Bioinformatics Sequence Analysis

Coiled Coil Prediction

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Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins. The individual α-helices twist and wind around each other to form a coiled bundle structure. The coiled coil conformation is important in easing inter- or intra protein interactions. Proteins having these structural domains are often involved in transcription regulation or in the maintenance of cytoskeletal integrity. Coiled coils have an typical repeat of seven residues (heptads) which consider a side-chain packing geometry at facing residues. For every seven residues, the first and fourth are hydrophobic, facing the helical interface; the others are hydrophilic and exposed to the solvent. The sequence periodicity forms the basis for designing algorithms to predict this important structural domain. As a result of the regular structural features, if the location of coiled coils can be predicted precisely, the three-dimensional structure for the coiled coil region can sometimes be built. 

Tools 

Coils is a web-based program that detects coiled coil regions in proteins. It scans a window of fourteen, twenty one, or twenty-eight residues and compares the sequence to a probability matrix compiled from known parallel two-stranded coiled coils. By comparing the similarity scores, the program calculates the probability of the sequence to adopt a coiled coil conformation. The program is accurate for solvent-exposed, left-handed coiled coils, but less sensitive for other types of coiled coil structures, such as buried or right handed coiled coils. 

Multicoil is a web-based program for predicting coiled coils. The scoring matrix is constructed based on a database of known two-stranded and three-stranded coiled coils. The program is more conservative than Coils. It has been recently used in several genome-wide studies to screen for protein–protein interactions mediated by coiled coil domains. Leucine zipper domains are a special type of coiled coils found in transcription regulatory proteins. They contain two antiparallelα-helices held together by hydrophobic interactions of leucine residues. 

2ZIP is a web-based server that predicts leucine zippers. It combines searching of the characteristic leucine repeats with coiled coil prediction using an algorithm similar to Coils to yield accurate results.

Marcoil is a program built on hidden Markov models, and PCOILS, a new COILS version that uses profiles as inputs. Overall it gives a slightly better performance over the reference database than PCOILS and is considerably faster, but it is sensitive to highly charged false positives, whereas the weighting option of PCOILS allows the identification of such sequences.

The coiled-coil is a widespread protein structural motif known to have a stabilization function and to be involved in key interactions in cells and organisms. 

PS-COILS have been generated to define a baseline approach for benchmarking new coiled-coil predictors. Furthermore, a new structurally-annotated and freely-available dataset of coiled-coil structures have been created. 

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