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The central building block of an intermediate filament is a pair of two intertwined proteins that is called a coiled-coil structure. This name reflects the fact that the structure of each protein is helical, and the intertwined pair is also a helical structure.
The generation of a protein sequence is much easier than the determination of a protein structure. However, the structure of a protein gives much more insight in the function of the protein than its sequence. Therefore, a number of methods for the computational prediction of protein structure from its sequence have been developed. [39]
Calculating contacts is an important task in structural bioinformatics, being important for the correct prediction of protein structure and folding, thermodynamic stability, protein-protein and protein-ligand interactions, docking and molecular dynamics analyses, and so on.
Currently, the gap between known protein sequences and confirmed protein structures is immense. At the beginning of 2008, only about 1% of the sequences listed in the UniProtKB database corresponded to structures in the Protein Data Bank (PDB), leaving a gap between sequence and structure of approximately five million. [4]
Protein domains allow protein classification by a combination of sequence, structure and function, and they can be combined in many ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more ...
Protein function depends on 3-D structure and these 3-D structures are more highly conserved than sequences. Thus, the high-throughput structure determination methods of structural genomics have the potential to inform our understanding of protein functions. This also has potential implications for drug discovery and protein engineering. [2]
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
Kinesin is a protein functioning as a molecular biological machine. It uses protein domain dynamics on nanoscales. A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multidomain enzymes, in which multiple catalytic domains are found in a single polypeptide chain ...