The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade

We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein signal transduction cascades, renders stochastic signaling dynamics in cytosol biochemical networks distinct from the usual description of stochastic dynamics in gene regulatory networks. For a simple 2-step enzymatic cascade which underlies many important protein signaling pathways, we demonstrated that the commonly used techniques such as the linear noise approximation and the Langevin equation become inadequate when the number of proteins becomes too low. Consequently, we developed a new analytical approximation, based on mixing the generating function and distribution function approaches, to the solution of the master equation that describes nonlinear chemical signaling kinetics for this important class of biochemical reactions. Our techniques work in a much wider range of protein number fluctuations than the methods used previously. We found that under certain conditions the burst-phase noise may be injected into the downstream signaling network dynamics, resulting possibly in unusually large macroscopic fluctuations. In addition to computing first and second moments, which is the goal of commonly used analytical techniques, our new approach provides the full time-dependent probability distributions of the colored non-Gaussian processes in a nonlinear signal transduction cascade.Comment: 16 pages, 9 figure

Effects of electron transfer on the stability of hydrogen bonds.

The measurement of the dimerization constants of hydrogen-bonded ruthenium complexes (12, 22, 32) linked by a self-complementary pair of 4-pyridylcarboxylic acid ligands in different redox states is reported. Using a combination of FTIR and UV/vis/NIR spectroscopies, the dimerization constants (KD) of the isovalent, neutral states, 12, 22, 32, were found to range from 75 to 130 M-1 (ΔG0 = -2.56 to -2.88 kcal mol-1), while the dimerization constants (K2-) of the isovalent, doubly-reduced states, (12)2-, (22)2-, (32)2-, were found to range from 2000 to 2500 M-1 (ΔG0 = -4.5 to -4.63 kcal mol-1). From the aforementioned values and the comproportionation constant for the mixed-valent dimers, the dimerization constants (KMV) of the mixed-valent, hydrogen-bonded dimers, (12)-, (22)-, (32)-, were found to range from 0.5 × 106 to 1.2 × 106 M-1 (ΔG0 = -7.78 to -8.31 kcal mol-1). On average, the hydrogen-bonded, mixed-valent states are stabilized by -5.27 (0.04) kcal mol-1 relative to the isovalent, neutral, hydrogen-bonded dimers and -3.47 (0.06) kcal mol-1 relative to the isovalent, dianionic hydrogen bonded dimers. Electron exchange in the mixed valence states imparts significant stability to hydrogen bonding. This is the first quantitative measurement of the strength of hydrogen bonds in the presence and absence of electronic exchange

Identification of the prebiotic translation apparatus within the contemporary ribosome

A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the proto-ribosome emergence hypothesis and show that the tendency for dimerization, a prerequisite for obtaining the catalytic centre, is linked to the fold of its two components, indicating functional selection at the molecular level in the prebiotic era and supporting the existence of dimeric proto-ribosome

Oligorotaxane radicals under orders

A strategy for creating foldameric oligorotaxanes composed of only positively charged components is reported. Threadlike components-namely oligoviologens-in which different numbers of 4,4'-bipyridinium (BIPY(2+)) subunits are linked by p-xylylene bridges, are shown to be capable of being threaded by cyclobis(paraquat-p-phenylene) (CBPQT(4+)) rings following the introduction of radical-pairing interactions under reducing conditions. UV/vis/NIR spectroscopic and electrochemical investigations suggest that the reduced oligopseudorotaxanes fold into highly ordered secondary structures as a result of the formation of BIPY(\u2022+) radical cation pairs. Furthermore, by installing bulky stoppers at each end of the oligopseudorotaxanes by means of Cu-free alkyne-azide cycloadditions, their analogous oligorotaxanes, which retain the same stoichiometries as their progenitors, can be prepared. Solution-state studies of the oligorotaxanes indicate that their mechanically interlocked structures lead to the enforced interactions between the dumbbell and ring components, allowing them to fold (contract) in their reduced states and unfold (expand) in their fully oxidized states as a result of Coulombic repulsions. This electrochemically controlled reversible folding and unfolding process, during which the oligorotaxanes experience length contractions and expansions, is reminiscent of the mechanisms of actuation associated with muscle fibers

Exploring DNA Compaction Via Bacillus Subtilis ParB Protein by Single Molecule Investigation

