The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra

Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO-(l-Ala)(5)-NH2 in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide C?O and N-H groups. Hydrogen bonding of water with the C?O group determines the shape and position of the amide I band. The C?O bond length increases upon formation of C?OH2O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the C?O and N-H group, but their contributions to this spectral region differ: geometrically, the formation of a C?OH2O bond decreases the C-N bond length, while upon forming a N-HH2O hydrogen bond, the N-H bond length increases

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

In the past few decades, Raman optical activity (ROA) spectroscopy has been shown to be very sensitive to the solution structure of peptides and proteins. A major and urgent challenge remains the need to make detailed assignments of experimental ROA patterns and relate those to the solution structure adopted by the protein. In the past few years, theoretical developments and implementations of ROA theory have made it possible to use quantum chemical methods to compute the ROA spectra of peptides. In this work, a large database of ROA spectra of peptide model structures describing the allowed backbone conformations of proteins was systematically calculated and used to make unprecedented detailed assignments of experimental ROA patterns to the conformational elements of the peptide in solution. By using a similarity index to compare an experimental spectrum to the database spectra (2902 theoretical spectra), the conformational preference of the peptide in solution can be assigned to a very specific region in the Ramachandran space. For six (poly)peptides this approach was validated and gives excellent agreement between experiment and theory. Additionally, hydrogen/deuterium exchanged structures and the conformational dependence of the amide modes in Raman spectra can be analysed using the new database. The excellent agreement between experiment and theory demonstrates the power of the newly developed database as a tool to study Raman and ROA patterns of peptides and proteins. The interpretation of experimental ROA patterns of different proteins published in the scientific literature is discussed based on the spectral trends observed in the database

Surface enhanced Raman optical activity as an ultra sensitive tool for ligand binding analysis

Abstract. The Surface Enhanced Resonance Raman Scattering (SERRS) and Surface Enhanced Resonance Raman Optical Activity (SERROA) spectra of myoglobin and the myoglobin-azide complex were measured on very dilute samples (100 nM protein) in order to analyze the sensitivity of SERROA spectroscopy when inducing small structural changes. While the SERRS spectra of the two compounds were virtually identical, comparison of the SERROA spectra revealed several differences, including frequency shifts and changes in signal intensity, consistent with structural change in the porphyrin prosthetic group of the protein upon azide complexation. Application of this method allows for rapid analysis of ligand binding in metalloproteins in dilute aqueous solution and could in the future, when combined with theoretical studies, increase the obtainable structural resolution of proteins beyond that of X-ray analysis

Comparative study of the vibrational optical activity techniques in structure elucidation : the case of galantamine

The absolute configuration of the alkaloid galantamine was studied using a range of solution-state techniques; nuclear magnetic resonance (NMR), vibrational circular dichroism (VCD), and Raman optical activity (ROA). While the combined use of NMR and VCD does provide a fast, high-resolution methodology for determining the absolute configuration of galantamine, both techniques were needed in concert to achieve this goal. ROA, on the other hand, proved to be sensitive enough to assign the full absolute configuration without relying on other techniques. In both cases, statistical validation was applied to aid the determination of absolute configuration. In the case of galantamine, ROA combined with statistical validation is shown to be a powerful stand-alone tool for absolute configuration determination

Conformational disorder and dynamics of proteins sensed by Raman optical activity

Raman optical activity (ROA) spectra of proteins hold a lot of information about their structure in solution. To create a better understanding of the ROA spectra of, among others, the intrinsically disordered proteins (IDPs), involved in neurodegenerative diseases, the effect of conformational disorder and dynamics on the ROA spectra was studied. Density functional theory (DFT) calculations of small ensembles of model peptides with increasing disorder show that the ROA patterns of alpha-helical and polyproline II (PPII) structure reflect the average backbone angles in the ensemble. The amide III region in the ROA spectra of the alpha-helical peptides is shown to retain its typical -/+/+ pattern, while the amide III region of PPII secondary structure diminishes in intensity with increasing structural disorder. The results show that the ROA spectra of IDPs hence more likely stem from short stretches of well-defined PPII helices rather than a very flexible chain. Further DFT calculations support that mixing of PPII with helical secondary structure is consistent with experimental spectra of IDPs, while mixing with beta-strand results in spectral patterns that are not observed experimentally. The detailed information obtained from these results contributes to a better understanding of the spectrum-structure relation

Norwegian salmon in the European market: An assessment of competitive avantages

Masteroppgave i International Business and Marketing - Nord universitet 202

Med film på pakningen : bruk av merkevareallianser mellom annonsører og filmdistributører

