Increased expression of heat shock protein 105 in rat uterus of early pregnancy and its significance in embryo implantation

Background  

Heat shock proteins (Hsps) are a set of highly conserved proteins, Hsp105, has been suggested to play a role in reproduction.     

Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin

Background  

Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins.     

Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues

Background  

The emergence of structural genomics presents significant challenges in the annotation of biologically uncharacterized proteins. Unfortunately, our ability to analyze these proteins is restricted by the limited catalog of known molecular functions and their associated 3D motifs.     

Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location

Background  

Two-hybrid screening for proteins that interact with the core domain of human topoisomerase I identified two novel proteins, BTBD1 and BTBD2, which share 80% amino acid identities.     

Molecular cloning and tissue expression of the fatty acid-binding protein (<Emphasis Type="Italic">Es-FABP</Emphasis>) gene in female Chinese mitten crab (<Emphasis Type="Italic">Eriocheir sinensis</Emphasis>)

Background  

Fatty acid-binding proteins (FABPs), small cytosolic proteins that function in the uptake and utilization of fatty acids, have been extensively studied in higher vertebrates while invertebrates have received little attention despite similar nutritional requirements during periods of reproductive activity.     

Identification of DNA-binding proteins using support vector machines and evolutionary profiles

Background  

Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation, as these proteins play a crucial role in gene-regulation. In this paper, we developed various SVM modules for predicting DNA-binding domains and proteins. All models were trained and tested on multiple datasets of non-redundant proteins.     

Definition of novel cell envelope associated proteins in Triton X-114 extracts of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> H37Rv

Background  

Membrane- and membrane-associated proteins are important for the pathogenicity of bacteria. We have analysed the content of these proteins in virulent Mycobacterium tuberculosis H37Rv using Triton X-114 detergent-phase separation for extraction of lipophilic proteins, followed by their identification with high resolution mass spectrometry.     

ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files

Background  

Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins.     

Structural and functional diversification in the teleost S100 family of calcium-binding proteins

Background  

Among the EF-Hand calcium-binding proteins the subgroup of S100 proteins constitute a large family with numerous and diverse functions in calcium-mediated signaling. The evolutionary origin of this family is still uncertain and most studies have examined mammalian family members.     

Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles

Background  

Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing motif-based methods have got limited success due to lack of universal motif in all secretory proteins of malaria parasite.     

Outer membrane proteins can be simply identified using secondary structure element alignment

Background  

Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery.     

Computational identification of strain-, species- and genus-specific proteins

Background  

The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets.     

Prediction of β-barrel membrane proteins by searching for restricted domains

Background  

The identification of β-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses.     

The signaling helix: a common functional theme in diverse signaling proteins

Background  

The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood.     

Prediction of transmembrane helix orientation in polytopic membrane proteins

Background  

Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins.     

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Background  

The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins.     

Casein phosphopeptides drastically increase the secretion of extracellular proteins in <Emphasis Type="Italic">Aspergillus awamori</Emphasis>. Proteomics studies reveal changes in the secretory pathway

Background  

The secretion of heterologous animal proteins in filamentous fungi is usually limited by bottlenecks in the vesicle-mediated secretory pathway.     

Rapid glycation with D-ribose induces globular amyloid-like aggregations of BSA with high cytotoxicity to SH-SY5Y cells

Background  

D-ribose in cells and human serum participates in glycation of proteins resulting in advanced glycation end products (AGEs) that affect cell metabolism and induce cell death. However, the mechanism by which D-ribose-glycated proteins induce cell death is still unclear.