MMDB: annotating protein sequences with Entrez's 3D-structure database

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ()

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences

Enhanced furfural production from raw corn stover employing a novel heterogeneous acid catalyst

With the aim to enhance the direct conversion of raw corn stover into furfural, a promising approach was proposed employing a novel heterogeneous strong acid catalyst (SC-CaCt-700) in different solvents. The novel catalyst was characterized by elemental analysis, N-2 adsorption-desorption, FT-IR, XPS, TEM and SEM. The developed catalytic system demonstrated superior efficacy for furfural production from raw corn stover. The effects of reaction temperature, residence time, catalyst loading, substrate concentration and solvent were investigated and optimized. 93% furfural yield was obtained from 150 mg corn stover at 200 degrees C in 100 min using 45 mg catalyst in gamma-valerolactone (GVL). In comparison, 51.5% furfural yield was achieved in aqueous media under the same conditions (200 degrees C, 5 h, and 45 mg catalyst), which is of great industrial interest. Furfural was obtained from both hemicelluloses and cellulose in corn stover, which demonstrated a promising routine to make the full use of biomass

Large-Scale Identification of Protein Crotonylation Reveals Its Role in Multiple Cellular Functions

Lysine crotonylation on histones is a recently identified post-translational modification that has been demonstrated to associate with active promoters and to directly stimulate transcription. Given that crotonyl-CoA is essential for the acyl transfer reaction and it is a metabolic intermediate widely localized within the cell, we postulate that lysine crotonylation on nonhistone proteins could also widely exist. Using specific antibody enrichment followed by high-resolution mass spectrometry analysis, we identified hundreds of crotonylated proteins and lysine residues. Bioinformatics analysis reveals that crotonylated proteins are particularly enriched for nuclear proteins involved in RNA processing, nucleic acid metabolism, chromosome organization, and gene expression. Furthermore, we demonstrate that crotonylation regulates HDAC1 activity, expels HP1α from heterochromatin, and inhibits cell cycle progression through S-phase. Our data thus indicate that lysine crotonylation could occur in a large number of proteins and could have important regulatory roles in multiple nuclei-related cellular processes

Pre-eclampsia

Pre-eclampsia is a multisystem disorder of pregnancy, characterised by hypertension and proteinuria, occurring after 20 weeks of gestation. As well as being associated with pregnancy complications such as preterm delivery and foetal growth restriction, pre-eclampsia is now increasingly known to be associated with cardiovascular diseases in later life. Despite decades of research into the condition, it remains difficult to predict, difficult to diagnose and difficult to treat. In this chapter pathophysiological mechanisms and origins of disease will be discussed, with a focus on placental and cardiovascular factors. Potential markers to improve early prediction of disease and therapeutic strategies will be discussed, as well as the relationship between pre-eclampsia and future maternal health problems