Expansion of Auxiliary Activity Family 5 sequence space via biochemical characterization of six new copper radical oxidases.

Bacterial and fungal copper radical oxidases (CROs) from Auxiliary Activity Family 5 (AA5) are implicated in morphogenesis and pathogenesis. The unique catalytic properties of CROs also make these enzymes attractive biocatalysts for the transformation of small molecules and biopolymers. Despite a recent increase in the number of characterized AA5 members, especially from subfamily 2 (AA5_2), the catalytic diversity of the family as a whole remains underexplored.

Thomson-Einstein's Tea Leaf Paradox Revisited: Aggregation in Rings.

A distinct particle focusing spot occurs in the center of a rotating fluid, presenting an apparent paradox given the presence of particle inertia. It is recognized, however, that the presence of a secondary flow with a radial component drives this particle aggregation. In this study, we expand on the examination of this "Thomson-Einstein's tea leaf paradox" phenomenon, where we use a combined experimental and computational approach to investigate particle aggregation dynamics.

Copper radical oxidases: galactose oxidase, glyoxal oxidase, and beyond!

The copper radical oxidases (CROs) are an evolutionary and functionally diverse group of enzymes established by the historically significant galactose 6-oxidase and glyoxal oxidase from fungi. Inducted in 2013, CROs now constitute Auxiliary Activity Family 5 (AA5) in the Carbohydrate-Active Enzymes (CAZy) classification. CROs catalyse the two-electron oxidation of their substrates using oxygen as the final electron acceptor and are particularly distinguished by a cross-linked tyrosine-cysteine co-factor that is integral to radical stabilization.

Diamond in the Rough: Toward Improved Materials for the Bone-Implant Interface.

The ability of an orthopedic implant to integrate successfully with the surrounding bone tissue is imperative for optimal patient outcomes. Here, the recent advances and future prospects for diamond-based coatings of conventional osteo-implant materials (primarily titanium) are explored. The ability of these diamond coatings to enhance integration into existing bone, improved implant mechanical properties, facilitate surface chemical functionalization, and provide anti-microbial properties are discussed in context of orthopedic implants.

Revisiting Infectious Complications Following Total Parenteral Nutrition Use During Hematopoietic Stem Cell Transplantation.

Background: Total parenteral nutrition (TPN) is frequently used to manage caloric needs during hematopoietic stem cell transplantation (HSCT). Previous studies in transplant patients who received TPN have reported widely discordant results with regard to infection and mortality, and risk factors for TPN-related infection remain unclear.

Method: We conducted a retrospective study of all HSCT recipients treated with TPN between 2005 to 2014 at Northwestern Memorial Hospital to determine the incidence and epidemiology of infections.

Directed evolution and biophysical characterization of a full-length, soluble, human caveolin-1 variant.

Protein engineering by directed evolution can alter proteins' structures, properties, and functions. However, membrane proteins, despite their importance to living organisms, remain relatively unexplored as targets for protein engineering and directed evolution. This gap in capabilities likely results from the tendency of membrane proteins to aggregate and fail to overexpress in bacteria cells.

A unique "turn-on" fluorescence signalling strategy for highly specific detection of ascorbic acid using carbon dots as sensing probe.

Carbon dots (CDs) that showed strong blue fluorescence were successfully synthesised from sodium alginate via furnace pyrolysis. The single step pyrolytic synthesis was simple to perform while yielded CDs with high photostability, good water solubility and minimum by-products. In order to design the probe with "turn-on" sensing capability, the CDs were screened against a series of metal cations to first "turn-off" the fluorescence.

One-pot synthesis of carbon dots using two different acids and their respective unique photoluminescence property.

Carbon dots, a new class of nanomaterial with unique optical property and have great potential in various applications. This work demonstrated the possibility of tuning the emission wavelength of carbon dots by simply changing the acid type used during synthesis. In particular, sulfuric and phosphoric acids and a mixture of the two were used to carbonize the same starting precursor, sucrose.

