Studies on metal complex formation of environmentally friendly aminopolycarboxylate chelating agents

Aminopolykarboksyylaatteja, kuten etyleenidiamiinitetraetikkahappoa (EDTA), on käytetty useiden vuosikymmenien ajan erinomaisen metalli-ionien sitomiskyvyn vuoksi kelatointiaineena lukuisissa sovelluksissa sekä analytiikassa että monilla teollisisuuden aloilla. Näiden yhdisteiden biohajoamattomuus on kuitenkin herättänyt huolta viime aikoina, sillä niiden on havaittu olevan hyvin pysyviä luonnossa. Tämä työ on osa laajempaa tutkimushanketta, jossa on tavoitteena löytää korvaavia kelatointiaineita EDTA:lle. Tutkimuksen aiheena on kuuden kelatointiaineen metalli-ionien sitomiskyvyn kartoitus. EDTA:a paremmin luonnossa hajoavina nämä ovat ympäristöystävällisiä ehdokkaita korvaaviksi kelatointiaineiksi useisiin sovelluksiin. Työssä tutkittiin niiden kompleksinmuodostusta useiden metalli-ionien kanssa potentiometrisella titrauksella. Metalli-ionivalikoima vaihteli hieman kelatointiaineesta riippuen sisältäen magnesium-, kalsium-, mangaani-, rauta-, kupari-, sinkki-, kadmium-, elohopea-, lyijy- ja lantaani-ionit. Tutkittavat metallit oli valittu tähtäimessä olevien sovellusten, synteesissä ilmenneiden ongelmien tai ympäristönäkökohtien perusteella. Tulokset osoittavat näiden yhdisteiden metallinsitomiskyvyn olevan jonkin verran heikompi kuin EDTA:lla, mutta kuitenkin riittävän useisiin sovelluksiin kuten sellunvalkaisuprosessiin. Myrkyllisten raskasmetallien, kadmiumin, elohopen ja lyijyn kohdalla EDTA:a heikompi sitoutuminen on eduksikin, koska se yhdistettynä parempaan biohajoavuuteen saattaa alentaa tutkittujen yhdisteiden kykyä mobilisoida kyseisiä metalleja sedimenteistä. Useimmilla tutkituista yhdisteistä on ympäristönäkökulmasta etuna myös EDTA:a pienempi typpipitoisuus.

Modelling the manager: Representing rule-based management in farming systems simulation models

We trace the evolution of the representation of management in cropping and grazing systems models, from fixed annual schedules of identical actions in single paddocks toward flexible scripts of rules. Attempts to define higher-level organizing concepts in management policies, and to analyse them to identify optimal plans, have focussed on questions relating to grazing management owing to its inherent complexity. “Rule templates” assist the re-use of complex management scripts by bundling commonly-used collections of rules with an interface through which key parameters can be input by a simulation builder. Standard issues relating to parameter estimation and uncertainty apply to management sub-models and need to be addressed. Techniques for embodying farmers' expectations and plans for the future within modelling analyses need to be further developed, especially better linking planning- and rule-based approaches to farm management and analysing the ways that managers can learn.

Contested Lands: Land Disputes in Semi-Arid Parts of Northern Tanzania : Case Studies of the Loliondo and Sale Divisions

This study Contested Lands: Land disputes in semi-arid parts of northern Tanzania. Case Studies of the Loliondo and Sale Division in the Ngorongoro District concentrates on describing the specific land disputes which took place in the 1990s in the Loliondo and Sale Divisions of the Ngorongoro District in northern Tanzania. The study shows the territorial and historical transformation of territories and property and their relation to the land disputes of the 1990s'. It was assumed that land disputes have been firstly linked to changing spatiality due to the zoning policies of the State territoriality and, secondly, they can be related to the State control of property where the ownership of land property has been redefined through statutory laws. In the analysis of the land disputes issues such as use of territoriality, boundary construction and property claims, in geographical space, are highlighted. Generally, from the 1980s onwards, increases in human population within both Divisions have put pressure on land/resources. This has led to the increased control of land/resource, to the construction of boundaries and finally to formalized land rights on village lands of the Loliondo Division. The land disputes have thus been linked to the use of legal power and to the re-creation of the boundary (informal or formal) either by the Maasai or the Sonjo on the Loliondo and Sale village lands. In Loliondo Division land disputes have been resource-based and related to multiple allocations of land or game resource concessions. Land disputes became clearly political and legal struggles with an ecological reference.Land disputes were stimulated when the common land/resource rights on village lands of the Maasai pastoralists became regulated and insecure. The analysis of past land disputes showed that space-place tensions on village lands can be presented as a platform on which spatial and property issues with complex power relations have been debated. The reduction of future land disputes will succeed only when/if local property rights to land and resources are acknowledged, especially in rural lands of the Tanzanian State.

