Targeting protein with the aim of ubiquitin-labelling for degradation is a new and upand coming field of drug discovery. Proteolysis targeting chimeras (PROTACs) areheterobifunctional linker molecules that connects the target molecule to an E3ubiquitin ligase, subsequent ubiquitination of the target protein initiates the proteindegradation by the proteosome system. The functional nature or mechanism ofPROTACs have the potential to reach previously undruggable proteins with shallowbinding pockets where traditionally designed inhibitors have failed. This projectexamines the possibility to develop a biophysical strategy for characterization andranking of PROTAC compounds. During the project biophysical methods such as SPRwith BIAcore T200, GCI with WAVE, switchSense and MST have been used todevelop a PROTAC ranking assay. Limited solubility of the PROTAC compoundshindered the development of a PROTAC ranking assay, the concentrations neededfor affinity estimation could not be reached due to the solubility of the PROTACcompounds under given condition. Hence further development of the PROTACranking assay is required. There is potentially a great deal of knowledge that can begathered from a working biophysical PROTAC ranking assay that can assist in thedevelopment of new therapeutic compounds.

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Recent developments in x-ray single particle imaging and diffraction pattern analysis would benefit if the analysis can be made easier and less computationally costly. One way of doing this is to control the orientation of the sample molecules. Therefore pre-orientation of a protein in an electric field is investigated to determine if it is a viable option for experimental set-ups. Previous simulations have shown that this is possible, but the protein can become unstable during the orientation process and deform. By adding a thin water film (3 Å thick) the aim is to stabilize the protein, increasing the orientation speed and make it more resilient to conformational changes. In 2022 simu-lations were performed, but due to energy leaking from the system no new conclusions could be drawn. The aim of the project was first to discover why the energy was leaking, and then re-do the simulations. The energy problem was solved by sourcing a neutral protein and removing the center of mass motion removal-setting in the simulation software GROMACS. For the second part, the simulations clearly shows that the water both increases the speed of orientation and stabilises the protein, both when looking at the root mean square deviation and the radius of gyration.

<p>Vi har identifierat flexibelt utbyte och lagring av data i databaser, tillsammans med långvarig satsning på olika existerande och framtida modeller som nyckar till förståelse av det regler nätverk som utgör bron mellan geno- och fenotyp. Denna pilot studie av modellering av stora cellulära kontroll nätverk utgår från en intressant medicinsk frågeställning inom molekylär cellbiologi: Är framtvingad expression av Cdc6, aktivering av Cdk4/6 och Cdk2 tillräcklig för förankringsfri entré av cell cykelns S fas? Vi försöker konstruera en modell för att besvara denna fråga, på så sätt att vi kan detektera problem vid modellering av stora kontroll nätverk, diskutera implikationer och möjliga lösningar.</p><p>Vår modell är baserad på 1447 reaktioner och innehåller 1343 olika molekyler. Vi använde graf teori för att studera dess topologi och gjorde följande fynd: Nätverket är skalfritt och avtar enligt en potensfunktion, som var väntat baserat på tidigare arbeten. Nätverket består av ett stort väl förenat kluster. Det kan inte bli modulariserat i form av starka komponenter eller block i en användbar form. Detta eftersom vi fann en stor komponent eller ett stort block som innehöll majoriteten av alla molekyler och mer än hundra små komponenter eller block med en eller några molekyler. Vårt nätverk stämmer inte överens med en hierarkisk nätverks modell bestående av block förenade av cut-vertices.</p> / <p>We have identified flexible exchange and storage of data in databases, together with prolonged investment in different existing and future modelling formalisms as key issues in successful understanding of the regulatory network responsible for the connection between geno- and phenotype. This pilot study of modelling of large-scale regulatory networks starts with a medically interesting question from molecular cell biology: Is enforced expression of Cdc6, activation of Cdk4/6 and Cdk2 sufficient for anchorage-independent entry of the S phase of the cell cycle? We try to construct a model for answering this question, in such a way that we can reveal obstacles of large-scale regulatory modelling, discuss their implications and possible solutions.</p><p>Our model is based on 1447 reactions and contains 1343 different molecules. We used graph theory to study its topology and made the following findings: The network is scale-free and decays as a power-law, as could be expected based on earlier works. The network consists of one huge well connected cluster. It cannot be modularised into strong components or blocks in a useful way, since we get one big component or block containing a majority of all molecules and more than a hundred tiny components or blocks with one or a few molecules. Our network does not agree with a hierarchical network model consisting of blocks linked by cut-vertices.</p>

