Zobrazeno 1 - 10
of 149
pro vyhledávání: '"Shakhnovich, E. I."'
Publikováno v:
J. Chem. Phys. 129, 095108 (2008)
We apply a simulational proxy of the phi-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding reactions of two small lattice Go polymers with different native geometries. These results are co
Externí odkaz:
http://arxiv.org/abs/0806.3064
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar structures. The effe
Externí odkaz:
http://arxiv.org/abs/q-bio/0609048
In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns have always t
Externí odkaz:
http://arxiv.org/abs/q-bio/0607050
Autor:
Lyjatsky, D. B., Shakhnovich, E. I.
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81] demonstrat
Externí odkaz:
http://arxiv.org/abs/q-bio/0603017
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein structure, with the
Externí odkaz:
http://arxiv.org/abs/cond-mat/0108357
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and uses a Go p
Externí odkaz:
http://arxiv.org/abs/cond-mat/0011369
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space of sequen
Externí odkaz:
http://arxiv.org/abs/cond-mat/9905309
Autor:
Gutman, L., Shakhnovich, E. I.
Phase separation of sequence-disordered liquid crystalline polymers, a promising class of technological and biological relevance, is studied by field theory, and thermodynamic mechanisms responsible for orientational ordering observed in experiments,
Externí odkaz:
http://arxiv.org/abs/cond-mat/9904333
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the total numb
Externí odkaz:
http://arxiv.org/abs/cond-mat/9809410
Autor:
Gutman, L., Shakhnovich, E. I.
We study the phase behavior of random heteropolymers (RHPs) with quenched cross-links, a novel polymer class of technological and biological relevance, and show the possible occurrence of freezing with few chain conformations sampled. The sensitivity
Externí odkaz:
http://arxiv.org/abs/cond-mat/9805111