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Introdution:
Ubiquitin is a highly conserved 8547Da protein with 76 amino acid residues which is found only in eukaryotes. This protein is also stable to heat and folds into a compact globular structure. It is prevalent in numerous different tissues and organisms, hence its name Ubiquitin, originating from the Latin ubique,''everywhere''. Ubiquitin is involved in manay cell processes, namely DNA repair, embryogenesis, regulation of transcription, and apoptosis(cell death). It can exist either in free form or as part of a complex with other proteins. This protein attaches itself to other proteins by covalent bond formation between glycine at its C-terminus end and the side chains of lysine on the proteins it forms conjugation with. The importance of this protein can not be downsized, and this has been delineated by the recent Nobel prize in Chemistry been awarded to Aaron, Avram and Irwin for the discovery of Ubiquitin mediated protein degradation.
Structural Features:
Primary structure:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EEEEE TTS EEEEE TT BHHHHHHHH HHHH GGG EEEEETTEE EDGRTLSDYN IQKESTLHLV LRLRGG TTSBTGGGT TT EEEEE E S
Basically every protein is composed of a backbone attached with side chains.
Ubiquitin has 1 alpha helix and 5 beta strands which are all antiparallel.
Structural motif can simply be defined as supersecondary structure and Ubiquitin exhibits a hairpin motif where a loop region connects 2 antiparallel beta strands.
Ubiquitin exhibits an alpha/beta domain which looks more of a twist.The loop that connects the carboxylic end of the beta strand with the amino end of the alpha helix usually have conserved amino acid sequences in homologous proteins. It is also involved in forming the functional binding sites in other proteins.
Amino acid side chains interactions with each other and water influence their contribution to protein stability and function.
Ubiquitin has 27 hydrophobic amino acid side chains which interact with one another through van der Waal interactions to form a hydrophobic core.
The remaining 49 amino acid side chains are polar, neutral and charged amino acids and constitute to the solvent accessible regions of the protein which interacts with one another and water through hydrogen bonding. A combination of hydrophobic effect and polar interactions between amino acid side chains and with water drives Ubiquitin to fold in its native state.
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