Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and “snapshots” of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited “crowding” effect must be included in attempts to understand macromolecular behavior in vivo

How novel structures inform understanding of complement function

33 p.-3 fig.During the last decade, the complement field has experienced outstanding advancements in the mechanistic understanding of how complement activators are recognized, what C3 activation means, how protein complexes like the C3 convertases and the membrane attack complex are assembled, and how positive and negative complement regulators perform their function. All of this has been made possible mostly because of the contributions of structural biology to the study of the complement components. The wealth of novel structural data has frequently provided support to previously held knowledge, but often has added alternative and unexpected insights into complement function. Here we will review some of these findings focusing in the alternative and terminal complement pathways.SRdeC is supported by the Spanish “Ministerio de Economía y Competitividad-FEDER” (SAF2015-66287R), the Seventh Framework Programme European Union Project EURenOmics (305608) and the Autonomous Region of Madrid (S2010/BMD- 2316). SRdeC is member of the “CIB intramural Program “Molecular Machines for Better Life (MACBET)”. EGdeJ is supported by the Spanish “Ministerio de Economía y Competitividad-FEDER” (RYC-2013-13395 and SAF2014-52339P). OL is supported by the Spanish Ministry of Economy, Industry and Competitiveness (SAF2014-52301-R).AT and MS are supported by the Spanish “Ministerio de Economía y Competitividad-FEDER” (IJCI-2015-25222 and IJCI-2015-24388, respectively).Peer reviewe