Archaean crustal evolution in eastern Finland : New geochronological and geochemical constraints from the Kuhmo terrain and the Nurmes belt

This thesis summarises the results of four original papers concerning U-Pb geochronology and geochemical evolution of Archaean rocks from the Kuhmo terrain and the Nurmes belt, eastern Finland. The study area belongs to a typical Archaean granite-greenstone terrain, composed of metavolcanic and metasedimentary rocks in generally N-S trending greenstone belts as well as a granitoid-gneiss complex with intervening gneissic and migmatised supracrustal and plutonic rocks. U-Pb data on migmatite mesosomes indicate that the crust surrounding the Tipasjärvi-Kuhmo-Suomussalmi greenstone belt is of varying age. The oldest protolith detected for a migmatite mesosome from the granitoid-gneiss complex is 2.94 Ga, whereas the other dated migmatites protoliths have ages of 2.84 2.79 Ga. The latter protoliths are syngenetic with the majority of volcanic rocks in the adjacent Tipasjärvi-Kuhmo-Suomussalmi greenstone belt. This suggests that the genesis of some of the volcanic rocks within the greenstone belt and surrounding migmatite protoliths could be linked. Metamorphic zircon overgrowths with ages of 2.84 2.81 Ga were also obtained. The non-migmatised plutonic rocks in the Kuhmo terrain and in the Nurmes belt record secular geochemical evolution, typical of Archaean cratons. The studied tonalitic rocks have ages of 2.83 2.75 Ga and they have geochemical characteristics similar to low-Al and high-Al TTD (tonalite-trondhjemite-dacite). The granodiorites, diorites, and gabbros with high Mg/Fe and LILE-enriched characteristics were mostly emplaced between 2.74 2.70 Ga and they exhibit geochemical characteristics typical of Archaean sanukitoid suites. The latest identified plutonic episode took place at 2.70 2.68 Ga, when compositionally heterogeneous leucocratic granitoid rocks, with a variable crustal component, were emplaced. U-Pb data on migmatite leucosomes suggest that leucosome generation may have been coeval with this latest plutonic event. On the basis of available U-Pb and Sm-Nd isotopic data it appears that the plutonic rocks of the Kuhmo terrain and the Nurmes belt do not contain any significant input from Palaeoarchaean sources. A characteristic feature of the Nurmes belt is the presence of migmatised paragneisses, locally preserving primary edimentary structures, with sporadic amphibolite intercalations. U-Pb studies on zircons indicate that the precursors of the Nurmes paragneisses were graywackes that were deposited between 2.71 Ga and 2.69 Ga and that they had a prominent 2.75 2.70 Ga source. Nd isotopic and whole-rock geochemical data for the intercalated amphibolites imply MORB sources. U-Pb data on zircons from the plutonic rocks and paragneisses reveal that metamorphic zircon growth took place at 2.72 2.63 Ga. This was the last tectonothermal event related to cratonisation of the Archaean crust of eastern Finland.

Can teacher collaboration overcome barriers to interdisciplinary learning in a disciplinary university? A case study using climate change

A teacher network was formed at an Australian university in order to better promote interdisciplinary student learning on the complex social-environmental problem of climate change. Rather than leaving it to students to piece together disciplinary responses, eight teaching academics collaborated on the task of exposing students to different types of knowledge in a way that was more than the summing of disciplinary parts. With a part-time network facilitator providing cohesion, network members were able to teach into each other’s classes, and share material and student activities across a range of units that included business, zoology, marine science, geography and education. Participants reported that the most positive aspects of the project were the collegiality and support for teaching innovation provided by peers. However, participants also reported being time-poor and overworked. Maintaining the collaboration beyond the initial one year project proved difficult because without funding for the network facilitator, participants were unable to dedicate the time required to meet and collaborate on shared activities. In order to strengthen teacher collaboration in a university whose administrative structures are predominantly discipline-based, there is need for recognition of the benefits of interdisciplinary learning to be matched by recognition of the need for financial and other resources to support collaborative teaching initiatives.

