Chirality of coiled coils: elasticity matters.
نویسندگان
چکیده
Coiled coils are important protein-protein interaction motifs with high specificity that are used to assemble macromolecular complexes. Their simple geometric organization, consisting of alpha helices wrapped around each other, confers remarkable mechanical properties. A geometrical and mechanical continuous model taking into account sequence effects and based on the superhelical winding of the constituent helices is introduced, and a continuous family of solutions in which the oligomerization interactions are satisfied is derived. From these solutions, geometric and structural properties, such as the chirality and pitch of the coiled coil and the location of residues, are obtained. The theoretical predictions are compared to x-ray data from the leucine zipper motif.
منابع مشابه
Length-dependent force characteristics of coiled coils.
Coiled-coil domains within and between proteins play important structural roles in biology. They consist of two or more alpha helices that form a superhelical structure due to packing of the hydrophobic residues that pattern each helix. A recent continuum model showed that the correspondence between the chirality of the pack to that of the underlying hydrophobic pattern comes about because of t...
متن کاملMultiCoil: a program for predicting two- and three-stranded coiled coils.
A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two-stranded coiled-coil prediction program PairCoil to the identification of three-stranded coiled coils. The computations are based upon data gathered from a three-stranded coiled-coil database comprising 6,319 amino acid...
متن کاملAnti-parallel Coiled Coils Structure Prediction by Support Vector Machine Classification
Coiled coils is an important 3-D protein structure with two or more stranded alpha-helical motif wounded around to form a “knobs-into-holes” structure. In this paper we propose an SVM classification approach to predict the antiparallel coiled coils structure based on the primary amino acid sequence. The training dataset for the machine learning are collected from SOCKET database which is a SOCK...
متن کاملChiral elasticity of DNA
DNA has been described as a semiflexible polymer. But DNA is chiral, so its bending Hamiltonian contains nonlinear terms coupling the curvature κ to the torsion τ , leading to an average 〈τ〉 independent of κ, and variance 〈∆τ〉 scaling as 1/κ. We perform atomistic MD simulations of 31 base-pair DNA sequences with explicit solvent, in which “restraints” are imposed to “encourage” the DNA to bend....
متن کاملThe evolution and structure prediction of coiled coils across all genomes.
Coiled coils are α-helical interactions found in many natural proteins. Various sequence-based coiled-coil predictors are available, but key issues remain: oligomeric state and protein-protein interface prediction and extension to all genomes. We present SpiriCoil (http://supfam.org/SUPERFAMILY/spiricoil), which is based on a novel approach to the coiled-coil prediction problem for coiled coils...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Physical review letters
دوره 100 3 شماره
صفحات -
تاریخ انتشار 2008