Quantifying electron transfer reactions in biological systems:what interactions play the major role?

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor

Nettbaserte pengespill - en studie om valg av spillselskap basert på forbrukeridentitet og tilhørighet

Det nettbaserte pengespillmarkedet domineres av utenlandske aktører som med høy konkurranseevne og kompetanse truer Norsk Tipping sin posisjon som monopolist. Dette er kampen mellom de kommersielle tilbyderne og den samfunnsorienterte statlige virksomheten hvor ulike verdisyn og holdninger skiller deres praksis. Hensikten med denne bacheloroppgaven er å undersøke om identitet og tilhørighet har en betydning for valg av spillselskap. Norsk Tipping gir hele overskuddet tilbake til samfunnet, i motsetning til de utenlandske selskapene som ønsker å maksimere egen profitt. Vi mener det er interessant å undersøke i hvilken grad forbrukeridentitet, lokal tilhørighet og engasjement i breddeidretten har innvirkning på valgprosessen. På bakgrunn av temaet har vi valgt følgende problemstilling: “I hvilken grad påvirker identitet, tilhørighet og engasjement i breddeidretten valg av spillselskap” Det teoretiske grunnlaget for oppgaven tar utgangspunkt i studier av blant andre Tajfel (1982), Sirgy (1982) og Kihlstrom, Beer og Klein (2002) sine teorier om identiteter. Vi har også brukt Strizhakova og Coulter (2015) sin studie om preferanser mot lokale produkter og forskningsstudier fra andre land for å belyse oppgaven. Med utgangspunkt i tidligere forskning og teori utarbeidet vi fire hypoteser, hvorav to ble bekreftet og to avkreftet. Resultatene tyder på at det er viktigere faktorer som spiller inn på valget av spillselskap enn de vi har undersøkt, men hypotesene indikerer likevel en forklaringsverdi. Det er benyttet kvantitativ metode for innsamling av data gjennom en tverrsnittsundersøkelse. Undersøkelsen ble delt via Facebook som resulterte i et utvalg på 205 respondenter. Ettersom dette forskningstemaet er relativt ukjent og lite utbredt, mener vi at denne undersøkelsen danner grunnlag for videre forskning ved bruk av et forbedret spørreskjema som måler begrepene dypere og et mer representativt utvalg

Introducing VIKING:A Novel Online Platform for Multiscale Modeling

Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.</p

Computational investigations of Cryptochrome as a magnetoreceptor

At nogle dyr er i stand til at navigere ved at bruge jordens magnetfelt har længe været et mysterie for forskere, og det har været omgivet af skepsis og interesse fra mange grene af videnskaben. I de seneste år har den generelle forståelse af dette fænomen steget betydeligt, men der er stadig mange ubesvarede spørgsmål med hensyn til den nøjagtige mekanisme.Generelt er der to hovedhypoteser, den første er at dyr bruger magnetit, eller andre magnetiske materialer, til at mærke jordens magnetfelt. Den anden teori er radikalpar teorien, hvor dyr kan føle jordens magnetfelt ved at anvende de kvantemekaniske egenskaber af radikalpar.Begge disse teorier er sandsynligvis korrekte. Nogle dyr bruger magnetit, andre bruger den mere eksotiske radikalpar mekanisme.Denne afhandling er en computer baseret undersøgelse af det formodede værtsmolekyle for radikalpar mekanismen, cryptochrome proteinet, i henhold til dets egenskab som magnetfelts sensor. Afhandlingen kan deles op i to hovedmål. Undersøgelsen af hvordan radikalpar bliver dannet i cryptochrome, og en undersøgelse af forskellige strukturelle modeller af cryptochrome proteiner fra trækfugle. De konstruerede modeller undersøges ved hjælp af molekylær dynamik, hvorved deres dynamiske egenskaber, som stammer fra atomernes bevægelse i proteinet, kan studeres. Ved at bruge molekylær dynamik på kendte krystal strukturer af cryptochrome proteiner fra andre dyr, samt de konstruerede modeller af cryptochrome fra trækfugle, kan vi undersøge de forskellige dynamiske egenskaber proteinerne kan have. For at undersøge dannelsen af radikalpar bruger vi kvantemekaniske metoder, der beskriver den elektroniske struktur i proteinet, og muliggør undersøgelse af bevægelsen af de elektroner der danner de pågældende radikalpar.Når det er muligt, knytter vi vores resultater med eksperimenter, for at forstå funktionerne in vivo.Magnetic field sensing in animals has been a long standing scientific question, historically surrounded with scepticism and interest from many different fields. In recent years the general understanding of this phenomena has expanded significantly, however, there are still many unanswered questions, as to the exact mechanism. In general there are two main hypothesis, the first being that animals use magnetite, or other magnetic materials, to sense the magnetic field. The other theory is the radical pair mechanism, where animals would sense the magnetic field by using the quantum mechanical properties of radical pairs.Both of these theories are likely true, some animals using magnetite, and some using the more exotic radical pair mechanism. This thesis is a computational study of the believed host molecule for the radical pair mechanism, the cryptochrome protein, in relation to magnetoreception. It has two main objectives. The investigation of the creation of the radical pair in cryptochrome, and the study of different structural models of avian cryptochrome proteins.The created models are investigated using molecular dynamics, to study their dynamic properties, which arise from the motions of the atoms in the protein. By subjecting known crystal structures of the cryptochrome proteins from non-migratory species, and the models of avian cryptochrome tomolecular dynamics simulations we probe the different dynamics and functions these proteins might have.To investigate the creation of the radical pair formation we utilize quantum mechanical methods that accounts for the electronic structure in the protein, and allows for investigation of the movement of the electrons that form the radical pairs in question. When possible the investigations are linked to experimental results, to heighten the understand of the in vivo activity