Filgrastim versus TBO-filgrastim to reduce the duration of neutropenia after autologous hematopoietic stem cell transplantation: TBO, or not TBO, that is the question.

After a hospital-wide formulary change resulted in the replacement of filgrastim with TBO-filgrastim for all on- and off-label indications, we performed a retrospective comparison of patients with myeloma receiving 200 mg/m(2) melphalan with autologous hematopoietic stem cell transplantation to see whether the type of growth factor used post-transplant made a difference. One hundred and eighty-two consecutive patients with myeloma were studied, 91 receiving filgrastim immediately prior to the change and 91 receiving TBO-filgrastim afterward. The CD34(+) cell dose was comparable, as were other characteristics.

The effects of an informational video on patient knowledge, satisfaction and compliance with venous thromboembolism prophylaxis: a pilot study.

Objective: Venous thromboembolism (VTE) is the leading cause of preventable death in hospitalized patients. Educational videos have been effectively used to increase patient satisfaction and knowledge. This study examined possible benefits of an educational video about VTE.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Background: Advances in high-throughput sequencing technology have yielded a large number of publicly available vertebrate genomes, many of which are selected for inclusion in NCBI's RefSeq project and subsequently processed by NCBI's eukaryotic annotation pipeline. Genome annotation results are affected by differences in available support evidence and may be impacted by annotation pipeline software changes over time. The RefSeq project has not previously assessed annotation trends across organisms or over time.

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.

Phosphorylation offers a dynamic way to regulate protein activity, subcellular localization, and stability. The majority of signaling pathways involve an extensive set of protein-protein interactions, and phosphorylation is widely used to regulate protein-protein binding by affecting the stability, kinetics and specificity of interactions. Previously it was found that phosphorylation sites tend to be located on protein-protein binding interfaces and may orthosterically modulate the strength of interactions.

MMDB: 3D structures and macromolecular interactions.

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions.

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.

We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types.

Intrinsic protein disorder in human pathways.

We analyze human-specific KEGG pathways trying to understand the functional role of intrinsic disorder in proteins. Pathways provide a comprehensive picture of biological processes and allow better understanding of a protein's function within the specific context of its surroundings. Our study pinpoints a few specific pathways significantly enriched in disorder-containing proteins and identifies the role of these proteins within the framework of pathway relationships.

Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.

Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication.

CDD: a Conserved Domain Database for the functional annotation of proteins.

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent.

Intrinsic disorder and protein multibinding in domain, terminal, and linker regions.

Intrinsic disorder is believed to contribute to the ability of some proteins to interact with multiple partners which is important for protein functional promiscuity and regulation of the cross-talk between pathways. To better understand the mechanisms of molecular recognition through disordered regions, here, we systematically investigate the coupling between disorder and binding within domain families in a structure interaction network and in terminal and inter-domain linker regions. We showed that the canonical domain-domain interaction model should take into account contributions of N- and C-termini and inter-domain linkers, which may form all or part of the binding interfaces.

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder.

Most of the proteins in a cell assemble into complexes to carry out their function. In this work, we have created a new database (named ComSin) of protein structures in bound (complex) and unbound (single) states to provide a researcher with exhaustive information on structures of the same or homologous proteins in bound and unbound states. From the complete Protein Data Bank (PDB), we selected 24 910 pairs of protein structures in bound and unbound states, and identified regions of intrinsic disorder.

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.

IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query.

CORAL: aligning conserved core regions across domain families.

Motivation: Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units.

Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis.

We perform a large-scale study of intrinsically disordered regions in proteins and protein complexes using a non-redundant set of hundreds of different protein complexes. In accordance with the conventional view that folding and binding are coupled, in many of our cases the disorder-to-order transition occurs upon complex formation and can be localized to binding interfaces. Moreover, analysis of disorder in protein complexes depicts a significant fraction of intrinsically disordered regions, with up to one third of all residues being disordered.

Protein subfamily assignment using the Conserved Domain Database.

Background: Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein.

CDD: specific functional annotation with the Conserved Domain Database.

NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.