Supplementary data are available at Bioinformatics online.

Protein structures often feature β-sheets in which adjacent β-strands have large sequence separation. How the folding process orchestrates the formation and correct arrangement of these strands is not comprehensively understood. Particularly challenging are proteins in which β-strands at the N and C termini are neighbors in a β-sheet. The N-terminal β-strand is synthesized early on, but it can not bind to the C terminus before the chain is fully synthesized. During this time, there is a danger that the β-strand at the N terminus interacts with nearby molecules, leading to potentially harmful aggregates of incompletely folded proteins. Simulations of the C-terminal fragment of Top7 show that this risk of misfolding and aggregation can be avoided by a "caching" mechanism that relies on the "chameleon" behavior of certain segments.protein folding | all-atom simulation | folding mechanism | chameleon segment | nonnative intermediates S tructure and function of proteins are determined by their amino acid sequence. How proteins find their functional native form is a long-standing question (1-3). Protein synthesis is directional from the N to the C terminus. In proteins with end-toend β-sheets, there is a danger that the N-terminal strand binds to nearby molecules or other parts of the chain, as the strand cannot bind to the C-terminal strand until the molecule is fully synthesized. Misfolding and aggregation may be the consequence. In our simulations, the N terminus of fragment Glu-2-Leu-50 of the 59-residue CFr (Protein Data Bank ID code 2GJH) (4) avoids the risk of misfolding by growing first into a non-native extension of an existing α-helix. Only after the other structural elements have formed and correctly assembled, does the N terminus unfold and attach to the C-terminal β-sheet as its last closing strand. We speculate that such a temporary caching of β-strands is a common mechanism that eases folding and hinders aggregation.The C-terminal fragment (CFr) (5) of the designed protein Top7 (6) forms a stable homodimer, whose secondary structure remains nearly unchanged up to 98 • C and high concentrations of denaturant (4). It is a model for small fast-folding proteins with complex topology and diverse secondary structure elements (see Fig. 1). Such proteins often have long-distance (in sequence) contacts between β-strands. Unlike helix contacts, these depend on the conformation of a large segment between the strands. It is unlikely that these contacts form before the intermediate segment has folded, as this would lead to a large entropic cost, or even interfere with the folding of the connecting segment. For slowfolding proteins, one can conjecture a "backtracking" mechanism (7) where folding succeeds only after breaking of prematurely formed β-contacts. In this study, we explore in silico the behavior of fast-folding proteins, as computational approaches (8, 9) can resolve details of folding that are beyond the reach of experiments. Results and DiscussionWe find that the CFr monomer folds to a native-like conform...

DHPRED has been implemented as a web service, which academic researchers can access from our webpage http://www.fz-juelich.de/nic/cbb

We study diffusion of macromolecules in a crowded cytoplasm-like environment, focusing on its dependence on composition and its crossover to the anomalous subdiffusion. The crossover and the diffusion itself depend on both the volume fraction and the relative concentration of macromolecules. In accordance with previous theoretical and experimental studies, diffusion slows down when the volume fraction increases. Contrary to expectations, however, the diffusion is also strongly dependent on the molecular composition. The crossover time decreases and diffusion slows down when the smaller macromolecules start to dominate. Interestingly, diffusion is faster in a cytoplasm-like (more polydisperse) system than it is in a two-component system, at comparable packing fractions, or even when the cytoplasm packing fraction is larger.