The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.
Database Search: A customizable interface was developed to permit complex queries that include the name of the protein, tissue, mitochondrial compartment, chromosome number, molecular weight range, pI range, and keywords. Users can also restrict the data being searched to 2D-PAGE images, Locus links, the Genome Database, OMIM, or RefSeq information. The query results, along with the protein sequence, and journal reference(s) is presented as an easy to read HTML page. The protein sequence is highlighted by using a mouse-over option that provides annotation such as the mitochondrion localization signal, variant information, etc. A selected protein sequence of interest can be used to search directly the SwissProt site for related proteins.
Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence.
Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations.
Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM.
3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT , Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage.
Links to other web sites relevant to mitochondrial proteins are provided.
Users are encouraged to contact us with corrections, preprints, reprints, and other information related to mitochondrial proteins to be included in this database.
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