mass spectrometry have been undertaken. Also in this thesis, mass spectrometric methodology was developed and applied to the identification of the proteins specifically phosphorylated in response to cCMP. Structural information of Ginkgo biloba flavonoids and terpene lactones, the fragment of compounds were obtained on both a LCQ ion trap and Q-TOF mass spectrometer. The tentative fragment pathways were proposed and used for structural elucidation of some unknown components in Ginkgo biloba commercial products. Capillary column separation of Ginkgo biloba commercial product was evaluated and fingerprint profiles of five Ginkgo biloba commercial products were compared. A reverse-phase high-performance liquid chromatography electrospray ionisation (RP-HPLC/ESI) mass spectrometry method was developed and validated for the simultaneous determination of ten major active components in Ginkgo biloba extract (bilobalide, ginkgolides A, B, C, quercetin, kaempferol, isorhamnetin, rutin hydrate, quercetin-3-beta-D-glucoside and quercitrin hydrate). The quantitative determination of flavonoids and terpene lactones by LC/MS in human urine after consumption of Ginkgo biloba product was developed. The online solid-phase extraction and capillary column with column-switch technique require minimum sample pre-treatment and both flavonoids and terpene lactones can be detected simultaneously. The mass accuracy at high molecular weight by matrix-assisted laser desoiption/ionisation time-of-flight mass spectrometry was investigated to resolve a question on mass accuracy which had been observed to be relatively low for high mss proteins. Bovine serum albumin (BSA) was employed as a model compound and strategies to improve mass measurement at high mass were examined. LC/MS was applied in part of the cyclic nucleotide project in the School of Biological Science. Since cAMP and cGMP are recognized second messengers and play important roles in signal transduction, to elucidate the function of cCMP in signal transduction, efforts were made to identify the cCMP-responsive protein kinase substrates. Methodology of specific enrichment of phosphopeptides using immobilized metal affinity chromatography (IMAC) was developed, phosphorylated proteins responding specifically to cCMP were proposed, and this supports the relationship of cCMP with cell hyperproliferation

Post-translational modifications near the quinone binding site of mammalian complex I.

Complex I (NADH:ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 protein subunits with one arm buried in the inner membrane of the mitochondrion and the orthogonal arm protruding about 100 Å into the matrix. The protruding arm contains the binding sites for NADH, the primary acceptor of electrons flavin mononucleotide (FMN), and a chain of seven iron-sulfur clusters that carries the electrons one at a time from FMN to a coenzyme Q molecule bound in the vicinity of the junction between the two arms. In the structure of the closely related bacterial enzyme from Thermus thermophilus, the quinone is thought to bind in a tunnel that spans the interface between the two arms, with the quinone head group close to the terminal iron-sulfur cluster, N2. The tail of the bound quinone is thought to extend from the tunnel into the lipid bilayer. In the mammalian enzyme, it is likely that this tunnel involves three of the subunits of the complex, ND1, PSST, and the 49-kDa subunit. An arginine residue in the 49-kDa subunit is symmetrically dimethylated on the ω-N(G) and ω-N(G') nitrogen atoms of the guanidino group and is likely to be close to cluster N2 and to influence its properties. Another arginine residue in the PSST subunit is hydroxylated and probably lies near to the quinone. Both modifications are conserved in mammalian enzymes, and the former is additionally conserved in Pichia pastoris and Paracoccus denitrificans, suggesting that they are functionally significant

NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I.

Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ∼100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-β-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ω-N(G),N(G') atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm

Assembly of the peripheral stalk of ATP synthase in human mitochondria.

The adenosine triphosphate (ATP) synthase in human mitochondria is a membrane bound assembly of 29 proteins of 18 kinds organized into F1-catalytic, peripheral stalk (PS), and c8-rotor ring modules. All but two membrane components are encoded in nuclear genes, synthesized on cytoplasmic ribosomes, imported into the mitochondrial matrix, and assembled into the complex with the mitochondrial gene products ATP6 and ATP8. Intermediate vestigial ATPase complexes formed by disruption of nuclear genes for individual subunits provide a description of how the various domains are introduced into the enzyme. From this approach, it is evident that three alternative pathways operate to introduce the PS module (including associated membrane subunits e, f, and g). In one pathway, the PS is built up by addition to the core subunit b of membrane subunits e and g together, followed by membrane subunit f. Then this b-e-g-f complex is bound to the preformed F1-c8 module by subunits OSCP and F6 The final component of the PS, subunit d, is added subsequently to form a key intermediate that accepts the two mitochondrially encoded subunits. In another route to this key intermediate, first e and g together and then f are added to a preformed F1-c8-OSCP-F6-b-d complex. A third route involves the addition of the c8-ring module to the complete F1-PS complex. The key intermediate then accepts the two mitochondrially encoded subunits, stabilized by the addition of subunit j, leading to an ATP synthase complex that is coupled to the proton motive force and capable of making ATP

