Database-Driven Identification of Structurally Similar Protein-Protein Interfaces

Analyzing the similarity of protein interfaces in protein-protein interactions gives new insights into protein function and assists in discovering new drugs. Usually, tools that assess the similarity focus on the interactions between two protein interfaces, while sometimes we only have one predicted interface. Herein, we present PiMine, a database-driven protein interface similarity search. It compares interface residues of one or two interacting chains by calculating and searching tetrahedral geometric patterns of α-carbon atoms and calculating physicochemical and shape-based similarity. On a dedicated, tailor-made dataset, we show that PiMine outperforms commonly used comparison tools in terms of early enrichment when considering interfaces of sequentially and structurally unrelated proteins. In an application example, we demonstrate its usability for protein interaction partner prediction by comparing predicted interfaces to known protein-protein interfaces.

SiteMine: Large-scale binding site similarity searching in protein structure databases

Drug discovery and design challenges, such as drug repurposing, analyzing protein-ligand and protein-protein complexes, ligand promiscuity studies, or function prediction, can be addressed by protein binding site similarity analysis. Although numerous tools exist, they all have individual strengths and drawbacks with regard to run time, provision of structure superpositions, and applicability to diverse application domains. Here, we introduce SiteMine, an all-in-one database-driven, alignment-providing binding site similarity search tool to tackle the most pressing challenges of binding site comparison. The performance of SiteMine is evaluated on the ProSPECCTs benchmark, showing a promising performance on most of the data sets. The method performs convincingly regarding all quality criteria for reliable binding site comparison, offering a novel state-of-the-art approach for structure-based molecular design based on binding site comparisons. In a SiteMine showcase, we discuss the high structural similarity between cathepsin L and calpain 1 binding sites and give an outlook on the impact of this finding on structure-based drug design. SiteMine is available at https://uhh.de/naomi.

Division of labour in honey bees: age- and task-related changes in the expression of octopamine receptor genes

The honey bee (Apis mellifera L.) has developed into an important ethological model organism for social behaviour and behavioural plasticity. Bees perform a complex age-dependent division of labour with the most pronounced behavioural differences occurring between in-hive bees and foragers. Whereas nurse bees, for example, stay inside the hive and provide the larvae with food, foragers leave the hive to collect pollen and nectar for the entire colony. The biogenic amine octopamine appears to play a major role in division of labour but the molecular mechanisms involved are unknown. We here investigated the role of two characterized octopamine receptors in honey bee division of labour. AmOctαR1 codes for a Ca(2+) -linked octopamine receptor. AmOctβR3/4 codes for a cyclic adenosine monophosphate-coupled octopamine receptor. Messenger RNA expression of AmOctαR1 in different brain neuropils correlates with social task, whereas expression of AmOctβR3/4 changes with age rather than with social role per se. Our results for the first time link the regulatory role of octopamine in division of labour to specific receptors and brain regions. They are an important step forward in our understanding of complex behavioural organization in social groups.

New horizons in military dental laboratory training

Dental laboratory training has taken on a new look for the military. As a result of numerous cost analyses Air Force, Navy, and Army training has been combined under one roof. All three services have molded their courses together to form a tri-service training program at Sheppard AFB in Wichita Falls, Texas. Graduation of the first class occurred on June 24, 1998. A 6 month basic course, as well as several advanced concept courses are offered by the program. Instructors from all branches of service are represented on staff to teach. The facility is state of the art and was built in 1991 to provide for Air Force Dental Training. Downsizing of today's military has resulted in dental training coming together to provide one quality course to military individuals qualified to enroll, thus ensuring tomorrow's laboratory technicians will be as qualified as those in the past.