Sequence determinants of protein phase behavior from a coarse-grained model
نویسندگان
چکیده
منابع مشابه
Sequence determinants of protein phase behavior from a coarse-grained model
Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation (LLPS). However, many proteins involved in this phase separation are at least partially disordered. The molecular mechanism and the sequence determinants of this process are challenging to determine experimentally owing ...
متن کاملSequence Design in Coarse-Grained Protein Models
Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences. In this paper we discuss an alternative Monte Carlo approach, multisequence design, where conformation and sequ...
متن کاملSequence-dependent thermodynamics of a coarse-grained DNA model.
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperat...
متن کاملCoarse-grained lattice model simulations of sequence-structure fitness of a ribosome-inactivating protein.
Many realistic protein-engineering design problems extend beyond the computational limits of what is considered practical when applying all-atom molecular-dynamics simulation methods. Lattice models provide computationally robust alternatives, yet most are regarded as too simplistic to accurately capture the details of complex designs. We revisit a coarse-grained lattice simulation model and de...
متن کاملSequence determines degree of knottedness in a coarse-grained protein model.
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show t...
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: PLOS Computational Biology
سال: 2018
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1005941