Protein tertiary structure
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the backbone may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.[1][2] A number of these structures may bind to each other, forming a quaternary structure.[3]
This article is about tertiary structure in protein. For the article about tertiary structure in nucleic acid, see Nucleic acid tertiary structure.History[edit]
The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. Wrinch demonstrated this with the Cyclol model, the first prediction of the structure of a globular protein.[4] Contemporary methods are able to determine, without prediction, tertiary structures to within 5 Å (0.5 nm) for small proteins (<120 residues) and, under favorable conditions, confident secondary structure predictions.
Projects[edit]
Prediction algorithm[edit]
The Folding@home project at the University of Pennsylvania is a distributed computing research effort which uses approximately 5 petaFLOPS (≈10 x86 petaFLOPS) of available computing. It aims to find an algorithm which will consistently predict protein tertiary and quaternary structures given the protein's amino acid sequence and its cellular conditions.[9][10]
A list of software for protein tertiary structure prediction can be found at
List of protein structure prediction software.
Protein aggregation diseases[edit]
Protein aggregation diseases such as Alzheimer's disease and Huntington's disease and prion diseases such as bovine spongiform encephalopathy can be better understood by constructing (and reconstructing) disease models. This is done by causing the disease in laboratory animals, for example, by administering a toxin, such as MPTP to cause Parkinson's disease, or through genetic manipulation.[11][12] Protein structure prediction is a new way to create disease models, which may avoid the use of animals.[13]
Protein Tertiary Structure Retrieval Project (CoMOGrad)[edit]
Matching patterns in tertiary structure of a given protein to huge number of known protein tertiary structures and retrieve most similar ones in ranked order is in the heart of many research areas like function prediction of novel proteins, study of evolution, disease diagnosis, drug discovery, antibody design etc. The CoMOGrad project at BUET is a research effort to device an extremely fast and much precise method for protein tertiary structure retrieval and develop online tool based on research outcome.[14][15]