Biomedical subjects

Markus Elsner

Publications and source records attributed to Markus Elsner.

5 recordsLinked to original sources

PubMed2005

Commuting between Golgi cisternae--mind the GAP!

Intracellular transport has remained central to cell biology now for more than 40 years. Despite this, we still lack an overall mechanistic framework that describes transport in different parts of the cell. In the secretory pathway, basic questions, such as how biosynthetic cargo traverses the pathway, are still debated. Historically, emphasis was first put on interpreting function from morphology at the ultrastructural level revealing membrane structures such as the transitional ER, vesicular carriers, vesicular tubular clusters, Golgi cisternae, Golgi stacks and the Golgi ribbon. This emphasis on morphology later switched to biochemistry and yeast genetics yielding many of the key molecular players and their associated functions that we know today. More recently, microscopy studies of living cells incorporating biophysics and system analysis has proven useful and is often used to readdress earlier findings, sometimes with surprising outcomes.

Animals↗

PubMed2004

Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices.

Specific non-covalent interactions between transmembrane (TM) alpha-helices are important in a variety of biological processes. Experimental and computational studies have shown that van der Waals interactions play an important role in the tight packing between TM alpha-helices, although polar interactions can also be important in some instances. Based on the assumption that van der Waals interaction alone is sufficient for a meso-scale (residue-scale) description of the interaction between TM alpha-helices, we have designed a novel residue-scale scoring function for modeling structures of oligomers of TM alpha-helices. We first calculated atomistic van der Waals interaction energies between two amino acids, X and Y, of a pair of parallel alpha-helices, glycine-X-glycine and glycine-Y-glycine and compiled them according to three variables, the distance between the two C(alpha) atoms and the rotational angles of X and Y about their helical axes. Upon averaging over the rotational angles, we obtained one-dimensional interaction energy profiles that are functions of the distance between C(alpha) atoms only. Each of the interaction energy profiles was fitted with a generic fitting function of the distance between C(alpha) atoms, yielding analytical scoring functions for all possible amino acid pairs. For glycophorin A, neu/erbB-2, and phospholamban, lowest-energy conformations obtained through exhaustive scanning of the entire conformational space using the scoring functions were compatible with available experimental data.

Amino Acid Sequence↗

PubMed2004

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Macromolecular crowding dramatically affects cellular processes such as protein folding and assembly, regulation of metabolic pathways, and condensation of DNA. Despite increased attention, we still lack a definition for how crowded a heterogeneous environment is at the molecular scale and how this manifests in basic physical phenomena like diffusion. Here, we show by means of fluorescence correlation spectroscopy and computer simulations that crowding manifests itself through the emergence of anomalous subdiffusion of cytoplasmic macromolecules. In other words, the mean square displacement of a protein will grow less than linear in time and the degree of this anomality depends on the size and conformation of the traced particle and on the total protein concentration of the solution. We therefore propose that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale.

Computer Simulation↗

PubMed2003

Spatiotemporal dynamics of the COPI vesicle machinery.

Assembly of the coat protein I (COPI) vesicle coat is controlled by the small GTPase ADP ribosylation factor 1 (ARF1) and its GTPase-activating protein, ARFGAP1. Here, we investigate the diffusional behaviours of coatomer, the main component of the coat, and also those of ARF1 and ARFGAP1. Using fluorescence-correlation spectroscopy, we found that most ARF1 and ARFGAP1 molecules are highly mobile in the cytosol (diffusion constant D approximately equal to 15 microm(2) s(-1)), whereas coatomer diffuses 5-10 times more slowly than expected (D approximately equal to 1 microm(2) s(-1)). This slow diffusion causes diffusion-limited binding kinetics to Golgi membranes, which, in FRAP (fluorescence recovery after photobleaching) experiments, translates into a twofold slower binding rate. The addition of aluminium fluoride locks coatomer onto Golgi membranes and also decreases the binding kinetics of both ARF1 and ARFGAP1, suggesting that these proteins function in concert to mediate sorting and vesicle formation.

ADP-Ribosylation Factor 1↗

PubMedDate not supplied

Cisternal maturation and vesicle transport: join the band wagon! (Review).

'No cellular organelle has been the subject of as many, as long-lasting or as diverse polemics as the Golgi apparatus'. This statement was made by Whaley almost 30 years ago in the book The Golgi Apparatus and still holds true today, perhaps more then ever. Why is this? How come something as mundane as a series of intracellular membrane bound structures continues to fascinate and captivate a large section of the cell biology community? One simple reason (putting polemics aside) is that the secretory pathway appears deceptively simple. Once probed, however, it has a persistent habit of developing into an enigma. Is one then not closer than 30 years ago? In a sense yes, in that one has more components and a better understanding of inherent membrane dynamics, but it is still not known how newly synthesized proteins and lipids make their way from the ER to the plasma membrane. Is it by vesicles, cisternal carriers or transient tubular connections? It has also been learned that newly synthesized proteins are segregated away from the resident components throughout the pathway, but not how. Do coat proteins hold the key? It is understood that the cytoskeleton is important, but not really why. It is known that each Golgi stack is a fully functional unit, but not why stacks are connected laterally into a large ribbon (the Golgi apparatus). This review focuses on how proteins make their way through the pathway, a basic question that remains to be answered.

Animals↗