Conservation of complete trimethylation of lysine-43 in the rotor ring of c-subunits of metazoan adenosine triphosphate (ATP) synthases.

The rotors of ATP synthases turn about 100 times every second. One essential component of the rotor is a ring of hydrophobic c-subunits in the membrane domain of the enzyme. The rotation of these c-rings is driven by a transmembrane proton-motive force, and they turn against a surface provided by another membrane protein, known as subunit a. Together, the rotating c-ring and the static subunit a provide a pathway for protons through the membrane in which the c-ring and subunit a are embedded. Vertebrate and invertebrate c-subunits are well conserved. In the structure of the bovine F1-ATPase-c-ring subcomplex, the 75 amino acid c-subunit is folded into two transmembrane α-helices linked by a short loop. Each bovine rotor-ring consists of eight c-subunits with the N- and C-terminal α-helices forming concentric inner and outer rings, with the loop regions exposed to the phospholipid head-group region on the matrix side of the inner membrane. Lysine-43 is in the loop region and its ε-amino group is completely trimethylated. The role of this modification is unknown. If the trimethylated lysine-43 plays some important role in the functioning, assembly or degradation of the c-ring, it would be expected to persist throughout vertebrates and possibly invertebrates also. Therefore, we have carried out a proteomic analysis of c-subunits across representative species from different classes of vertebrates and from invertebrate phyla. In the twenty-nine metazoan species that have been examined, the complete methylation of lysine-43 is conserved, and it is likely to be conserved throughout the more than two million extant metazoan species. In unicellular eukaryotes and prokaryotes, when the lysine is conserved it is unmethylated, and the stoichiometries of c-subunits vary from 9-15. One possible role for the trimethylated residue is to provide a site for the specific binding of cardiolipin, an essential component of ATP synthases in mitochondria

Organization of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking.

The F-ATPase in bovine mitochondria is a membrane-bound complex of about 30 subunits of 18 different kinds. Currently, ∼85% of its structure is known. The enzyme has a membrane extrinsic catalytic domain, and a membrane intrinsic domain where the turning of the enzyme's rotor is generated from the transmembrane proton-motive force. The domains are linked by central and peripheral stalks. The central stalk and a hydrophobic ring of c-subunits in the membrane domain constitute the enzyme's rotor. The external surface of the catalytic domain and membrane subunit a are linked by the peripheral stalk, holding them static relative to the rotor. The membrane domain contains six additional subunits named ATP8, e, f, g, DAPIT (diabetes-associated protein in insulin-sensitive tissues), and 6.8PL (6.8-kDa proteolipid), each with a single predicted transmembrane α-helix, but their orientation and topography are unknown. Mutations in ATP8 uncouple the enzyme and interfere with its assembly, but its roles and the roles of the other five subunits are largely unknown. We have reacted accessible amino groups in the enzyme with bifunctional cross-linking agents and identified the linked residues. Cross-links involving the supernumerary subunits, where the structures are not known, show that the C terminus of ATP8 extends ∼70 Å from the membrane into the peripheral stalk and that the N termini of the other supernumerary subunits are on the same side of the membrane, probably in the mitochondrial matrix. These experiments contribute significantly toward building up a complete structural picture of the F-ATPase.This work was supported by the intramural program of the Medical Research Council (MRC Grant U105663150 (to J. E. W.)

