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Structural Genomics
Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. Because protein structure is closely linked with protein function, the structural genomics has the potential to inform knowledge of prote ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Nuclear Magnetic Resonance Spectroscopy
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated. NMR involves the quantum-mechanical properties of the central core ("nucleus") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how the atoms are linked chemically, how close they are in space, and how rapid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of ''individual'' genes and their roles in inheritance, genomics aims at the collective characterization and quantification of ''all'' of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CATH
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and colleagues including Janet Thornton and David Jones, and continues to be developed by the Orengo group at University College London. CATH shares many broad features with the SCOP resource, however there are also many areas in which the detailed classification differs greatly. Hierarchical organization Experimentally-determined protein three-dimensional structures are obtained from the Protein Data Bank and split into their consecutive polypeptide chains, where applicable. Protein domains are identified within these chains using a mixture of automatic methods and manual curation. The domains are then classified within the CATH structural hierarchy: at the Class (C) level, domains are assigned according to their secondary structure content, i. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Classification Of Proteins
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor. Similar to CATH and Pfam databases, SCOP provides a classification of individual structural domains of proteins, rather than a classification of the entire proteins which may include a significant number of different domains. The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Labo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UniProt
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Geor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multi-drug-resistant Tuberculosis
Multidrug-resistant tuberculosis (MDR-TB) is a form of tuberculosis (TB) infection caused by bacteria that are resistant to treatment with at least two of the most powerful first-line anti-TB medications (drugs): isoniazid and rifampin. Some forms of TB are also resistant to second-line medications, and are called extensively drug-resistant TB ( XDR-TB). Tuberculosis is caused by infection with the bacterium ''Mycobacterium tuberculosis''. Almost one in four people in the world are infected with TB bacteria. Only when the bacteria become active do people become ill with TB. Bacteria become active as a result of anything that can reduce the person's immunity, such as HIV, advancing age, diabetes or other immunocompromising illnesses. TB can usually be treated with a course of four standard, or first-line, anti-TB drugs (i.e., isoniazid, rifampin, pyrazinamide and ethambutol). However, beginning with the first antibiotic treatment for TB in 1943, some strains of the TB bacteri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mycobacterium Tuberculosis
''Mycobacterium tuberculosis'' (M. tb) is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, ''M. tuberculosis'' has an unusual, waxy coating on its cell surface primarily due to the presence of mycolic acid. This coating makes the cells impervious to Gram staining, and as a result, ''M. tuberculosis'' can appear weakly Gram-positive. Acid-fastness, Acid-fast stains such as Ziehl–Neelsen stain, Ziehl–Neelsen, or Fluorescence, fluorescent stains such as Auramine O, auramine are used instead to identify ''M. tuberculosis'' with a microscope. The physiology of ''M. tuberculosis'' is highly aerobic organism, aerobic and requires high levels of oxygen. Primarily a pathogen of the mammalian respiratory system, it infects the lungs. The most frequently used diagnostic methods for tuberculosis are the Mantoux test, tuberculin skin test, Acid-Fast Stain, acid-fast stain, Microbiological cultu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mycobacterium Tuberculosis Structural Genomics Consortium
The TB Structural Genomics Consortium (TBSGC) is a worldwide consortium of scientists developing a foundation for tuberculosis diagnosis and treatment by determining the three-dimensional structures of proteins from ''M. tuberculosis'' founded in 2000 as a part of the Protein Structure Initiative. The consortium seeks to solve structures of proteins that are of great interest to the TB biology community. A major goal of the consortium is to have a putative function for every ORF in the TB genome. __TOC__ Activities As of June 2006, 82 TB protein structures have been determined, 15 since January 1, 2006. The database of linked structural and functional information that has been constructed using this information can form a lasting basis for understanding ''M. tuberculosis'' pathogenesis and for structure-based drug design. As of June 2006, the TB Structural Genomics Consortium consists of 430 active members in 148 laboratories from 83 institutions across 15 countries. Consortium la ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Escherichia Coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly found in the lower intestine of warm-blooded organisms. Most ''E. coli'' strains are harmless, but some serotypes ( EPEC, ETEC etc.) can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains do not cause disease in humans and are part of the normal microbiota of the gut; such strains are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between ''E. col ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermotoga
''Thermotoga'' is a genus of the phylum ''Thermotogota''. Members of ''Thermotoga'' are hyperthermophilic bacteria whose cell is wrapped in a unique sheath-like outer membrane, called a "toga". The members of the phylum stain Gram-negative as they possess a thin peptidoglycan in between two lipid bilayers, albeit both peculiar. The peptidoglycan is unusual as the crosslink is not only meso-diaminopimelate as occurs in Pseudomonadota, but D-lysine.All proteinogenic amino acids have the L- configuration; in peptidoglycan some amino acids with the D- configuration are present. Lysine is synthesised from meso-diaminopimelate by Diaminopimelate decarboxylase The species are anaerobes with varying degrees of oxygen tolerance. They are capable of reducing elemental sulphur (S0) to hydrogen sulphide, which in turn can be used. Whether thermophily is an innovation of the lineage or an ancestral trait is unclear and cannot be determined. The genome of '' Thermotoga maritima'' was sequen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