Faithful chromosome segregation involves ParB, a DNA-binding and compacting protein that specifically recognizes parS DNA sites near the replication origin. ParB spreads 10-20 kb from parS sites, which recruitments additional ParB molecules to neighboring DNA, forming higher-order nucleoprotein complexes. ParB is also a novel CTPase enzyme and hydrolyses CTP to self-dimerization and create a clamp that slides along DNA. To understand the roles of CTP in Bacillus subtilis ParB (BsParB), we purified wild type ParB (BsParB (WT)) and recombinant ParB (BsParB(R80A)) mutant. BsParB(R80A) was known to prevent CTP binding and not compact DNA. Proteins N- and C-terminally appended with a lysine-cysteine-lysine (KCK) tag were tested. We performed single-molecule DNA flow-stretching experiments both in the absence and presence of CTP. Both CTP binding and CTP hydrolysis impacts ParB-mediated DNA compaction, with parS sites modulating compaction rates, while BsParB(R80A) could compact DNA in a CTP-dependent manner. The KCK tag influenced DNA compaction

LATS1 but not LATS2 represses autophagy by a kinase-independent scaffold function

Autophagy perturbation represents an emerging therapeutic strategy in cancer. Although LATS1 and LATS2 kinases, core components of the mammalian Hippo pathway, have been shown to exert tumor suppressive activities, here we report a pro-survival role of LATS1 but not LATS2 in hepatocellular carcinoma (HCC) cells. Specifically, LATS1 restricts lethal autophagy in HCC cells induced by sorafenib, the standard of care for advanced HCC patients. Notably, autophagy regulation by LATS1 is independent of its kinase activity. Instead, LATS1 stabilizes the autophagy core-machinery component Beclin-1 by promoting K27-linked ubiquitination at lysine residues K32 and K263 on Beclin-1. Consequently, ubiquitination of Beclin-1 negatively regulates autophagy by promoting inactive dimer formation of Beclin-1. Our study highlights a functional diversity between LATS1 and LATS2, and uncovers a scaffolding role of LATS1 in mediating a cross-talk between the Hippo signaling pathway and autophagy

The true story of Yeti, the "abominable" heterochromatic gene of drosophila melanogaster

The Drosophila Yeti gene (CG40218) was originally identified by recessive lethal mutation and subsequently mapped to the deep pericentromeric heterochromatin of chromosome 2. Functional studies have shown that Yeti encodes a 241 amino acid protein called YETI belonging to the evolutionarily conserved family of Bucentaur (BCNT) proteins and exhibiting a widespread distribution in animals and plants. Later studies have demonstrated that YETI protein: (i) is able to bind both subunits of the microtubule-based motor kinesin-I; (ii) is required for proper chromosome organization in both mitosis and meiosis divisions; and more recently (iii) is a new subunit of dTip60 chromatin remodeling complex. To date, other functions of YETI counterparts in chicken (CENtromere Protein 29, CENP-29), mouse (Cranio Protein 27, CP27), zebrafish and human (CranioFacial Development Protein 1, CFDP1) have been reported in literature, but the fully understanding of the multifaceted molecular function of this protein family remains still unclear. In this review we comprehensively highlight recent work and provide a more extensive hypothesis suggesting a broader range of YETI protein functions in different cellular processes

Research on the Dimerization Sequence of Exo70 and Its Role in Breast Cancer Cell Metastasis

Exo70是胞外分泌复合体Exocyst的关键亚基,可通过参与Exocyst复合体或自身聚合促进细胞迁移。我们在研究中发现,Exo70自身形成二聚体的能力显著强于与Exocyst其它7个亚基的结合,提示Exo70二聚化的重要作用。进一步构建Exo70缺失突变体,并通过一系列免疫共沉淀实验确定了Exo70形成二聚体的关键位置是位于氨基酸31~35与505~509的两段同样的序列SLEKS。进而利用这两个序列的缺失突变体,通过transwell迁移实验,证实这两段SLEKS序列在Exo70二聚化及乳腺癌细胞迁移过程中的关键作用。以上结果为Exo70独立于Exocyst复合体功能之外的新功能研究提供了依据,也为乳腺癌及其转移的治疗提供潜在的靶点。Exo70,the key subunit of Exocyst protein complex,promotes cell metastasisby self-dimerization or by involving in the Exocyst complex formation.In this research,we found that Exo70 was dramatically more capable of forming self-dimerization than binding to the other subunits of exocyst complex,and aindicative of the important roles of its self-dimerization.Then we constructed a set of truncation mutants of Exo70 in order to determine the core sequence for its dimerization.With co-immun oprecipitation analysis,we identified two identical protein sequences"SLEKS"located at amino acid 31~35 and 505~509 as critical sequencesfor the dimerization of Exo70.By "cell transwell"essay,we further found that the full length Exo70 significantly promotes breast cancer metastasis,while the two truncation mutants of Exo70(Δ31~35 and Δ505~509) don't process such ability,indicating that these two "SLEKS"sequences play pivotal role in breast cancer cell metastasis and invasion.Together,these results provide fundamental basis for researches on novel functions of Exo70 besides its well-known role in Exocyst complex formation and provide potential drug target for treating breast cancer and its metastasis.国家自然科学基金青年项目(31300970);; 福州大学科研启动项目(510402)共同资