The three-dimensional structure of the chemotactic peptide Nformyl-L-Met-L-Leu-L-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16 13 C-15 N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly 13 C, 15 N-and 15 N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.

The emergence of small open reading frame (sORF)-encoded peptides (SEPs) is rapidly expanding the known proteome at the lower end of the size distribution. Here, we show that the mitochondrial proteome, particularly the respiratory chain, is enriched for small proteins. Using a prediction and validation pipeline for SEPs, we report the discovery of 16 endogenous nuclear encoded, mitochondrial-localized SEPs (mito-SEPs). Through functional prediction, proteomics, metabolomics and metabolic flux modeling, we demonstrate that BRAWNIN, a 71 a.a. peptide encoded by C12orf73, is essential for respiratory chain complex III (CIII) assembly. In human cells, BRAWNIN is induced by the energy-sensing AMPK pathway, and its depletion impairs mitochondrial ATP production. In zebrafish, Brawnin deletion causes complete CIII loss, resulting in severe growth retardation, lactic acidosis and early death. Our findings demonstrate that BRAWNIN is essential for vertebrate oxidative phosphorylation. We propose that mito-SEPs are an untapped resource for essential regulators of oxidative metabolism.

A local rule-based theory is developed which shows that the self-assembly of icosahedral virus shells may depend on only the lower-level Interactions of a protein subunit with its neighbors-i.e., on local rules rather than on larger structural building blocks. The local rule theory provides a framework for understanding the assembly of icosahedral viruses. These include both viruses that fall in the quasiequivalence theory of Caspar and KMug and the polyoma virus structure, which violates quasi-equivalence and has puzzled researchers since it was first observed. Local rules are essentially templates for energetically favorable arrangements. The tolerance margins for these rules are investigated through computer simulations. When these tolerance margins are exceeded in a particular way, the result is a "spiraling" malformation that has been observed in nature.It was also generally believed that proteins took on only one conformation, particularly very stable proteins such as those that form virus shells. Recent evidence indicates that virus-shell proteins in fact take on several conformations (10-12) as has been proposed (5, 13). This important observation informs the approach to virus-shell assembly presented below.The primary idea behind a local rule-based theory is that, if the protein subunits assume different conformations during the assembly process depending on their relative positions, a protein binding to the structure has enough local information to "know" where to bind. In particular, possible assembly pathways can be given that depend only on the interactions ofa protein with its immediate neighbors rather than on larger structural building blocks.

The structural context provided by the folding and docking of the engrailed homeodomain allows Lys50 to make remarkably favorable contacts with the guanines at base pairs 5 and 6 of the binding site. Although many different residues occur at position 50 in different homeodomains, and although numerous position 50 variants have been constructed, the most striking examples of altered specificity usually involve introducing or removing a lysine sidechain from position 50. This high-resolution structure also confirms the critical role of Asn51 in homeodomain-DNA recognition and further clarifies the roles of water molecules near residues 50 and 51.

Pontes et al. show that plasma membrane mechanics exerts an upstream control during cell motility. Variations in plasma membrane tension orchestrate the behavior of the cell leading edge, with increase–decrease cycles in tension promoting adhesion row positioning.