Folding a Protein with Equal Probability of Being Helix or Hairpin
نویسندگان
چکیده
منابع مشابه
Folding a protein with equal probability of being helix or hairpin.
We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hair...
متن کاملFolding pathways of a helix-turn-helix model protein
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a β-strand conformation or two different loop conformations of the protein glutamine synthetase, six trajectories are generated using the so-called window move in dihe...
متن کاملCorrect folding of an α-helix and a β-hairpin using a polarized 2D torsional potential
A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-l...
متن کاملDynamic folding pathway models of a-helix and b-hairpin structures
We present dynamic folding pathway models of a-helix and b-hairpin structures at atomistic details by using the action-derived molecular dynamics method. The present formulation is free from common assumptions widely used in molecular dynamics such as high temperature simulations, a choice of order parameter set, an arbitrary identification of the folded configuration, or an exponential kinetic...
متن کاملCommon fold in helix-hairpin-helix proteins.
Helix-hairpin-helix (HhH) is a widespread motif involved in non-sequence-specific DNA binding. The majority of HhH motifs function as DNA-binding modules, however, some of them are used to mediate protein-protein interactions or have acquired enzymatic activity by incorporating catalytic residues (DNA glycosylases). From sequence and structural analysis of HhH-containing proteins we conclude th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2012.05.029