Nuclear magnetic resonance studies of protein conformation: I. Ribonuclease S. II. Hemoglobin

Fluorine nuclear magnetic resonance techniques have been used to study conformational processes in two proteins labeled specifically in strategic regions with covalently attached fluorinated molecules. In ribonuclease S, the ϵ-amino groups of lysines 1 and 7 were trifluoroacetylated without diminishing enzymatic activity. As inhibitors bound to the enzyme, changes in orientation of the peptide segment containing the trifluoroacetyl groups were detected in the nuclear magnetic resonance spectrum. pH Titration of one of the histidines in the active site produced a reversal of the conformational process.

Hemoglobin was trifluoroacetonylated at the reactive cysteine 93 of each β chain. The nuclear magnetic resonance spectrum of the fluorine moiety reflected changes in the equilibrium position of the β chain carboxy terminus upon binding of heme ligands and allosteric effectors. The chemical shift positions observed in deoxy- and methemoglobin were pH dependent, undergoing an abnormally steep apparent titration which was not observed in hemoglobin from which histidine β 146 had been removed enzymatically. The abnormal sharpness of these pH dependent processes is probably due to interactions between several ionizing groups.

The carbon monoxide binding process was studied by concurrent observation of the visible and nuclear magnetic resonance spectra of trifluoroacetonylated hemoglobin at fractional ligand saturations throughout the range 0-1.0. Comparison of the ligand binding process observed in these two ways yields evidence for a specific order of ligand binding. The sequence of events is sensitive to the pH and organic phosphate concentration of the medium, demonstrating the delicately balanced control system produced by interactions between the hemoglobin subunits and the effectors.

Specific Interaction with Cardiolipin Triggers Functional Activation of Dynamin-Related Protein 1

Dynamin-Related Protein 1 (Drp1), a large GTPase of the dynamin superfamily, is required for mitochondrial fission in healthy and apoptotic cells. Drp1 activation is a complex process that involves translocation from the cytosol to the mitochondrial outer membrane (MOM) and assembly into rings/spirals at the MOM, leading to membrane constriction/division. Similar to dynamins, Drp1 contains GTPase (G), bundle signaling element (BSE) and stalk domains. However, instead of the lipid-interacting Pleckstrin Homology (PH) domain present in the dynamins, Drp1 contains the so-called B insert or variable domain that has been suggested to play an important role in Drp1 regulation. Different proteins have been implicated in Drp1 recruitment to the MOM, although how MOM-localized Drp1 acquires its fully functional status remains poorly understood. We found that Drp1 can interact with pure lipid bilayers enriched in the mitochondrion-specific phospholipid cardiolipin (CL). Building on our previous study, we now explore the specificity and functional consequences of this interaction. We show that a four lysine module located within the B insert of Drp1 interacts preferentially with CL over other anionic lipids. This interaction dramatically enhances Drp1 oligomerization and assembly-stimulated GTP hydrolysis. Our results add significantly to a growing body of evidence indicating that CL is an important regulator of many essential mitochondrial functions.

Identifizierung der Welsart in Filetware durch Protein- und DNA-Analyse

Zusammenfassung Zur Identifizierung der folgenden vier Welsarten bzw. zwei Hybriden (Clarias gariepinus, Pangasius hypophthalmus, Pseudoplatystoma spp., Silurus glanis, Claresse® und Melander®) wurden die isolektrische Fokussierung (IEF) der wasserlöslichen Muskelproteine und die Polymerase-Kettenreaktion (PCR) zur Vervielfältigung und Sequenzierung eines Abschnittes aus dem Cytochrom b – Gen eingesetzt. Die IEF ergab artspezifische Proteinmuster mit hitzestabilen Proteinbanden im anodalen Gelbereich. Der afrikanische Wels (C. gariepinus) und das Hybriderzeugnis Melander® wiesen das gleiche Proteinmuster auf. Mittels DNA-Analyse ließen sich die Welsarten anhand ihrer Cytochrom b Gensequenzen eindeutig identifizieren. Auch hier zeigte der Welshybrid Melander® ein identisches Ergebnis wie der afrikanische Wels. Die Schwierigkeiten der Identifizierung von Tigerwelsen südamerikanischer Herkunft aus der Gattung Pseudoplatystoma werden diskutiert. Abstract Isoelectric focusing (IEF) of water soluble proteins and PCR-based DNA- analysis were used to differentiate between four catfish species (Clarias gariepinus, Pangasius hypophthalmus, Pseudoplatystoma spp., Silurus glanis) and two hybrids Claresse® and Melander®. Specific protein patterns have been obtained for all species and Claresse®, but in case of Melander® the identical pattern was observed as for the African catfish Clarias gariepinus. By sequencing the PCR products and application of BLAST, authenticity of the different catfish samples was confirmed. The cytochrome b gene sequences of Melander® and African catfish were identical. The difficulties of identifying catfishes of the genus Pseudoplatystoma are discussed.

Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

Membrane activities of Dynamin-related protein 1 (DRP1) and BCL2-related Ovarian Killer (BOK)

311 p.

Cuando el miedo invade la ficción. Análisis de Perdidos (Lost) y de otros quality dramas de la era Post 11S.

521 p.