A Probabilistic Approach to the Primary Visual Cortex

What can the statistical structure of natural images teach us about the human brain? Even though the visual cortex is one of the most studied parts of the brain, surprisingly little is known about how exactly images are processed to leave us with a coherent percept of the world around us, so we can recognize a friend or drive on a crowded street without any effort. By constructing probabilistic models of natural images, the goal of this thesis is to understand the structure of the stimulus that is the raison d etre for the visual system. Following the hypothesis that the optimal processing has to be matched to the structure of that stimulus, we attempt to derive computational principles, features that the visual system should compute, and properties that cells in the visual system should have. Starting from machine learning techniques such as principal component analysis and independent component analysis we construct a variety of sta- tistical models to discover structure in natural images that can be linked to receptive field properties of neurons in primary visual cortex such as simple and complex cells. We show that by representing images with phase invariant, complex cell-like units, a better statistical description of the vi- sual environment is obtained than with linear simple cell units, and that complex cell pooling can be learned by estimating both layers of a two-layer model of natural images. We investigate how a simplified model of the processing in the retina, where adaptation and contrast normalization take place, is connected to the nat- ural stimulus statistics. Analyzing the effect that retinal gain control has on later cortical processing, we propose a novel method to perform gain control in a data-driven way. Finally we show how models like those pre- sented here can be extended to capture whole visual scenes rather than just small image patches. By using a Markov random field approach we can model images of arbitrary size, while still being able to estimate the model parameters from the data.

Service-based Requirements for Future Mobile Networks

The mobile phone has, as a device, taken the world by storm in the past decade; from only 136 million phones globally in 1996, it is now estimated that by the end of 2008 roughly half of the worlds population will own a mobile phone. Over the years, the capabilities of the phones as well as the networks have increased tremendously, reaching the point where the devices are better called miniature computers rather than simply mobile phones. The mobile industry is currently undertaking several initiatives of developing new generations of mobile network technologies; technologies that to a large extent focus at offering ever-increasing data rates. This thesis seeks to answer the question of whether the future mobile networks in development and the future mobile services are in sync; taking a forward-looking timeframe of five to eight years into the future, will there be services that will need the high-performance new networks being planned? The question is seen to be especially pertinent in light of slower-than-expected takeoff of 3G data services. Current and future mobile services are analyzed from two viewpoints; first, looking at the gradual, evolutionary development of the services and second, through seeking to identify potential revolutionary new mobile services. With information on both current and future mobile networks as well as services, a network capability - service requirements mapping is performed to identify which services will work in which networks. Based on the analysis, it is far from certain whether the new mobile networks, especially those planned for deployment after HSPA, will be needed as soon as they are being currently roadmapped. The true service-based demand for the "beyond HSPA" technologies may be many years into the future - or, indeed, may never materialize thanks to the increasing deployment of local area wireless broadband technologies.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

VisArchive: a time and relevance based visual interface for searching, browsing, and exploring project archives

Background Project archives are becoming increasingly large and complex. On construction projects in particular, the increasing amount of information and the increasing complexity of its structure make searching and exploring information in the project archive challenging and time-consuming. Methods This research investigates a query-driven approach that represents new forms of contextual information to help users understand the set of documents resulting from queries of construction project archives. Specifically, this research extends query-driven interface research by representing three types of contextual information: (1) the temporal context is represented in the form of a timeline to show when each document was created; (2) the search-relevance context shows exactly which of the entered keywords matched each document; and (3) the usage context shows which project participants have accessed or modified a file. Results We implemented and tested these ideas within a prototype query-driven interface we call VisArchive. VisArchive employs a combination of multi-scale and multi-dimensional timelines, color-coded stacked bar charts, additional supporting visual cues and filters to support searching and exploring historical project archives. The timeline-based interface integrates three interactive timelines as focus + context visualizations. Conclusions The feasibility of using these visual design principles is tested in two types of project archives: searching construction project archives of an educational building project and tracking of software defects in the Mozilla Thunderbird project. These case studies demonstrate the applicability, usefulness and generality of the design principles implemented.