Computational reconstruction reveals a candidate magnetic biocompass to be likely irrelevant for magnetoreception

Abstract Birds use the magnetic field of the Earth to navigate during their annual migratory travel. The possible mechanism to explain the biophysics of this compass sense involves electron transfers within the photoreceptive protein cryptochrome. The magnetoreceptive functioning of cryptochromes is supposedly facilitated through an iron rich polymer complex which couples to multiple cryptochromes. The present investigation aims to independently reconstruct this complex and describe its interaction with Drosophila melanogaster cryptochromes. The polymer complex consists of ISCA1 protein monomers with internally bound iron sulphur clusters and simultaneously binds ten cryptochromes. Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. It is found that the cryptochrome binding to the ISCA1 polymer is not uniform and that the binding affinity depends on its placement along the ISCA1 polymer. This finding supports the claim that the individual ISCA1 monomer acts as possible intracellular interaction partner of cryptochrome, but the proposed existence of an elongated ISCA1 polymer with multiple attached cryptochromes appears to be questionable

Applications of molecular modeling to flavoproteins:Insights and challenges

The general field of molecular simulation provides a wide spectrum of methods for studying the structure and function of biomolecules. Depending on the scale and question of interest, appropriate approaches may range from ab initio quantum mechanical calculations (when detailed aspects of and changes in electronic structure must be considered) to Brownian dynamics and coarse-grained molecular dynamics (to track large scale conformational motions, diffusion, and inter-molecular interactions). The entire range of molecular simulation methods has been fruitfully applied to a range of flavoenzymes, allowing researchers to address everything from the specific intermediates involved in the photoreactions of flavin chromophore-containing light sensors, to the very long timescale motions induced by covalent modifications to bound flavin. The unique challenge posed by flavoproteins to all types of molecular simulation arises from the chemistry of the flavin isoalloxazine moiety, which presents an unusually large delocalized electron system which must be carefully treated in order to represent its contributions to the overall behavior of the system. Here we outline the particular considerations required for appropriate treatment of flavoproteins in simulations ranging from electronic structure calculations to long-timescale modeling of flavoprotein conformational transitions.</p

Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome

Cryptochrome proteins are activated by the absorption of blue light, leading to the formation of radical pairs through electron transfer in the active site. Recent experimental studies have shown that once some of the amino acid residues in the active site of Xenopus laevis cryptochrome DASH are mutated, radical-pair formation is still observed. In this study, we computationally investigate electron-transfer pathways in the X. laevis cryptochrome DASH by extensively equilibrating a previously established homology model using molecular dynamics simulations and then mutating key amino acids involved in the electron transfer. The electron-transfer pathways are then probed by using tight-binding density-functional theory. We report the alternative electron-transfer pathways resolved at the molecular level and, through comparison of amino acid sequences for cryptochromes from different species, we demonstrate that one of these alternative electron-transfer pathways could be general for all cryptochrome DASH proteins.</p