Vi har identifierat flexibelt utbyte och lagring av data i databaser, tillsammans med långvarig satsning på olika existerande och framtida modeller som nyckar till förståelse av det regler nätverk som utgör bron mellan geno- och fenotyp. Denna pilot studie av modellering av stora cellulära kontroll nätverk utgår från en intressant medicinsk frågeställning inom molekylär cellbiologi: Är framtvingad expression av Cdc6, aktivering av Cdk4/6 och Cdk2 tillräcklig för förankringsfri entré av cell cykelns S fas? Vi försöker konstruera en modell för att besvara denna fråga, på så sätt att vi kan detektera problem vid modellering av stora kontroll nätverk, diskutera implikationer och möjliga lösningar. Vår modell är baserad på 1447 reaktioner och innehåller 1343 olika molekyler. Vi använde graf teori för att studera dess topologi och gjorde följande fynd: Nätverket är skalfritt och avtar enligt en potensfunktion, som var väntat baserat på tidigare arbeten. Nätverket består av ett stort väl förenat kluster. Det kan inte bli modulariserat i form av starka komponenter eller block i en användbar form. Detta eftersom vi fann en stor komponent eller ett stort block som innehöll majoriteten av alla molekyler och mer än hundra små komponenter eller block med en eller några molekyler. Vårt nätverk stämmer inte överens med en hierarkisk nätverks modell bestående av block förenade av cut-vertices. / We have identified flexible exchange and storage of data in databases, together with prolonged investment in different existing and future modelling formalisms as key issues in successful understanding of the regulatory network responsible for the connection between geno- and phenotype. This pilot study of modelling of large-scale regulatory networks starts with a medically interesting question from molecular cell biology: Is enforced expression of Cdc6, activation of Cdk4/6 and Cdk2 sufficient for anchorage-independent entry of the S phase of the cell cycle? We try to construct a model for answering this question, in such a way that we can reveal obstacles of large-scale regulatory modelling, discuss their implications and possible solutions. Our model is based on 1447 reactions and contains 1343 different molecules. We used graph theory to study its topology and made the following findings: The network is scale-free and decays as a power-law, as could be expected based on earlier works. The network consists of one huge well connected cluster. It cannot be modularised into strong components or blocks in a useful way, since we get one big component or block containing a majority of all molecules and more than a hundred tiny components or blocks with one or a few molecules. Our network does not agree with a hierarchical network model consisting of blocks linked by cut-vertices.

This work aims to investigate the fragmentation of an ionized Cystine molecule, as simulated in the framework of molecular dynamics and quantum mechanics. Cystine is viewed as a model system for larger sets of peptides -- ultimately contributing to the understanding of protein photofragmentation, which is crucial for determining the structure of a protein using new methods. The analysis software was written in Python, partly in conjunction with another student. The photofragmentation of the molecule is analyzed in terms of bond integrity versus time and mass-to-charge ratios for the resulting fragments. Generally, the molecule disintegrates into more and smaller fragments the higher the degree of ionization is. / I det föreliggande arbetet undersöks fragmenteringen av en joniserad molekyl Cystin, som simulerats medelst molekyldynamik och kvantmekanik. Cystin betraktas som ett modellsystem för större peptidstrukturer -- något som i längden kan bidra till större förståelse för fotofragmentering av proteiner, vilket i sin tur är avgörande inom nya metoder för strukturbestämning. Analysprogrammet skrevs i Python och delvis i samarbete med en annan student. Molekylens fotofragmentering analyseras med avseende på bindningsintegritet över tid, samt mass-laddningskvot hos de resulterande fragmenten. I allmänhet sönderfaller molekylen till fler och mindre fragment ju högre joniseringsnivån är.