Cellular Membranes as a Playground for Semliki Forest Virus Replication Complex

All positive-strand RNA viruses utilize cellular membranes for the assembly of their replication complexes, which results in extensive membrane modification in infected host cells. These alterations act as structural and functional scaffolds for RNA replication, providing protection for the viral double-stranded RNA against host defences. It is known that different positive-strand RNA viruses alter different cellular membranes. However, the origin of the targeted membranes, the mechanisms that direct replication proteins to specific membranes and the steps in the formation of the membrane bound replication complex are not completely understood. Alphaviruses (including Semliki Forest virus, SFV), members of family Togaviridae, replicate their RNA in association with membranes derived from the endosomal and lysosomal compartment, inducing membrane invaginations called spherules. Spherule structures have been shown to be the specific sites for RNA synthesis. Four replication proteins, nsP1-nsP4, are translated as a polyprotein (P1234) which is processed autocatalytically and gives rise to a membrane-bound replication complex. Membrane binding is mediated via nsP1 which possesses an amphipathic α-helix (binding peptide) in the central region of the protein. The aim of this thesis was to characterize the association of the SFV replication complex with cellular membranes and the modification of the membranes during virus infection. Therefore, it was necessary to set up the system for determining which viral components are needed for inducing the spherules. In addition, the targeting of the replication complex, the formation site of the spherules and their intracellular trafficking were studied in detail. The results of current work demonstrate that mutations in the binding peptide region of nsP1 are lethal for virus replication and change the localization of the polyprotein precursor P123. The replication complex is first targeted to the plasma membrane where membrane invaginations, spherules, are induced. Using a specific regulated endocytosis event the spherules are internalized from the plasma membrane in neutral carrier vesicles and transported via an actin-and microtubule-dependent manner to the pericentriolar area. Homotypic fusions and fusions with pre-existing acidic organelles lead to the maturation of previously described cytopathic vacuoles with hundreds of spherules on their limiting membranes. This work provides new insights into the membrane binding mechanism of SFV replication complex and its role in the virus life cycle. Development of plasmid-driven system for studying the formation of the replication complex described in this thesis allows various applications to address different steps in SFV life cycle and virus-host interactions in the future. This trans-replication system could be applied for many different viruses. In addition, the current work brings up new aspects of membranes and cellular components involved in SFV replication leading to further understanding in the formation and dynamics of the membrane-associated replication complex.

ORP1L, a new Rab7 effector and regulator of late endosome functions

Oxysterol binding protein (OSBP) homologues have been found in eukaryotic organisms ranging from yeast to humans. These evolutionary conserved proteins have in common the presence of an OSBP-related domain (ORD) which contains the fully conserved EQVSHHPP sequence motif. The ORD forms a barrel structure that binds sterols in its interior. Other domains and sequence elements found in OSBP-homologues include pleckstrin homology domains, ankyrin repeats and two phenylalanines in an acidic tract (FFAT) motifs, which target the proteins to distinct subcellular compartments. OSBP homologues have been implicated in a wide range of intracellular processes, including vesicle trafficking, lipid metabolism and cell signaling, but little is known about the functional mechanisms of these proteins. The human family of OSBP homologues consists of twelve OSBP-related proteins (ORP). This thesis work is focused on one of the family members, ORP1, of which two variants were found to be expressed tissue-specifically in humans. The shorter variant, ORP1S contains an ORD only. The N-terminally extended variant, ORP1L, comprises a pleckstrin homology domain and three ankyrin repeats in addition to the ORD. The two ORP1 variants differ in intracellular localization. ORP1S is cytosolic, while the ankyrin repeat region of ORP1L targets the protein to late endosomes/lysosomes. This part of ORP1L also has profound effects on late endosomal morphology, inducing perinuclear clustering of late endosomes. A central aim of this study was to identify molecular interactions of ORP1L on late endosomes. The morphological changes of late endosomes induced by overexpressed ORP1L implies involvement of small Rab GTPases, regulators of organelle motility, tethering, docking and/or fusion, in generation of the phenotype. A direct interaction was demonstrated between ORP1L and active Rab7. ORP1L prolongs the active state of Rab7 by stabilizing its GTP-bound form. The clustering of late endosomes/lysosomes was also shown to be linked to the minus end-directed microtubule-based dynein-dynactin motor complex through the ankyrin repeat region of ORP1L. ORP1L, Rab7 and the Rab7-interacting lysosomal protein (RILP) were found to be part of the same effector complex recruiting the dynein-dynactin complex to late endosomes, thereby promoting minus end-directed movement. The proteins were found to be physically close to each other on late endosomes and RILP was found to stabilize the ORP1L-Rab7 interaction. It is possible that ORP1L and RILP bind to each other through their C-terminal and N-terminal regions, respectively, when they are bridged by Rab7. With the results of this study we have been able to place a member of the uncharacterized OSBP-family, ORP1L, in the endocytic pathway, where it regulates motility and possibly fusion of late endosomes through interaction with the small GTPase Rab7.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.

