Including H-Bonding in Depth-Dependent Membrane Burial Potentials for Improving Folding Simulations
نویسندگان
چکیده
منابع مشابه
On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations
Significant progress has recently been made in de novo protein structure prediction. The Rosetta method by Baker and colleagues, which is based on the idea of assembling putative models from a library of k-mer fragments derived from known three-dimensional protein structures, proved to be particularly successful. Critical components of the Rosetta approach are various sequence-dependent as well...
متن کاملMonte Carlo simulations of protein folding under confining potentials
We present a theoretical investigation of the folding of small proteins assisted by chaperones. We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom. The cage of chaperonins is modeled by an external confining potential which is also able to take into account hydrophobic and hydrophilic effects inside the cavity. ...
متن کاملEffective potentials for folding proteins.
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydr...
متن کاملComputer simulations of membrane protein folding: structure and dynamics.
A lattice model of membrane proteins with a composite energy function is proposed to study their folding dynamics and native structures using Monte Carlo simulations. This model successfully predicts the seven helix bundle structure of sensory rhodopsin I by practicing a three-stage folding. Folding dynamics of a transmembrane segment into a helix is further investigated by varying the cooperat...
متن کاملFolding and assembly of h-barrel membrane proteins
Beta-barrel membrane proteins occur in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. The membrane-spanning sequences of h-barrel membrane proteins are less hydrophobic than those of a-helical membrane proteins, which is probably the main reason why completely different folding and membrane assembly pathways have evolved for these two classes of membrane proteins....
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: 2016
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2015.11.378