<p>A proof-of-concept for a novel microarray used to study protein-ligand interaction in real-time using label-free detection is presented. Many of todays commercially available instruments lack the ability to immobilize membrane proteins. At the same time, the pharmaceutical industry develops drugs directed towards membrane-bound receptors. The need to study drug-target kinetics and to be able to screen for new medical substances is high. To study the biomolecular interactions in real-time, imaging surface plasmon resonance (iSPR) is used. A patterned sensor surface with hydrophobic barriers assisting in the piezodispensing of NeutrAvidin with complex-bound biotin-ssDNA is created. Histidine-tagged proteins are immobilized at the vesicle surface using divalent nitrilotriacetic acid. The concept of the vesicle immobilization, the protein-binding to vesicles and the protein-ligand interaction is initially studied using a Biacore instrument. The dissociation of the ligand IFNα2 from its receptor ifnar-2 (wt) are in accordance with the literature. In the imaging SPR experiments, it is found that the dissociation of IFNα2 from the ifnar-2 (wt) receptor is slower than expected, probably due to rebinding of the ligand. It is also found that imidazole is needed to avoid vesicle-vesicle interaction. The immobilization of proteins had to be done on-line i.e. when the vesicles were bound to the surface. Depending on the mixture of receptors at the vesicle surface the affinity for the ligand was changed. The results achieved were reproducible.</p>

<p>Syfte</p><p>Studien syftade till att undersöka om långvarig ihållande submaximal aktivering av Transversus Abdominis (TrA) påverkar dess anticipatoriska aktivering vid snabba viljemässigt utförda armrörelser.</p><p>Metod</p><p>I stående position utförde nio fysiskt aktiva kvinnor fem st snabba bilaterala armlyft från 0º till 90º axelflexion före och efter cirka 10 minuters ihållande submaximal aktivet i TrA samt efter 5 minuters vila. Elektromyografisk aktivitet (EMG) registrerades via två intramuskulära trådelektroder, placerade i höger TrA och två ytelektroder placerade på höger Deltoideus anterior. Buktrycket tros tillsammans med TrA stabilisera ryggraden vilket registrerades genom att en tryckgivare placerades i magsäcken.</p><p>Resultat</p><p>TrA aktiverades före Deltoideus både före och efter den långvariga aktiveringen. Initieringen av EMG-signalen i höger TrA hade oförändrat förhållande till initieringen av EMG-signalen i Deltoideus före och efter ihållande aktivitet samt efter 5 minuters vila. EMG amplituden i TrA var oförändrad både i baslinjefasen (600 ms före till 250 ms före deltoideus aktivering) och i den anticipatoriska fasen (100 ms före till 50 ms efter Deltoideus aktivering). Även buktrycksvärdet förblev oförändrat såväl vid baslinjen som i den anticipatoriska fasen.</p><p>Slutsats</p><p>Denna studie visade att centrala nervsystemet påbörjar aktiveringen av de innersta bukmusklerna före initieringen av armrörelserna och att detta förhållande ej påverkas av 10 minuters ihållande submaximal aktivering av TrA. Det finns inga tillgängliga metoder för direkt mätning av TrA:s mekaniska effekt, men eftersom buktrycket förblev oförändrad är det rimligt att tro att TrA:s kontraktilitet inte försämrats av den submaximala aktiveringen.</p> / <p>Aim</p><p>The aim of the study was to investigate whether prolonged sustained sub maximal activation of Transversu Abdominis (TrA) influences its anticipitatory activation associated with fast voluntary shoulder flexion.</p><p>Method</p><p>In a standing position nine physically active female subjects (mean age of 26 ± 3 y) performed five rapid bilateral shoulder flexion from 0° to 90° shoulder flexion, before and after approximately 10 minutes of sustained submaximal activity in TrA as well as after 5 minutes rest. Electromyographic activity (EMG) was recorded using two intramuscular fine-wire electrodes placed in the right TrA and two surface electrodes placed over the Deltoideus anterior. Intra-abdominal pressure (IAP) was recorded intra-gastrically.</p><p>Results</p><p>TrA was activated prior to Deltoideus, before as well as after the sustained activation. The onset of TrA muscle activation relative to the onset of Deltoideus activation was not significantly different between before, directly after, or 5 minutes after the end of the sustained activity. The root mean square of the TrA EMG was unchanged both before arm lifts (baseline) and within the anticipatory window (100 ms before until 50 ms after Deltoideus onset). The IAP-value was unaffected in the baseline as well as in the anticipatory phase.</p><p>Conclusion</p><p>This study shows that the central nervous system begins activating the TrA slightly before initiating arm movements and that this behaviour is unaffected by a 10 min. sustained submaximal activation of TrA. There are no methods available for direct measurement of the mechanical output from TrA activation, but since IAP was unaffected it appears reasonable to conclude that the contractility of TrA is not deteriorated by the submaximal activation of TrA.</p>

