A direct hydrogen bond between ubiquinone/quinol bound at the QO site and a cluster-ligand histidine of the iron-sulfur protein (ISP) is described as a major determining factor explaining much experimental data on position of the ISP ectodomain, EPR lineshape and midpoint potential of the iron-sulfur cluster, and the mechanism of the bifurcated electron transfer from ubiquinol to the high and low potential chains of the bc1 complex.

A significant fraction of the proteins in any genome are membrane proteins, and membrane proteins are vital to many fundamental processes of life. While many membrane proteins have now been crystallized in three dimensions, membrane proteins have proven considerably more difficult to crystallize than soluble proteins, and some have not yielded after extensive efforts at crystallization, e.g., the mitochondrial adenine nucleotide transporter, the bacterial chemotaxis receptor, and lactose permease.One membrane protein that crystallizes fairly readily is the mitochondrial cytochrome bc1 complex. This 11-subunit respiratory enzyme has been crystallized in at least eight different crystal forms. We here review conditions that lead to crystallization in various forms, and provide some of the history of our crystallization attempts.

Ubihydroquinone: cytochrome (cyt) c oxidoreductase, or cyt bc1, is a widespread, membrane integral enzyme that plays a crucial role during photosynthesis and respiration. It is one of the major contributors of the electrochemical proton gradient, which is subsequently used for ATP synthesis. The simplest form of the cyt bc1 is found in bacteria, and it contains only the three ubiquitously conserved catalytic subunits: the FeS protein, cyt b and cyt c1. Here we present a preliminary X-ray structure of Rhodobacter capsulatus cyt bc1 at 3.8 Angstrom, and compare it to the available structures of its homologues from mitochondria and chloroplast. Using the bacterial enzyme structure, we highlight the structural similarities and differences that are found among the three catalytic subunits between the the different members of this family of enzymes. In addition, we discuss the locations of currently known critical mutations, and their implications in terms of the cyt bc1 catalysis.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.