Advances in the analysis of dynamic protein complexes by proteomics and data processing

Signal transduction governs virtually every cellular function of multicellular organisms, and its deregulation leads to a variety of diseases. This intricate network of molecular interactions is mediated by proteins that are assembled into complexes within individual signaling pathways, and their composition and function is often regulated by different post-translational modifications. Proteomic approaches are commonly used to analyze biological complexes and networks, but often lack the specificity to address the dynamic and hence transient nature of the interactions and the influence of the multiple post-translational modifications that govern these processes. Here we review recent developments in proteomic research to address these limitations, and discuss several technologies that have been developed for this purpose. The synergy between these proteomic and computational tools, when applied together with global methods to the analysis of individual proteins, complexes and pathways, may allow researchers to unravel the underlying mechanisms of signaling networks in greater detail than previously possible.     

Cytokinin and auxin interactions in plant development: metabolism, signalling, transport and gene expression

Auxin and cytokinins have been identified as key regulators of plant development. Recently, these phytohormones have been shown to interact during important developmental processes, including positioning, identity acquisition and maintenance of meristem organizing centres, regulation of balance between cell division and differentiation, and postembryonic de novo organogenesis. Here, we discuss recent advances in our understanding of the underlying molecular mechanisms at the levels of regulating metabolism, signalling, gene expression and protein stability.     

Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers

We address the question of what are the molecular mechanisms providing discrimination between seemingly similar counterions binding to various biomolecular surfaces. In the case of protein association with Na (+) and K (+) ions, recent works proposed that specificity of carboxylate functional groups interacting with these mobile ions rationalizes the observed ionic discrimination. We probe in this work whether similar arguments may be used to explain higher propensity of Na (+) ions to associate with DNA compared with K (+) ions, which was suggested by our simulations and some experiments. By comparing our extensive molecular dynamics simulations of Na (+) and K (+) distributions around a 16-base-pair DNA oligomer, [(CGAGGTTTAAACCTCG)] 2, with additional simulations where DNA is replaced by a "soup" of monomers (dimethylphosphate anion), we conclude that DNA specificity toward Na (+)/K (+) is not determined by the underlying functional group specificity. Instead, the collective effect of DNA charges drives larger Na (+) association. To gain additional microscopic insights into the mechanisms of specificity on ionic associations in these systems, we carried out energetic analysis of the association between Na (+) and K (+) with chloride and dimethylphosphate anions. The insights gained from our computational work shed light on a number of experiments on electrolyte solutions of monovalent salts and DNA.     

Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single‐wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical‐chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.     

Chemical 'Jekyll and Hyde's: small-molecule inhibitors of developmental signaling pathways

Small molecules that perturb developmental signaling pathways can have devastating effects on embryonic patterning, as evidenced by the chemically induced onset of cyclopic lambs and children with severely shortened limbs during the 1950s. Recent studies, however, have revealed critical roles for these pathways in human disorders and diseases, spurring the re-examination of these compounds as new targeted therapies. In this tutorial review, we describe four case studies of teratogenic compounds, including inhibitors of the Hedgehog (Hh), Wnt, and bone morphogenetic protein (BMP) pathways. We discuss how these teratogens were discovered, their mechanisms of action, their utility as molecular probes, and their potential as therapeutic agents. We also consider current challenges in the field and possible directions for future research.     

In silico Analysis of Molecular Mechanisms of Galanthus nivalis Agglutinin-Related Lectin-Induced Cancer Cell Death from Carbohydrate-Binding Motif Evolution Hypothesis

Galanthus nivalis agglutinin-related lectins, a superfamily of strictly mannose-binding-specific lectins widespread amongst monotyledonous plants, have drawn a rising attention for their remarkable anti-proliferative and apoptosis-inducing activities toward various types of cancer cells; however, the precise molecular mechanisms by which they induce tumor cell apoptosis are still only rudimentarily understood. Herein, we found that the three conserved motifs "QXDXNXVXY," the mannose-specific binding sites, could mutate at one or more amino acid sites, which might be a driving force for the sequential evolution and thus ultimately leading to the complete disappearance of the three conserved motifs. In addition, we found that the motif evolution could result in the diversification of sugar-binding types that G. nivalis agglutinin-related lectins could bind from specific mannose receptors to more types of sugar-containing receptors in cancer cells. Subsequently, we indicated that some sugar-containing receptors such as TNFR1, EGFR, Hsp90, and Hsp70 could block downstream anti-apoptotic or survival signaling pathways, which, in turn, resulted in tumor cell apoptosis. Taken together, our hypothesis that carbohydrate-binding motif evolution may impact the G. nivalis agglutinin-related lectin-induced survival or anti-apoptotic pathways would provide a new perspective for further elucidating the intricate relationships between the carbohydrate-binding specificities and complex molecular mechanisms by which G. nivalis agglutinin-related lectins induce cancer cell death.     