En merkevareallianse innebærer at to eller flere merkevarer eksponeres sammen i reklamen og/eller på produktene. I flere artikler fra de senere år har bransjemagasinet Kampanje omtalt en bestemt form for merkevareallianser de mener vi kommer til å se mer av her til lands i årene som kommer. Denne typen merkevareallianser kjennetegnes av at en kinofilm utgjør den ene av to merkevarer. I denne oppgaven vil jeg undersøke hva jeg anser for å være sentrale aspekter vedrørende den norske praksisen med merkevareallianser og kinofilm. For det første vil jeg gjøre rede for hva som kjennetegner slike allianser, og hvilke aktører som er representert i feltet. Hva som utgjør partenes motivasjon, og hvilke kriterier som må være oppfylt dersom partene skal komme til enighet, er andre temaer som vies oppmerksomhet. Gjennom en analyse av innsamlet data, vil denne oppgaven også søke å belyse hvilket omfang og hvilken utbredelse denne samarbeidsformen har her til lands. Helt til slutt rettes oppmerksomheten mot hvilke filmer som kan være mest ettertraktet for merkevareallianser, og hva slags varer og tjenester som tilknyttes filmer

Når Jonas blir Støre : En retorisk analyse av Jonas Gahr Støres rolle i den TVsendte partilederdebatten 14. august 2017

Masteroppgave samfunnskommunikasjon KOM500 - Universitetet i Agder 2018This thesis project is a rhetorical analysis of Jonas Gahr Støre, leader of the Norwegian Labour Party, in the televised party leader debate on 08.14.2017. Støre had been accused of being unclear in his communication style for a long time, but was named the winner of this debate in several major Media. With a hermeneutic approach, the task examines the rhetorical devices Støre used in the debate. By using theoretical perspectives from political communication and mediation, the project also explores why Støre appeared the way he did. The analysis shows that Støre assumed an active role in the debate, especially when the debate was dealing with matters where the party is seeking issue ownership. He repeatedly attacks the government and the prime minister, framing issues to stress the need for a change of government

PKM2 Interacts With the Cdk1-CyclinB Complex to Facilitate Cell Cycle Progression in Gliomas

PKM2 is a phosphotyrosine-binding glycolytic enzyme upregulated in many cancers, including glioma, and contributes to tumor growth by regulating cell cycle progression. We noted, however, that in multiple glioma cell lines, PKM2 knock-down resulted in an accumulation of cells in G2-M phase. Moreover, PKM2 knock-down decreased Cdk1 activity while introducing a constitutively active Cdk1 reversed the effects of PKM2 knock-down on cell cycle progression. The means by which PKM2 increases Cdk1 activity have not been described. Transient interaction of T14/Y15-phosphorylated Cdk1 with cyclin B allows Cdk7-mediated pT161 Cdk1 phosphorylation followed by cdc25C-mediated removal of pT14/Y15 and activation of Cdk1 in cycling cells. In the present course of investigation, PKM2 modulation did not influence Cdk7 activity, but phosphotyrosine binding forms of PKM2 co-immunoprecipitated with pY15-containing Cdk1-cyclinB and enhanced formation of active pT161 Cdk1-cyclin B complexes. Moreover, exogenous expression of phosphotyrosine binding forms of PKM2 reversed the effects of PKM2 knock-down on G2-M arrest. We here show that PKM2 binds and stabilize otherwise transient pY15-containing Cdk1-cyclinB complexes that in turn facilitate Cdk1-cyclin B activation and entry of cells into mitosis. These results, therefore, establish metabolic enzyme PKM2 as a direct interactor and activator of Cdk1-cyclin B complex and thereby directly controls mitotic progression and the growth of brain tumor cells.publishedVersio

Higher than expected and significantly increasing incidence of upper tract urothelial carcinoma. A population based study

Purpose: To register all cases of urothelial cancer and renal cell carcinoma (RCC) in Norway during 1999–2018 to obtain the contemporary incidence of UTUC and UTUC incidence relative to other urothelial cancers and RCC. Further to analyse possible changes over time regarding UTUC incidence, UTUC patient characteristics, tumour characteristics and survival. Methods: 3502 cases registered with ICD code C65 and C66 during 1999–2018 at the Norwegian cancer registry were entered into a database. After a selection process 3096 cases were included in the study. The crude incidences of UTUC were calculated for each year adjusting for the corresponding population data. Age-standardized rates adjusting to the European standard population (2013) were calculated. Comparisons were made with other cases of urothelial cancer and RCC. For changes over time, the material was split into 5-year periods. Regression analysis was used to calculate yearly changes and for assessing statistical significance. Survival outcomes were calculated using the Kaplan–Meier method. Results: The overall age-standardized incidence rate was 3.88, increasing from 3.21 to 4.70 from first to last 5-year periods. The increase affected all ages except those < 60 years of age, and were observed regardless of gender or anatomical location. UTUC constituted 11.8% of all urothelial cancers, increasing from 9.9 to 12.8%. Mean patient age at diagnosis increased from 71.5 to 73.4 years. The 5-years Cancer-specific survival improved from 57.4 to 65.4%. Conclusion: The incidence of UTUC was higher than expected and increasing. Patient age at diagnosis was increasing.publishedVersio