Helix folding simulations with various initial conformations
نویسندگان
چکیده
منابع مشابه
Folding thermodynamics of pseudoknotted chain conformations.
We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information...
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 کاملFolding simulations and computer redesign of protein A three-helix bundle motifs.
In solution, the B domain of protein A from Staphylococcus aureus (B domain) possesses a three-helix bundle structure. This simple motif has been previously reproduced by Kolinski and Skolnick (Proteins 18: 353-366, 1994) using a reduced representation lattice model of proteins with a statistical interaction scheme. In this paper, an improved version of the potential has been used, and the robu...
متن کاملFolding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model.
Vpu is an 81-amino-acid auxiliary membrane protein encoded by human immunodeficiency virus type 1 (HIV-1). One of its roles is to amplify viral release by self-assembling in homo-oligomers to form functional water-filled pores enabling the flux of ions across the membrane. Various NMR and CD studies have shown that the transmembrane domain of Vpu has a helical conformation. With a recently deve...
متن کاملSimulations of Protein Folding
A protein is a linear chain of amino acids. The proteins of natural living organisms are composed of 20 different types of amino acids. A typical protein is a polymer of 300 amino acids, of which there are 20 = 2× 10 different possibilities. The human body uses about 80,000 different proteins for most of its functionality, including structure, communication, transport, and catalysis. The order ...
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: 1994
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(94)80973-7