Deciphering UV-induced DNA Damage Responses to Prevent and Treat Skin Cancer

Ultraviolet (UV) radiation is among the most prevalent environmental factors that influence human health and disease. Even 1 h of UV irradiation extensively damages the genome. To cope with resulting deleterious DNA lesions, cells activate a multitude of DNA damage response pathways, including DNA repair. Strikingly, UV-induced DNA damage formation and repair are affected by chromatin state. When cells enter S phase with these lesions, a distinct mutation signature is created via error-prone translesion synthesis. Chronic UV exposure leads to high mutation burden in skin and consequently the development of skin cancer, the most common cancer in the United States. Intriguingly, UV-induced oxidative stress has opposing effects on carcinogenesis. Elucidating the molecular mechanisms of UV-induced DNA damage responses will be useful for preventing and treating skin cancer with greater precision. Excitingly, recent studies have uncovered substantial depth of novel findings regarding the molecular and cellular consequences of UV irradiation. In this review, we will discuss updated mechanisms of UV-induced DNA damage responses including the ATR pathway, which maintains genome integrity following UV irradiation. We will also present current strategies for preventing and treating nonmelanoma skin cancer, including ATR pathway inhibition for prevention and photodynamic therapy for treatment.     

Prediction of vibrational frequencies of possible intermediates and side products of the methanol synthesis on ZnO(0001) by ab initio calculations

We used ab initio density functional theory in combination with an embedded cluster approach to calculate vibrational spectra and formation enthalpies of possible intermediates and side products (spectator species) in the synthesis of methanol out of syngas on the ZnO(0001) surface. Our investigations are based upon our previous work on possible reaction pathways and activation barriers for this reaction at oxygen vacancies on ZnO(0001). We present and discuss calculated vibrational frequencies of short-living formyl, hydroxymethylene, formaldehyde, acetale, and hydroxymethyl intermediates and compare the calculated frequencies of formate and methoxy species as well as CO and CO(2) species, at the defect free surface and at oxygen vacancies, with recent experimental findings. All investigated species show characteristic features in their spectra. Therefore, the analysis of their vibrational frequencies is a suitable mean to distinguish them and gain new insights in this reaction which is of recent experimental interest. We are able to identify the structure and characteristics of different surface species, such as monodentate and polydentate carbonate and formate species, in agreement with experimental results.     

Efficient and robust strong-field control of population transfer in sensitizer dyes with designed femtosecond laser pulses

We demonstrate control of electronic population transfer in molecules with the help of appropriately shaped femtosecond laser pulses. To this end we investigate two photosensitizer dyes in solution being prepared in the triplet ground state. Excitation within the triplet system is followed by intersystem crossing and the corresponding singlet fluorescence is monitored as a measure of population transfer in the triplet system. We record control landscapes with respect to the fluorescence intensity on both dyes by a systematic variation of laser pulse shapes combining second order and third order dispersion. In the strong-field regime we find highly structured topologies with large areas of maximum or minimum population transfer being insensitive over a certain range of applied laser intensities thus demonstrating robustness. We then compare our experimental results with simulations on generic molecular potentials by solving the time-dependent Schr?dinger equation for excitation with shaped pulses. Control landscapes with respect to population transfer confirm the general trends from experiments. An analysis of regions with maximum or minimum population transfer indicates that coherent processes are responsible for the outcome of our excitation process. The physical mechanisms of joint motion of ground and excited state wave packets or population of a vibrational eigenstate in the excited state permit us to discuss the molecular dynamics in an atom-like picture.     

Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.     

Enzymatic catalysis of urea decomposition: elimination or hydrolysis?

We present a high-level quantum chemical study of possible reaction mechanisms associated with the catalytic decomposition of urea by a bioinorganic mimetic of the dinickel active site of urease. We chose the phthalazine-dinickel complexes of Lippard and co-workers, because these mimetics have been shown to hydrolytically degrade urea. High-level quantum chemical methodologies were utilized to identify stable intermediates and transition-state structures along several possible reaction pathways. The computed results were then used to further analyze what may occur in the active site of urease. Valuable information on the latter has been extracted from experimental data, computational approaches, and unpublished molecular dynamics simulations. On the basis of these comparative studies, we propose that both the elimination and hydrolytic pathways may compete for urea decomposition in the active site of urease.     

Is Curcumin the Answer to Future Chemotherapy Cocktail?