A number of diseases are linked to protein folding problems which lead to the deposition of insoluble protein plaques in the brain or other organs. These diseases include prion diseases such as Creutzfeld-Jakob disease, Alzheimer's disease, Parkinson's disease and type II (non-insulin dependent) diabetes. The protein plaques are found to consist of amyloid fibrils - cross-beta-sheet polymers with the beta-strands arranged perpendicular to the long axis of the fibre. Studies of ex vivo fibrils and fibrils produced in vitro showed that amyloid structures possess similar tinctorial and morphological properties. These suggest that the ability to form amyloid fibrils is an inherent property of polypeptide chains. The aims of this thesis were to investigate the structural properties of cytotoxic amyloid and examine the involved mechanisms. The model proteins used in the studies were the equine and hen lysozymes and de novo designed protein albebetin. Lysozymes are naturally ubiquitous proteins. Equine lysozyme belongs to an extended family of structurally related lysozymes and α-lactalbumins and can be considered as an evolutional bridge between them. Hen lysozyme is one of the most characterized protein and its amyloidogenic properties were described earlier. De novo protein albebetin and its constructs are designed to perform the function of grafted polypeptide sequence. Fibrils of equine lysozyme are formed at acidic pH and elevated temperatures where a partially folded molten globule state is populated. We have shown that lysozyme assembles into annular and linear protofilaments in a calcium-dependent manner. We showed that albebetin and its constructs are inherently highly amyloidogenic under physiological conditions. Fibrillation proceeds via multiple pathways and includes a hierarchy of amyloid structures ranging from oligomers to protofilaments and fibrils, among which two distinct types of oligomeric intermediates were characterized. Pivotal oligomers comprise of 10-12 monomers and on-pathway amyloid-prone oligomers constitute of 26-30 molecules. We suggest that transformation of the pivotal oligomers into the amyloid-prone ones is a limiting stage in albebetin fibrillation. Cytotoxic studies of albebetin amyloid species have revealed that initial, pivotal oligomers do not effect on cell viability while amyloid-prone ones induce cell death. We suggest that oligomeric size is important for the stabilizing cross-beta-sheet core which is crucial for cell toxicity. Cytotoxic studies of both oligomers and fibrils of hen lysozyme have revealed that both species induce cell death. The amyloid sample containing cross-β-sheet oligomers induces an apoptosis-like cell death. The oligomers without cross-β-sheet appeared to be non-toxic, indicating that the stabilization of this structural pattern is critical for the induced toxicity. In contrast, the fibrils induce more rapid, necrosis-like death. These studies gained insights into a structure–function relationship of different forms of amyloid and general pathways of cell death. This is an important step in understanding the mechanisms of amyloid-associated degeneration and defining specific therapeutic targets.