Sphaerotilus natans: description of the morphology, growth and systematics of [Translation from: Schr. Ver. Zellstoff u. Pap.-Chem. u. -Ing., 26, 20-37, 1956]

The morphology, increase and systematica of Sphaerotilus natans is studied and culture methods examined

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations

Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full unbinding pathway is often lacking due, in part, to the static nature of atomic structures and ensemble averaging inherent to bulk biophysics approaches. Here we combine molecular dynamics and high-speed force spectroscopy on the streptavidin-biotin complex to determine the binding strength and unbinding pathways over the widest dynamic range. Experiment and simulation show excellent agreement at overlapping velocities and provided evidence of the unbinding mechanisms. During unbinding, biotin crosses multiple energy barriers and visits various intermediate states far from the binding pocket while streptavidin undergoes transient induced fits, all varying with loading rate. This multistate process slows down the transition to the unbound state and favors rebinding, thus explaining the long lifetime of the complex. We provide an atomistic, dynamic picture of the unbinding process, replacing a simple two-state picture with one that involves many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be relevant for other receptor-ligand bonds.Comment: 21 pages, 4 figure

BIOCONTRACT, mutualismusok, szerződések, térbeliség és diszperzió = BIOCONTRACT, mutualisms, contracts, space, and dispersa

A fogolydilemma és a hótorlasz játékok viselkedését vizsgáltuk rácson. Megmutattuk, hogy a térbeliség mindkét szociális dilemma esetén segíti a kooperátorokat. Vizsgáltuk továbbá a kooperatív stratégia fixációs valószínűségét dinamikus gráfokon. Kimutattuk, hogy a gráf élek nem-szelektív átrendezése a kooperatív stratégia elterjedését jelentősen csökkenti, míg a szelektív átrendezése növelheti azt. Vizsgáltuk a sztochasztikus normák kialakulásának lehetőségét. Kimutattuk, hogy a korai emberi társadalmakra jellemző csoportstruktúra mellett egy sajátos kooperatív norma válik dominánssá. Ez a norma akkor is megjelenik, ha az altruista akciókról csak közvetett megfigyelők által lehet tudomást szerezni. Kifejlesztettünk egy térben explicit modellt a Cordia nodosa- Allomerus- Azteca hangya növény mutualista rendszer evolúciójának vizsgálatára, ahol az Allomerus faj a védelem mellett egyben kasztrációs parazita is. A hangyafajok diszperziós ráfordításának és a kasztrációs szint evolúcióját vizsgáltuk a megfelelő csereviszonyokat feltételezve. Megmutattuk, hogy egy térbeli ciklikus dinamika tartja fenn a három faj együttélését. A terepi tapasztalatokkal összhangban a nagyobb növény sűrűség kisebb egyensúlyi kasztrációs szintet, valamint a kasztráló faj fokozott jelenlétét vonja maga után. Vizsgáltuk az N személyes nemlineáris szociális dilemma játékokat. Kimutattuk, hogy az együttműködők és az önzők stabil együttélése jellemző jól-kevert populációkban is. | We studied the prisoner's dilemma and snowdrift games on rectangular grids. We showed that spatial correlations help cooperators in both models. We studied the fixation probability of cooperative strategy on simple dynamical graphs by using prisoner's dilemma game. It is shown that non-selective re-linking of the edges decreases the fixation probability of the cooperative strategy while selective re-linking can increase it. We studied the possibilities of the evolution of cooperative norms. It is shown that a specific cooperative norm becomes dominant in populations having group structure which is observed in the ancient human societies. This norm evolves even if individuals are informed only by indirect observers about the altruistic acts. We worked out a spatially explicit model to study evolutionary dynamics of Cordia nodosa, Allomerus and Azteca plant-ant system, where Allomerus defenses the plant but castrates the flowers of it. We studied the evolution of castration level and dispersion level by assuming adequate trade-offs. It is shown that a spatial cyclic dynamics maintain the coexistence of the three species. In concordance with the results of field experiments, the higher the plant density the smaller the castration level and the higher the relative density of castrating ant in the equilibrium. We studied non-linear N-person social dilemma games. It is shown that coexistence of cooperators and defectors is typical in these games in well-mixed populations

High-Speed Atomic Force Microscopy Tracks Toxin Action

LetterIn this issue of Biophysical Journal, the article ''Real-Time Visualization of Assembling of a Sphingomyelin-Specific Toxin on Planar Lipid Membranes'' by Yilmaz et al. (1) describes a high-speed atomic force microscopy (HS-AFM) analysis of the assembly and the conformational changes of pore-forming toxin lysenin (2) on a supported lipid bilayer. Pore-forming toxins are ubiquitous in bacteria, fungi, and animals, inducing cell death through membrane permeation. They have been structurally (3) and functionally intensively studied (4). However, essential information concerning conforma-tional changes, assembly dynamics, and membrane insertion of the toxin action has remained unknown, probably due to the lack of a technique that can analyze molecules with both high spatial and temporal resolution. Using HS-AFM, pioneered by the authors (5), they study the addition of lysenin toxins onto supported lipid bilayers and report the subsequent steps of toxin action: Monomer diffusion is extremely fast, and HS-AFM imaging could not localize or track single subunits (which would quickly result in oligomer and cluster formations). These clusters are initially heterogeneously arranged and display a variety of short-distance orientations. The authors are able to capture pore sub-elements like half-rings within these initial clusters, probably the unique observation of assembly intermediates of the toxin self-assembly process. Subsequently, lysenin self-assembly adjusts interactions , a process that is rather slow and takes place from seconds to up to minutes, leading to the formation of hexagonal close-packed assemblies, reminiscent of hexagonal two-dimensional crystals. The authors state ''Initially, both individual and small domains of lysenin clusters formed randomly at different locations on the membrane. While some of these domains grew continuously, most of them reorganized by subsecond dissociation/reassociation of the clusters.'