Electron and proton transfer in NADH:ubiquinone oxidoreductase (Complex I) from Escherichia coli

Cells of every living organism on our planet − bacterium, plant or animal − are organized in such a way that despite differences in structure and function they utilize the same metabolic energy represented by electrochemical proton gradient across a membrane. This gradient of protons is generated by the series of membrane bound multisubunit proteins, Complex I, II, III and IV, organized in so-called respiratory or electron transport chain. In the eukaryotic cell it locates in the inner mitochondrial membrane while in the bacterial cell it locates in the cytoplasmic membrane. The function of the respiratory chain is to accept electrons from NADH and ubiquinol and transfer them to oxygen resulting in the formation of water. The free energy released upon these redox reactions is converted by respiratory enzymes into an electrochemical proton gradient, which is used for synthesis of ATP as well as for many other energy dependent processes. This thesis is focused on studies of the first member of the respiratory chain − NADH:ubiquinone oxidoreductase or Complex I. This enzyme has a boot-shape structure with hydrophilic and hydrophobic domains, the former of which has all redox groups of the protein, the flavin and eight to nine iron-sulfur clusters. Complex I serves as a proton pump coupling transfer of two electrons from NADH to ubiquinone to the translocation of four protons across the membrane. So far the mechanism of energy transduction by Complex I is unknown. In the present study we applied a set of different methods to study the electron and proton transfer reactions in Complex I from Escherichia coli. The main achievement was the experiment that showed that the electron transfer through the hydrophilic domain of Complex I is unlikely to be coupled to proton transfer directly or to conformational changes in the protein. In this work for the first time properties of all redox centers of Complex I were characterized in the intact purified bacterial enzyme. We also probed the role of several conserved amino acid residues in the electron transfer of Complex I. Finally, we found that highly conserved amino acid residues in several membrane subunits form a common pattern with a very prominent feature – the presence of a few lysines within the membrane. Based on the experimental data, we suggested a tentative principle which may govern the redox-coupled proton pumping in Complex I.

An engineering or behavioural approach? A study into employee’s perceptions regarding the effectiveness of occupational road safety initiatives

Background and Aims Considerable variation has been documented with fleet safety interventions’ abilities to create lasting behavioural change, and research has neglected to consider employees’ perceptions regarding the effectiveness of fleet interventions. This is a critical oversight as employees’ beliefs and acceptance levels (as well as the perceived organisational commitment to safety) can ultimately influence levels of effectiveness, and this study aimed to examine such perceptions in Australian fleet settings. Method 679 employees sourced from four Australian organisations completed a safety climate questionnaire as well as provided perspectives about the effectiveness of 35 different safety initiatives. Results Countermeasures that were perceived as most effective were a mix of human and engineering-based approaches: - (a) purchasing safer vehicles; - (b) investigating serious vehicle incidents, and; - (c) practical driver skills training. In contrast, least effective countermeasures were considered to be: - (a) signing a promise card; - (b) advertising a company’s phone number on the back of cars for complaints and compliments, and; - (c) communicating cost benefits of road safety to employees. No significant differences in employee perceptions were identified based on age, gender, employees’ self-reported crash involvement or employees’ self-reported traffic infringement history. Perceptions of safety climate were identified to be “moderate” but were not linked to self-reported crash or traffic infringement history. However, higher levels of safety climate were positively correlated with perceived effectiveness of some interventions. Conclusion Taken together, employees believed occupational road safety risks could best be managed by the employer by implementing a combination of engineering and human resource initiatives to enhance road safety. This paper will further outline the key findings in regards to practice as well as provide direction for future research.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.