The rise in cancer cases in recent years is an alarming situation worldwide. Despite the tremendous research and invention of new cancer therapies, the clinical outcomes are not always reassuring. Cancer cells could develop several evasive mechanisms for their survivability and render therapeutic failure. The continuous use of conventional cancer therapies leads to chemoresistance, and a higher dose of treatment results in even greater toxicities among cancer patients. Therefore, the search for an alternative treatment modality is crucial to break this viscous cycle. This paper explores the suitability of curcumin combination treatment with other cancer therapies to curb cancer growth. We provide a critical insight to the mechanisms of action of curcumin, its role in combination therapy in various cancers, along with the molecular targets involved. Curcumin combination treatments were found to enhance anticancer effects, mediated by the multitargeting of several signalling pathways by curcumin and the co-administered cancer therapies. The preclinical and clinical evidence in curcumin combination therapy is critically analysed, and the future research direction of curcumin combination therapy is discussed.     

A comparative thermodynamic study for both natural and artificial RNA/DNA-protein binary complexes

In recent years, Systematic Evolution of Ligands by EXponential enrichment (SELEX) technique has been developed into a fast growing field. In contrast to traditional recognition elements, like antibody, our interests focus on novel molecular recognition elements based on nucleic acids, which are of value both for the therapy and biosensors. A comparative study of thermodynamic for both natural and artificial RNA/DNA-protein complexes would establish bases for a specificity of complex formation. In particular, we have shown that aptamers could be used for a direct measuring of thrombin enzymatic activity in a solution.     

Strigolactones,from Plants to Human Health: Achievements and Challenges

Strigolactones (SLs) are a class of sesquiterpenoid plant hormones that play a role in the response of plants to various biotic and abiotic stresses. When released into the rhizosphere, they are perceived by both beneficial symbiotic mycorrhizal fungi and parasitic plants. Due to their multiple roles, SLs are potentially interesting agricultural targets. Indeed, the use of SLs as agrochemicals can favor sustainable agriculture via multiple mechanisms, including shaping root architecture, promoting ideal branching, stimulating nutrient assimilation, controlling parasitic weeds, mitigating drought and enhancing mycorrhization. Moreover, over the last few years, a number of studies have shed light onto the effects exerted by SLs on human cells and on their possible applications in medicine. For example, SLs have been demonstrated to play a key role in the control of pathways related to apoptosis and inflammation. The elucidation of the molecular mechanisms behind their action has inspired further investigations into their effects on human cells and their possible uses as anti-cancer and antimicrobial agents.     

Identifying cancer specific signaling pathways based on the dysregulation between genes

A large collection of studies has shown that the occurrence of cancer is related to the functional dysfunction of the pathways. Identification of cancer-related pathways could help researchers understand the mechanisms of complex diseases well. Whereas, most current signaling pathway analysis methods take no account of the gene interaction variations within pathways. Furthermore, considering that some pathways have connection with two or more cancer types, while some are likely to be cancer-type specific pathways. Identifying cancer-type specific pathways contributes to interpreting the different mechanisms of different cancer types. In this study, we first proposed a pathway analysis method named Pathway Analysis of Intergenic Regulation (PAIGR) to identify pathways with dysregulation between genes and compared the performance of this method with four existing methods on four colorectal cancer (CRC) datasets. The results showed that PAIGR could find cancer-related pathways more accurately. Moreover, in order to explore the relationship between the identified pathways and the cancer type, we constructed a pathway interaction network, in which nodes and edges represented pathways and interactions between pathways respectively. Highly connected pathways were considered to play a central role in an extensive range of biological processes, while sparsely connected pathways are considered to have certain specificity. Our results showed that pathways identified by PAIGR had a low nodal degree (i.e., a few numbers of interactions), which suggested that most of these pathways were cancer-type specific.     

Variation in the isotopic composition of zinc in the natural environment and the use of zinc isotopes in biogeosciences: a review

Zinc (Zn) is a trace element that is, as a building block in various enzymes, of vital importance for all living organisms. Zn concentrations are widely determined in dietary, biological and environmental studies. Recent papers report on the first efforts to use stable Zn isotopes in environmental studies, and initial results point to significant Zn isotope fractionation during various biological and chemical processes, and thus highlight their potential as valuable biogeochemical tracers. In this article, we discuss the state-of-the-art analytical methods for isotopic analysis of Zn and the procedures used to obtain accurate Zn isotope ratio results. We then review recent applications of Zn isotope measurements in environmental and life sciences, emphasizing the mechanisms and causes responsible for observed natural variation in the isotopic composition of Zn. We first discuss the Zn isotope variability in extraterrestrial and geological samples. We then focus on biological processes inducing Zn isotope fractionation in plants, animals and humans, and we assess the potential of Zn isotope ratio determination for elucidating sources of atmospheric particles and contamination. Finally, we discuss possible impediments and limitations of the application of Zn isotopes in (geo-) environmental studies and provide an outlook regarding future directions of Zn isotope research.     

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations

Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV—an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.