FG Modellierung biomolekularer Systeme

6 Items

Recent Submissions
Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations

Baserga, Federico ; Dragelj, Jovan ; Kozuch, Jacek ; Mohrmann, Hendrik ; Knapp, Ernst-Walter ; Stripp, Sven T. ; Heberle, Joachim (2021-04-27)

Cytochrome c oxidase (CcO) is a transmembrane protein complex that reduces molecular oxygen to water while translocating protons across the mitochondrial membrane. Changes in the redox states of its cofactors trigger both O2 reduction and vectorial proton transfer, which includes a proton-loading site, yet unidentified. In this work, we exploited carbon monoxide (CO) as a vibrational Stark effe...

Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster

Elghobashi-Meinhardt, Nadia ; Tombolelli, Daria ; Mroginski, Maria Andrea (2021-02-12)

The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein scaffold via six coordinating cysteine residues. In this study, the nature of spin coupling and the effect of spin states on the cluster’s geometry are i...

Cholesterol transport in wild-type NPC1 and P691S: Molecular dynamics simulations reveal changes in dynamical behavior

Elghobashi-Meinhardt, Nadia (2020-04-22)

The Niemann–Pick C1 (NPC1) protein is the main protein involved in NPC disease, a fatal lysosomal lipid storage disease. NPC1, containing 1278 amino acids, is comprised of three lumenal domains (N-terminal, middle lumenal, C-terminal) and a transmembrane (TM) domain that contains a five helix bundle referred to as the sterol-sensing domain (SSD). The exact purpose of the SSD is not known, but i...

Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations

Moubarak, Samah ; Elghobashi-Meinhardt, Nadia Said ; Tombolelli, Daria ; Mroginski, Maria Andrea (2020-01-22)

The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a ...

Theoretical studies for the development of a better understanding of cofactor-structure and mechanistic properties of photoreceptors and metallo-enzymes with quantum chemical and molecular dynamical approaches

Belger, Dennis Heinz (2020)

In this work two phytochromes, namely Cyanobacterial phytochrome Cph1 and Agrobacterium tumefaciens phytochrome Agp2, as well as formate dehydrogenase of Rhodobacter Capsulatus (RcFDH), are investigated. Part III shows the development and its application of a new polarized force field (polff) for the chromophore-binding domain (CBD) of Cph1, derived by QM-computations of Mulliken charges. This ...

3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function

Song, Chen ; Mroginski, Maria Andrea ; Lang, Christina ; Kopycki, Jakub ; Gärtner, Wolfgang ; Matysik, Jörg ; Hughes, Jon (2018-04-24)

We present structural information for oat phyA3 in the far-red-light-absorbing (Pfr) signaling state, to our knowledge the first three-dimensional (3D) information for a plant phytochrome as Pfr. Solid-state magic-angle spinning (MAS) NMR was used to detect interatomic contacts in the complete photosensory module [residues 1–595, including the NTE (N-terminal extension), PAS (Per/Arnt/Sim), GAF...