The Impact of Heterogeneous Shared Leadership in Scientific Teams

Leadership is evolving dynamically from an individual endeavor to shared efforts. This paper aims to advance our understanding of shared leadership in scientific teams. We define three kinds of leaders, junior (10-15), mid (15-20), and senior (20+) based on career age. By considering the combinations of any two leaders, we distinguish shared leadership as heterogeneous when leaders are in different age cohorts and homogeneous when leaders are in the same age cohort. Drawing on 1,845,351 CS, 254,039 Sociology, and 193,338 Business teams with two leaders in the OpenAlex dataset, we identify that heterogeneous shared leadership brings higher citation impact for teams than homogeneous shared leadership. Specifically, when junior leaders are paired with senior leaders, it significantly increases team citation ranking by 1-2%, in comparison with two leaders of similar age. We explore the patterns between homogeneous leaders and heterogeneous leaders from team scale, expertise composition, and knowledge recency perspectives. Compared with homogeneous leaders, heterogeneous leaders are more adaptive in large teams, have more diverse expertise, and trace both the newest and oldest references

Nucleotide-binding sites can enhance N-acylation of nearby protein lysine residues.

Acyl-CoAs are reactive metabolites that can non-enzymatically S-acylate and N-acylate protein cysteine and lysine residues, respectively. N-acylation is irreversible and enhanced if a nearby cysteine residue undergoes an initial reversible S-acylation, as proximity leads to rapid S → N-transfer of the acyl moiety. We reasoned that protein-bound acyl-CoA could also facilitate S → N-transfer of acyl groups to proximal lysine residues. Furthermore, as CoA contains an ADP backbone this may extend beyond CoA-binding sites and include abundant Rossmann-fold motifs that bind the ADP moiety of NADH, NADPH, FADH and ATP. Here, we show that excess nucleotides decrease protein lysine N-acetylation in vitro. Furthermore, by generating modelled structures of proteins N-acetylated in mouse liver, we show that proximity to a nucleotide-binding site increases the risk of N-acetylation and identify where nucleotide binding could enhance N-acylation in vivo. Finally, using glutamate dehydrogenase as a case study, we observe increased in vitro lysine N-malonylation by malonyl-CoA near nucleotide-binding sites which overlaps with in vivo N-acetylation and N-succinylation. Furthermore, excess NADPH, GTP and ADP greatly diminish N-malonylation near their nucleotide-binding sites, but not at distant lysine residues. Thus, lysine N-acylation by acyl-CoAs is enhanced by nucleotide-binding sites and may contribute to higher stoichiometry protein N-acylation in vivo

Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans.

The structures of F-ATPases have been determined predominantly with mitochondrial enzymes, but hitherto no F-ATPase has been crystallized intact. A high-resolution model of the bovine enzyme built up from separate sub-structures determined by X-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of ATP. Here the isolation, characterization and crystallization of an integral F-ATPase complex from the α-proteobacterium Paracoccus denitrificans are described. Unlike many eubacterial F-ATPases, which can both synthesize and hydrolyse ATP, the P. denitrificans enzyme can only carry out the synthetic reaction. The mechanism of inhibition of its ATP hydrolytic activity involves a ζ inhibitor protein, which binds to the catalytic F₁-domain of the enzyme. The complex that has been crystallized, and the crystals themselves, contain the nine core proteins of the complete F-ATPase complex plus the ζ inhibitor protein. The formation of crystals depends upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize. The experiments open the way to an atomic structure of an F-ATPase complex.his work was funded by the intramural programme of the Medical Research Council via MRC programme U105663150 to J.E.W., and by support from the Biotechnology and Biological Sciences Research Council to M.J.O.W

Application and progress of nomograms in gastric cancer

Gastric cancer, as one of the malignant tumors with a significant disease burden globally, emphasizes the importance of early diagnosis and personalized treatment for improving patient prognosis. In recent years, clinical prediction models (CPMs) have played a crucial role in predicting disease risks, assisting medical decision-making, and evaluating clinical prognosis and benefits as tools for risk–benefit assessment. Nomograms, as an important visualization form of clinical prediction models, have been increasingly applied in tumor-related research. Numerous studies have constructed multiple nomogram models by integrating clinical, pathological, laboratory, imaging data, and genetic characteristics, providing an accurate and effective tool for predicting the risk of gastric cancer, early diagnosis, treatment response assessment, and prognosis analysis. This article aims to review the current clinical applications and research progress of nomograms in gastric cancer, with the goal of providing robust references and theoretical support for clinical practice